3D1F

Crystal structure of E. coli sliding clamp (beta) bound to a polymerase III peptide

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3d1fa1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase III, beta subunit	DNA polymerase III, beta subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d3d1fb1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase III, beta subunit	DNA polymerase III, beta subunit	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DNA clamp	8038082	3000780	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA clamp	8038081	3000780	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA clamp	8038076	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8038082	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8038076	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8038081	3000780	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DNA_pol3_beta	e3d1fA1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: DNA_pol3_beta	ECOD (1.6)
A	DNA_pol3_beta_2	e3d1fA2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: DNA_pol3_beta_2	ECOD (1.6)
A	DNA_pol3_beta_3	e3d1fA3	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: DNA_pol3_beta_3	ECOD (1.6)
B	DNA_pol3_beta	e3d1fB1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: DNA_pol3_beta	ECOD (1.6)
B	DNA_pol3_beta_2	e3d1fB2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: DNA_pol3_beta_2	ECOD (1.6)
B	DNA_pol3_beta_3	e3d1fB3	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: DNA_pol3_beta_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.150.10	Alpha Beta	Roll	DNA Polymerase III	Chain A, domain 2	CATH (4.3.0)
B	3.10.150.10	Alpha Beta	Roll	DNA Polymerase III	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02768	DNA polymerase III beta subunit, C-terminal domain (DNA_pol3_beta_3)	DNA polymerase III beta subunit, C-terminal domain	A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.	Domain
A, B	PF02767	DNA polymerase III beta subunit, central domain (DNA_pol3_beta_2)	DNA polymerase III beta subunit, central domain	A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.	Domain
A, B	PF00712	DNA polymerase III beta subunit, N-terminal domain (DNA_pol3_beta)	DNA polymerase III beta subunit, N-terminal domain	A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth P], D [auth Q]	Nonapeptide from polymerase III C-terminal	-	-	-
A, B	DNA polymerase III subunit beta	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity identical protein binding protein binding protein homodimerization activity protein dimerization activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process DNA-templated DNA replication primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process DNA-templated DNA replication primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process DNA strand elongation involved in DNA replication macromolecule metabolic process translesion synthesis postreplication repair nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process error-prone translesion synthesis DNA biosynthetic process DNA repair regulation of DNA-templated DNA replication initiation regulation of cellular process negative regulation of biological process negative regulation of DNA-templated DNA replication initiation regulation of primary metabolic process negative regulation of DNA-templated DNA replication negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of biological process negative regulation of DNA replication DNA replication initiation negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process regulation of DNA-templated DNA replication negative regulation of DNA metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process bacterial-type DNA replication cell cycle DNA replication cell cycle cell cycle process	transferase complex, transferring phosphorus-containing groups DNA polymerase III complex protein-containing complex catalytic complex transferase complex DNA polymerase complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-DNA complex intracellular membraneless organelle chromosome transferase complex, transferring phosphorus-containing groups DNA polymerase III complex protein-containing complex catalytic complex transferase complex DNA polymerase complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-DNA complex intracellular membraneless organelle chromosome replication inhibiting complex intracellular organelle organelle membraneless organelle replication fork replisome Hda-beta clamp complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR046938	DNA clamp superfamily	Homologous Superfamily
A, B	IPR001001	DNA polymerase III, beta sliding clamp	Family
A, B	IPR022634	DNA polymerase III, beta sliding clamp, N-terminal	Domain
A, B	IPR022635	DNA polymerase III, beta sliding clamp, C-terminal	Domain
A, B	IPR022637	DNA polymerase III, beta sliding clamp, central	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.