6U9S

Crystal structure of human CD81 large extracellular loop in complex with 5A6 Fab

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
A	d6u9sa_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d6u9sd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d6u9sc1	All alpha proteins	Tetraspanin	Tetraspanin	Tetraspanin	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6u9sc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6u9sc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d6u9sf1	All alpha proteins	Tetraspanin	Tetraspanin	Tetraspanin	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d6u9sf2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6u9sb2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d6u9sb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d6u9se2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d6u9se1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Tetraspanin	8039070	3001736	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Tetraspanin	8039070	3001736	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	V-set_8	e6u9sA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
A	C1-set_1	e6u9sA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
D	V-set_8	e6u9sD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
D	C1-set_1	e6u9sD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C	CD81_like_LEL	e6u9sC1	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)
F	CD81_like_LEL	e6u9sF1	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	C1-set_4	e6u9sB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B	V-set	e6u9sB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
E	C1-set_4	e6u9sE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
E	V-set	e6u9sE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.10.1450.10	Mainly Alpha	Orthogonal Bundle	Cd81 Antigen, Extracellular Domain	Chain: A	CATH (utative)
F	1.10.1450.10	Mainly Alpha	Orthogonal Bundle	Cd81 Antigen, Extracellular Domain	Chain: A	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
A, D	5A6 FAB HEAVY CHAIN,B, E	VH-CH1	Homo sapiens (human)	IGHV7-4-102, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105, IGHG112, IGHG114, IGHG113, IGHG109, IGHG110, IGHG107, IGHG1*11	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202442-0)
B, E	5A6 FAB HEAVY CHAIN,B, E	L-KAPPA	Homo sapiens (human)	IGKV2-2801, IGKV2D-2801, IGKJ202, IGKJ204, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202442-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, D	Heavy Chain	IGHV7	-	cd81 antigen	SAbDab (2024-10-25)
B, E	Light Chain	IGKV2	Kappa	cd81 antigen	SAbDab (2024-10-25)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F	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, D	5A6 FAB Heavy Chain	-	-	-
C, F	CD81 antigen	protein binding binding virus receptor activity exogenous protein binding signaling receptor binding MHC class II protein binding MHC protein binding sterol binding organic cyclic compound binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding protein binding binding virus receptor activity exogenous protein binding signaling receptor binding MHC class II protein binding MHC protein binding sterol binding organic cyclic compound binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding transferrin receptor binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding cell adhesion molecule binding integrin binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains multicellular organismal process regulation of immune effector process lymphocyte mediated immunity T cell mediated immunity positive regulation of leukocyte mediated immunity regulation of cellular process response to stimulus T-helper 2 cell cytokine production T cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process type 2 immune response positive regulation of immune response regulation of T-helper 2 cell cytokine production adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains multicellular organismal process regulation of immune effector process lymphocyte mediated immunity T cell mediated immunity positive regulation of leukocyte mediated immunity regulation of cellular process response to stimulus T-helper 2 cell cytokine production T cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process type 2 immune response positive regulation of immune response regulation of T-helper 2 cell cytokine production regulation of type 2 immune response cytokine production leukocyte mediated immunity regulation of immune system process positive regulation of macromolecule metabolic process positive regulation of adaptive immune response positive regulation of T cell cytokine production positive regulation of immune system process regulation of T cell mediated immunity regulation of biological process regulation of cytokine production involved in immune response positive regulation of T-helper 2 cell cytokine production immune response regulation of adaptive immune response cellular metabolic process regulation of cellular metabolic process immune effector process regulation of gene expression regulation of leukocyte mediated immunity biosynthetic process regulation of response to stimulus regulation of immune response positive regulation of production of molecular mediator of immune response positive regulation of multicellular organismal process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response positive regulation of cytokine production regulation of metabolic process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of response to stimulus regulation of T cell cytokine production CD4-positive, alpha-beta T cell cytokine production regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of biosynthetic process regulation of cytokine production positive regulation of immune effector process regulation of multicellular organismal process cytokine production involved in immune response positive regulation of cellular process production of molecular mediator of immune response regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process adaptive immune response regulation of cellular biosynthetic process positive regulation of type 2 immune response regulation of lymphocyte mediated immunity positive regulation of gene expression immune system process positive regulation of T cell mediated immunity positive regulation of cytokine production involved in immune response cellular process positive regulation of cellular biosynthetic process protein localization regulation of localization cellular localization regulation of protein localization positive regulation of receptor clustering positive regulation of protein localization to membrane localization within membrane protein localization to membrane localization regulation of cellular localization cellular macromolecule localization macromolecule localization receptor clustering positive regulation of protein localization regulation of receptor clustering regulation of protein localization to membrane regulation of leukocyte activation regulation of cell activation cell activation involved in immune response T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell positive regulation of cell activation T cell activation positive regulation of leukocyte activation positive regulation of T cell activation positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell regulation of leukocyte cell-cell adhesion positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation cell adhesion cell-cell adhesion T cell activation involved in immune response leukocyte activation involved in immune response regulation of cell-cell adhesion lymphocyte activation involved in immune response positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell regulation of lymphocyte activation 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 regulation of protein catabolic process in the vacuole catabolic process positive regulation of protein metabolic process macromolecule catabolic process regulation of primary metabolic process protein metabolic process regulation of protein metabolic process protein catabolic process in the vacuole primary metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process positive regulation of protein catabolic process in the vacuole regulation of protein catabolic process import into cell receptor internalization transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport macrophage fusion myeloid leukocyte differentiation osteoclast fusion hemopoiesis cell development multinuclear osteoclast differentiation myeloid cell differentiation osteoclast differentiation leukocyte differentiation protein localization to cell periphery protein localization to plasma membrane regulation of protein exit from endoplasmic reticulum protein exit from endoplasmic reticulum establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization positive regulation of protein transport establishment of localization in cell positive regulation of intracellular transport regulation of intracellular transport regulation of transport regulation of establishment of protein localization intracellular transport regulation of protein transport positive regulation of protein exit from endoplasmic reticulum positive regulation of transport protein transport regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport regulation of alpha-beta T cell activation positive regulation of CD4-positive, alpha-beta T cell activation CD4-positive, alpha-beta T cell activation alpha-beta T cell activation positive regulation of alpha-beta T cell activation regulation of CD4-positive, alpha-beta T cell activation lymphocyte costimulation CD4-positive, alpha-beta T cell costimulation T cell costimulation cellular response to stimulus positive regulation of cell communication immune response-regulating cell surface receptor signaling pathway positive regulation of signal transduction positive regulation of T cell receptor signaling pathway signaling regulation of antigen receptor-mediated signaling pathway regulation of signal transduction cell communication immune response-activating signaling pathway immune response-regulating signaling pathway signal transduction regulation of signaling cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway regulation of T cell receptor signaling pathway T cell receptor signaling pathway regulation of cell communication antigen receptor-mediated signaling pathway activation of immune response positive regulation of antigen receptor-mediated signaling pathway positive regulation of signaling regulation of cell motility regulation of leukocyte migration macrophage migration leukocyte migration regulation of macrophage migration regulation of locomotion mononuclear cell migration regulation of cell migration myeloid leukocyte migration cell migration regulation of mononuclear cell migration cell motility locomotion regulation of protein stability regulation of biological quality regulation of B cell receptor signaling pathway B cell receptor signaling pathway positive regulation of B cell receptor signaling pathway intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade adaptive immune memory response regulation of adaptive immune memory response positive regulation of adaptive immune memory response immunological memory process 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 positive regulation of cell population proliferation positive regulation of alpha-beta T cell proliferation positive regulation of CD4-positive, alpha-beta T cell proliferation alpha-beta T cell proliferation lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation regulation of CD4-positive, alpha-beta T cell proliferation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation regulation of cell population proliferation mononuclear cell proliferation positive regulation of leukocyte proliferation leukocyte proliferation regulation of alpha-beta T cell proliferation positive regulation of mononuclear cell proliferation T cell proliferation regulation of lymphocyte proliferation CD4-positive, alpha-beta T cell proliferation regulation of T cell proliferation regulation of mononuclear cell proliferation protein localization to lysosome protein localization to organelle protein localization to vacuole immunological synapse formation cell-cell recognition cell recognition positive regulation of B cell proliferation regulation of B cell proliferation regulation of B cell activation B cell activation B cell proliferation positive regulation of B cell activation regulation of defense response regulation of response to external stimulus inflammatory response to antigenic stimulus positive regulation of response to external stimulus positive regulation of inflammatory response response to stress regulation of response to stress defense response regulation of inflammatory response to antigenic stimulus response to external stimulus regulation of inflammatory response positive regulation of inflammatory response to antigenic stimulus positive regulation of defense response inflammatory response humoral immune response immunoglobulin mediated immune response humoral immune response mediated by circulating immunoglobulin B cell mediated immunity positive regulation of DNA-templated transcription RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription	anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction membrane membrane-bounded organelle organelle vesicle cell periphery basal part of cell plasma membrane basal plasma membrane plasma membrane region anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction membrane membrane-bounded organelle organelle vesicle cell periphery basal part of cell plasma membrane basal plasma membrane plasma membrane region extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle basolateral plasma membrane immunological synapse tetraspanin-enriched microdomain
B, E	5A6 FAB Light Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F	Pharos: P60033	common variable immunodeficiency hepatitis C virus infection immunodeficiency, common variable, 6 pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis Acquired Hypogammaglobulinemia B cell deficiency glioblastoma lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia agammaglobulinemia B-cell chronic lymphocytic leukemia Duchenne muscular dystrophy juvenile dermatomyositis common variable immunodeficiency hepatitis C virus infection immunodeficiency, common variable, 6 pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis Acquired Hypogammaglobulinemia B cell deficiency glioblastoma lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia agammaglobulinemia B-cell chronic lymphocytic leukemia Duchenne muscular dystrophy juvenile dermatomyositis malignant ependymoma pancreatic intraductal papillary-mucinous carcinoma systemic sclerosis astrocytic tumor cancer Emery-Dreifuss muscular dystrophy lung adenocarcinoma oligodendroglioma

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.