6Z20

Structure of the EC2 domain of CD9 in complex with nanobody 4C8

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d6z20b_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
D	d6z20d_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	CD81_like_LEL	e6z20A1	A: few secondary structure elements	X: Tetraspanin extracellular domain (From Topology)	H: Tetraspanin extracellular domain (From Topology)	T: Tetraspanin extracellular domain	F: CD81_like_LEL	ECOD (1.6)
C	CD81_like_LEL	e6z20C1	A: few secondary structure elements	X: Tetraspanin extracellular domain (From Topology)	H: Tetraspanin extracellular domain (From Topology)	T: Tetraspanin extracellular domain	F: CD81_like_LEL	ECOD (1.6)
B	V-set_12	e6z20B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
D	V-set_12	e6z20D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.1450.10	Mainly Alpha	Orthogonal Bundle	Cd81 Antigen, Extracellular Domain	Chain: A	CATH (utative)
C	1.10.1450.10	Mainly Alpha	Orthogonal Bundle	Cd81 Antigen, Extracellular Domain	Chain: A	CATH (utative)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B, D	VHH 4E8, anti-cd9	VH	Lama glama (llama)	IGHV3-301, IGHJ401	V-DOMAIN VH	IG	VH	IMGT (202501-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D	Heavy Chain	IGHV1	-	cd9 antigen	SAbDab (2025-01-17)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00335	Tetraspanin family (Tetraspanin)	Tetraspanin family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	CD9 antigen	cell adhesion molecule binding protein-containing complex binding protein binding binding integrin binding signaling receptor binding	sperm-egg recognition sexual reproduction cell-cell recognition reproductive process fertilization cell recognition cellular process single fertilization developmental process tissue regeneration skeletal muscle tissue regeneration cellular developmental process developmental growth myoblast fusion sperm-egg recognition sexual reproduction cell-cell recognition reproductive process fertilization cell recognition cellular process single fertilization developmental process tissue regeneration skeletal muscle tissue regeneration cellular developmental process developmental growth myoblast fusion growth cell-cell fusion myotube differentiation involved in skeletal muscle regeneration muscle cell differentiation regeneration myotube differentiation muscle structure development syncytium formation by plasma membrane fusion anatomical structure morphogenesis cell differentiation myoblast fusion involved in skeletal muscle regeneration anatomical structure development anatomical structure formation involved in morphogenesis striated muscle cell differentiation syncytium formation localization import into cell receptor internalization transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport cell population proliferation multicellular organismal process regulation of body fluid levels regulation of cellular process response to stimulus negative regulation of biological process regulation of cell activation negative regulation of cell adhesion negative regulation of platelet activation regulation of coagulation regulation of biological quality response to wounding regulation of biological process negative regulation of homotypic cell-cell adhesion negative regulation of wound healing negative regulation of blood coagulation response to external stimulus blood coagulation negative regulation of hemostasis regulation of platelet activation regulation of response to stimulus negative regulation of response to external stimulus negative regulation of cell-cell adhesion regulation of wound healing negative regulation of multicellular organismal process platelet activation regulation of response to external stimulus homotypic cell-cell adhesion regulation of response to wounding cell adhesion cell-cell adhesion response to stress regulation of response to stress negative regulation of cellular process coagulation regulation of cell-cell adhesion regulation of multicellular organismal process regulation of hemostasis wound healing negative regulation of response to stimulus regulation of homotypic cell-cell adhesion regulation of cell adhesion regulation of blood coagulation biological regulation hemostasis cell activation negative regulation of platelet aggregation negative regulation of response to wounding platelet aggregation negative regulation of cell activation regulation of platelet aggregation negative regulation of coagulation regulation of cell motility regulation of leukocyte migration macrophage migration leukocyte migration regulation of macrophage migration immune system process regulation of locomotion mononuclear cell migration regulation of cell migration myeloid leukocyte migration cell migration regulation of immune system process regulation of mononuclear cell migration cell motility locomotion membrane organization membrane fusion plasma membrane fusion multicellular organismal reproductive process cellular process involved in reproduction in multicellular organism cellular component organization fusion of sperm to egg plasma membrane involved in single fertilization plasma membrane organization cellular component organization or biogenesis endomembrane system organization negative regulation of cell population proliferation regulation of cell population proliferation cellular response to stimulus cellular response to low-density lipoprotein particle stimulus response to endogenous stimulus response to chemical response to lipoprotein particle response to nitrogen compound cellular response to lipoprotein particle stimulus glial cell migration nervous system development neurogenesis multicellular organism development gliogenesis system development cellular component assembly involved in morphogenesis myelin assembly cellular component biogenesis cellular anatomical entity morphogenesis cellular component assembly cell junction assembly axon ensheathment ensheathment of neurons cell-cell junction assembly cell-cell junction organization myelination cell junction organization paranodal junction assembly	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle protein-containing complex platelet alpha granule membrane endomembrane system secretory granule secretory vesicle platelet alpha granule secretory granule membrane
B, D	Nanobody 4C8	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR042055	CD9, extracellular domain	Domain
A, C	IPR008952	Tetraspanin, EC2 domain superfamily	Homologous Superfamily
A, C	IPR000301	Tetraspanin, animals	Family
A, C	IPR018503	Tetraspanin, conserved site	Conserved Site
A, C	IPR018499	Tetraspanin/Peripherin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P21926	glioblastoma acute myeloid leukemia colorectal cancer giant cell glioblastoma Nerve Degeneration non-small cell lung carcinoma germ cell tumor cirrhosis of liver prostate cancer embryonal neoplasm tuberculosis facioscapulohumeral muscular dystrophy invasive ductal breast carcinoma limb-girdle muscular dystrophy malignant glioma glioblastoma acute myeloid leukemia colorectal cancer giant cell glioblastoma Nerve Degeneration non-small cell lung carcinoma germ cell tumor cirrhosis of liver prostate cancer embryonal neoplasm tuberculosis facioscapulohumeral muscular dystrophy invasive ductal breast carcinoma limb-girdle muscular dystrophy malignant glioma ankylosing spondylitis medulloblastoma colorectal adenoma ovarian cancer primary biliary cholangitis Duchenne muscular dystrophy Emery-Dreifuss muscular dystrophy juvenile dermatomyositis lung cancer malignant mesothelioma Becker muscular dystrophy pancreatic ductal adenocarcinoma dermatomyositis progressive supranuclear palsy ductal breast carcinoma in situ psoriasis esophageal adenocarcinoma gastric carcinoma interstitial cystitis large cell medulloblastoma malignant ependymoma malignant pancreatic neoplasm cancer osteosarcoma colorectal carcinoma pilocytic astrocytoma Down syndrome

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.