7QCD | pdb_00007qcd

CryoEM structure of the Smc5/6-holocomplex (composite structure)

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	COG5627	e7qcdC2	A: alpha bundles	X: Long alpha-hairpin	H: Endosomal sorting complex assembly domains (From Topology)	T: Endosomal sorting complex assembly domains	F: COG5627	ECOD (1.6)
C	zf-Nse	e7qcdC1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-Nse	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02463	RecF/RecN/SMC N terminal domain (SMC_N)	RecF/RecN/SMC N terminal domain	This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. Th ...	This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics [1]. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.	Domain
B	PF13476	AAA domain (AAA_23)	AAA domain		Domain
C	PF22326	E3 SUMO-protein ligase MMS21, N-terminal domain (MMS21_N)	E3 SUMO-protein ligase MMS21, N-terminal domain	This domain is found at the N-terminal end of E3 SUMO-protein ligase MMS21 from Saccharomyces cerevisiae and similar fungal proteins. MMS21 acts in a DNA repair pathway for removal of UV-induced DNA damage that is distinct from classical nucleotide e ...	This domain is found at the N-terminal end of E3 SUMO-protein ligase MMS21 from Saccharomyces cerevisiae and similar fungal proteins. MMS21 acts in a DNA repair pathway for removal of UV-induced DNA damage that is distinct from classical nucleotide excision repair and in repair of ionizing radiation damage. This domain forms an helix bundle with a coiled-coil structure. It is required for the binding to Smc5, which is essential for cell growth and resistance to DNA damage [1].	Domain
C	PF11789	Zinc-finger of the MIZ type in Nse subunit (zf-Nse)	Zinc-finger of the MIZ type in Nse subunit	Nse1 and Nse2 are novel non-SMC subunits of the fission yeast Smc5-6 DNA repair complex. This family is the zinc-finger domain similar to the MIZ type of zinc-finger [1].	Domain
D	PF07574	Nse1 non-SMC component of SMC5-6 complex (SMC_Nse1)	Nse1 non-SMC component of SMC5-6 complex	-	Family
D	PF08746	RING-like domain (zf-RING-like)	RING-like domain	This is a zinc finger domain that is related to the C3HC4 RING finger domain (Pfam:PF00097).	Domain
E	PF01454	MAGE homology domain (MAGE)	MAGE homology domain	The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this fam ...	The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex [2-3]. Nse3 has been demonstrated to be important for meiosis[3].	Domain
F	PF15412	Binding domain of Nse4/EID3 to Nse3-MAGE (Nse4-Nse3_bdg)	Binding domain of Nse4/EID3 to Nse3-MAGE	This family includes Nse4 and EID3 members [1], that bind over this region to the Nse3 pocket, in MAGE family Pfam:PF01454 [2].	Domain
F	PF08743	Nse4 C-terminal (Nse4_C)	Nse4 C-terminal	Nse4 is the kleisin component of the Smc5/6 DNA repair complex. It bridges the heads of Smc5 and Smc6 [1,2,3,4]. This is the C-terminal domain of Nse4 that interacts with the head domain of Smc5 [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Structural maintenance of chromosomes protein 5	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity DNA binding damaged DNA binding nucleic acid binding single-stranded DNA binding	nucleobase-containing compound metabolic process resolution of DNA recombination intermediates DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular component organization chromatin looping chromatin organization cellular component organization or biogenesis chromosome separation nucleobase-containing compound metabolic process resolution of DNA recombination intermediates DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular component organization chromatin looping chromatin organization cellular component organization or biogenesis chromosome separation cell cycle chromosome segregation cell cycle process cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair regulation of telomere maintenance regulation of cellular component organization regulation of cellular process telomere organization regulation of primary metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process biological regulation chromosome organization regulation of chromosome organization regulation of macromolecule metabolic process regulation of organelle organization telomere maintenance organelle organization regulation of metabolic process regulation of DNA metabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region protein-containing complex catalytic complex SUMO ligase complex transferase complex Smc5-Smc6 complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region protein-containing complex catalytic complex SUMO ligase complex transferase complex Smc5-Smc6 complex condensed chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B	Structural maintenance of chromosomes protein 6	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity DNA binding damaged DNA binding nucleic acid binding single-stranded DNA binding	nucleobase-containing compound metabolic process resolution of DNA recombination intermediates DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process localization DNA double-strand break attachment to nuclear envelope chromosome localization organelle localization chromosome attachment to the nuclear envelope nucleobase-containing compound metabolic process resolution of DNA recombination intermediates DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process localization DNA double-strand break attachment to nuclear envelope chromosome localization organelle localization chromosome attachment to the nuclear envelope cell cycle cell cycle process cellular component organization chromatin looping chromatin organization cellular component organization or biogenesis chromosome separation chromosome segregation cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair regulation of telomere maintenance regulation of cellular component organization regulation of cellular process telomere organization regulation of primary metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process biological regulation chromosome organization regulation of chromosome organization regulation of macromolecule metabolic process regulation of organelle organization telomere maintenance organelle organization regulation of metabolic process regulation of DNA metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle site of double-strand break membraneless organelle site of DNA damage intracellular membraneless organelle chromosome chromosome, telomeric region membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle site of double-strand break membraneless organelle site of DNA damage intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region protein-containing complex catalytic complex SUMO ligase complex transferase complex Smc5-Smc6 complex condensed chromosome nucleus
C	E3 SUMO-protein ligase MMS21	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO transferase activity transferase activity catalytic activity SUMO ligase activity ubiquitin-like protein ligase activity protein serine/threonine kinase activity enzyme regulator activity kinase activity protein kinase activity enzyme inhibitor activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO transferase activity transferase activity catalytic activity SUMO ligase activity ubiquitin-like protein ligase activity protein serine/threonine kinase activity enzyme regulator activity kinase activity protein kinase activity enzyme inhibitor activity protein kinase regulator activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein kinase inhibitor activity molecular function inhibitor activity molecular function regulator activity protein serine/threonine kinase inhibitor activity kinase inhibitor activity kinase regulator activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	localization DNA double-strand break attachment to nuclear envelope chromosome localization organelle localization chromosome attachment to the nuclear envelope cellular process cell cycle cell cycle process cellular component organization chromatin looping chromatin organization cellular component organization or biogenesis cellular response to stimulus double-strand break repair localization DNA double-strand break attachment to nuclear envelope chromosome localization organelle localization chromosome attachment to the nuclear envelope cellular process cell cycle cell cycle process cellular component organization chromatin looping chromatin organization cellular component organization or biogenesis cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair peptidyl-lysine modification protein sumoylation macromolecule modification peptidyl-amino acid modification protein metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of telomere maintenance regulation of cellular component organization regulation of cellular process telomere organization regulation of primary metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process biological regulation chromosome organization regulation of chromosome organization regulation of macromolecule metabolic process regulation of organelle organization telomere maintenance organelle organization regulation of metabolic process regulation of DNA metabolic process	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cytoplasm membraneless organelle intracellular membraneless organelle chromosome membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system cytoplasm membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region protein-containing complex catalytic complex SUMO ligase complex transferase complex Smc5-Smc6 complex condensed chromosome
D	Non-structural maintenance of chromosomes element 1	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	cellular component organization chromatin looping chromatin organization cellular process cellular component organization or biogenesis cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress cellular component organization chromatin looping chromatin organization cellular process cellular component organization or biogenesis cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair regulation of telomere maintenance regulation of cellular component organization regulation of cellular process telomere organization regulation of primary metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process biological regulation chromosome organization regulation of chromosome organization regulation of macromolecule metabolic process regulation of organelle organization telomere maintenance organelle organization regulation of metabolic process regulation of DNA metabolic process postreplication repair	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region protein-containing complex catalytic complex SUMO ligase complex transferase complex Smc5-Smc6 complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region protein-containing complex catalytic complex SUMO ligase complex transferase complex Smc5-Smc6 complex condensed chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle
E	Non-structural maintenance of chromosome element 3	-	cellular component organization chromatin looping chromatin organization cellular process cellular component organization or biogenesis cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress cellular component organization chromatin looping chromatin organization cellular process cellular component organization or biogenesis cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair regulation of telomere maintenance regulation of cellular component organization regulation of cellular process telomere organization regulation of primary metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process biological regulation chromosome organization regulation of chromosome organization regulation of macromolecule metabolic process regulation of organelle organization telomere maintenance organelle organization regulation of metabolic process regulation of DNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region protein-containing complex catalytic complex SUMO ligase complex transferase complex cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region protein-containing complex catalytic complex SUMO ligase complex transferase complex Smc5-Smc6 complex condensed chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle
F	Non-structural maintenance of chromosome element 4	-	cellular component organization chromatin looping chromatin organization cellular process cellular component organization or biogenesis cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress cellular component organization chromatin looping chromatin organization cellular process cellular component organization or biogenesis cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair regulation of telomere maintenance regulation of cellular component organization regulation of cellular process telomere organization regulation of primary metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process biological regulation chromosome organization regulation of chromosome organization regulation of macromolecule metabolic process regulation of organelle organization telomere maintenance organelle organization regulation of metabolic process regulation of DNA metabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region protein-containing complex catalytic complex SUMO ligase complex transferase complex Smc5-Smc6 complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region protein-containing complex catalytic complex SUMO ligase complex transferase complex Smc5-Smc6 complex condensed chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR003395	RecF/RecN/SMC, N-terminal	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR038729	Rad50/SbcC-type AAA domain	Domain
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C	IPR004181	Zinc finger, MIZ-type	Domain
C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
C	IPR054753	E3 SUMO-protein ligase MMS21, N-terminal domain	Domain
C	IPR026846	E3 SUMO-protein ligase Nse2 (Mms21)	Family
D	IPR011513	Non-structural maintenance of chromosomes element 1	Family
D	IPR014857	Non-structural maintenance of chromosomes element 1, RING C4HC3-type	Domain
D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
E	IPR041899	MAGE homology domain, winged helix WH2 motif	Homologous Superfamily
E	IPR002190	MAGE homology domain	Domain
E	IPR041898	MAGE homology domain, winged helix WH1 motif	Homologous Superfamily
E	IPR037445	Melanoma-associated antigen	Family
F	IPR027786	Nse4/EID family	Family
F	IPR014854	Non-structural maintenance of chromosome element 4, C-terminal	Domain
F	IPR029225	Nse4/EID protein, Nse3/MAGE-binding domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.