9IRU | pdb_00009iru

Cryo-em structure of TCR-4B1 complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth e]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054845	3000071	SCOP2B (2022-06-29)
G [auth f]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054845	3000071	SCOP2B (2022-06-29)
E [auth d]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054849	3000071	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)
J [auth n]	Beta-Casp	e9irun1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
I [auth m]	Beta-Casp	e9irum1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
H [auth g]	Beta-Casp	e9irug1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
F [auth e]	Beta-Casp	e9irue1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
G [auth f]	Beta-Casp	e9iruf1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
E [auth d]	Beta-Casp	e9irud1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
C [auth a]	Beta-Casp	e9irua1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)
D [auth b]	Beta-Casp	e9irub1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Beta-Casp	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF11628	T-cell surface glycoprotein CD3 zeta chain (TCR_zetazeta)	T-cell surface glycoprotein CD3 zeta chain	-	Family
A	PF11628	T-cell surface glycoprotein CD3 zeta chain (TCR_zetazeta)	T-cell surface glycoprotein CD3 zeta chain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
J [auth n]	TCR-b	-	-	-
I [auth m]	CD3-a	-	-	-
H [auth g]	T-cell surface glycoprotein CD3 gamma chain	protein-containing complex binding protein binding binding signaling receptor binding T cell receptor binding identical protein binding signaling receptor complex adaptor activity protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response biological regulation T cell receptor signaling pathway regulation of response to stimulus immune system process regulation of immune response antigen receptor-mediated signaling pathway activation of immune response adaptive immune response multicellular organismal process gamma-delta T cell activation T cell activation cell activation lymphocyte activation leukocyte activation localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization developmental process thymic T cell selection cellular developmental process hemopoiesis cell development mononuclear cell differentiation lymphocyte differentiation positive thymic T cell selection T cell differentiation in thymus cell differentiation positive T cell selection anatomical structure development T cell differentiation T cell selection leukocyte differentiation alpha-beta T cell activation regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process leukocyte apoptotic process regulation of apoptotic process regulation of programmed cell death cell death lymphocyte apoptotic process apoptotic process programmed cell death establishment or maintenance of cell polarity	protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex gamma-delta T cell receptor complex cell periphery cellular anatomical structure plasma membrane signaling receptor complex signaling receptor complex T cell receptor complex cell surface external side of plasma membrane side of membrane protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex gamma-delta T cell receptor complex cell periphery cellular anatomical structure plasma membrane signaling receptor complex signaling receptor complex T cell receptor complex cell surface 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 cytosol alpha-beta T cell receptor complex
F [auth e], G [auth f]	T-cell surface glycoprotein CD3 epsilon chain	protein-macromolecule adaptor activity molecular adaptor activity SH3 domain binding protein binding binding protein domain specific binding protein-containing complex binding signaling receptor binding T cell receptor binding identical protein binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity kinase binding protein-macromolecule adaptor activity molecular adaptor activity SH3 domain binding protein binding binding protein domain specific binding protein-containing complex binding signaling receptor binding T cell receptor binding identical protein binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity kinase binding enzyme binding protein kinase binding signaling receptor complex adaptor activity signaling adaptor activity	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of calcium-mediated signaling cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of calcium-mediated signaling positive regulation of calcium-mediated signaling signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction regulation of response to stimulus calcium-mediated signaling regulation of cell communication cellular process positive regulation of signaling developmental process thymic T cell selection multicellular organismal process cellular developmental process hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell differentiation in thymus T cell activation immune system process cell differentiation negative thymic T cell selection anatomical structure development T cell differentiation negative T cell selection T cell selection leukocyte differentiation immune response adaptive immune response regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion cell-substrate adhesion positive regulation of cell-matrix adhesion cell adhesion cell-matrix adhesion positive regulation of cell-substrate adhesion regulation of cell-matrix adhesion regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process gamma-delta T cell activation regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death head development animal organ development brain development nervous system development multicellular organism development cerebellum development central nervous system development metencephalon development hindbrain development system development alpha-beta T cell activation immune system development regulation of T cell anergy lymphocyte anergy regulation of lymphocyte anergy positive regulation of lymphocyte anergy positive regulation of T cell tolerance induction positive regulation of T cell anergy regulation of immune system process regulation of multicellular organismal process regulation of T cell tolerance induction positive regulation of immune system process T cell anergy T cell tolerance induction positive regulation of multicellular organismal process regulation of tolerance induction positive regulation of tolerance induction tolerance induction positive regulation of cell population proliferation regulation of leukocyte activation regulation of alpha-beta T cell activation positive regulation of alpha-beta T cell proliferation regulation of cell activation positive regulation of CD4-positive, alpha-beta T cell proliferation positive regulation of cell activation alpha-beta T cell proliferation lymphocyte proliferation positive regulation of leukocyte activation regulation of leukocyte proliferation cell population proliferation positive regulation of T cell activation regulation of CD4-positive, alpha-beta T cell proliferation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of alpha-beta T cell activation regulation of cell population proliferation mononuclear cell proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation positive regulation of leukocyte cell-cell adhesion leukocyte proliferation leukocyte cell-cell adhesion positive regulation of cell-cell adhesion regulation of alpha-beta T cell proliferation positive regulation of lymphocyte activation positive regulation of CD4-positive, alpha-beta T cell activation cell-cell adhesion CD4-positive, alpha-beta T cell activation positive regulation of mononuclear cell proliferation regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation CD4-positive, alpha-beta T cell proliferation regulation of T cell activation regulation of T cell proliferation regulation of CD4-positive, alpha-beta T cell activation regulation of mononuclear cell proliferation regulation of lymphocyte activation lymphocyte costimulation T cell costimulation protein-containing complex organization cellular component organization cellular component biogenesis signal complex assembly cellular component assembly protein-containing complex assembly cellular component organization or biogenesis cell surface receptor signaling pathway smoothened signaling pathway immune response-regulating cell surface receptor signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response immune response-activating cell surface receptor signaling pathway T cell receptor signaling pathway regulation of immune response antigen receptor-mediated signaling pathway activation of immune response cell-cell adhesion mediated by integrin positive regulation of cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin regulation of cell-cell adhesion mediated by integrin positive regulation of cell-cell adhesion mediated by integrin cell adhesion mediated by integrin positive thymic T cell selection positive T cell selection negative regulation of signaling negative regulation of biological process negative regulation of cell communication negative regulation of smoothened signaling pathway negative regulation of cellular process regulation of smoothened signaling pathway negative regulation of response to stimulus negative regulation of signal transduction plasma membrane bounded cell projection organization cell projection organization neuron projection development generation of neurons neurogenesis neuron differentiation dendrite development neuron development regulation of cytokine production cytokine production regulation of interleukin-2 production interleukin-2 production positive regulation of interleukin-2 production positive regulation of cytokine production cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway apoptotic signaling pathway G protein-coupled receptor signaling pathway negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of macromolecule metabolic process regulation of interleukin-4 production positive regulation of interleukin-4 production interleukin-4 production regulation of type II interferon production type II interferon production positive regulation of type II interferon production	protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex gamma-delta T cell receptor complex cell periphery cellular anatomical structure plasma membrane signaling receptor complex signaling receptor complex T cell receptor complex cell surface external side of plasma membrane side of membrane protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex gamma-delta T cell receptor complex cell periphery cellular anatomical structure plasma membrane signaling receptor complex signaling receptor complex T cell receptor complex cell surface external side of plasma membrane side of membrane cell-cell junction anchoring junction cell junction membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system alpha-beta T cell receptor complex neuron spine synapse neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection postsynapse dendrite dendritic tree cell body immunological synapse endoplasmic reticulum
E [auth d]	T-cell surface glycoprotein CD3 delta chain	identical protein binding protein binding binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cellular process signal transduction cell communication immune response-regulating cell surface receptor signaling pathway positive regulation of biological process positive regulation of response to stimulus immune response-activating signaling pathway cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cellular process signal transduction cell communication immune response-regulating cell surface receptor signaling pathway positive regulation of biological process positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process immune response-activating cell surface receptor signaling pathway immune response T cell receptor signaling pathway regulation of response to stimulus immune system process regulation of immune response antigen receptor-mediated signaling pathway activation of immune response adaptive immune response developmental process thymic T cell selection multicellular organismal process cellular developmental process hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation positive thymic T cell selection leukocyte activation T cell differentiation in thymus T cell activation cell differentiation positive T cell selection anatomical structure development T cell differentiation T cell selection leukocyte differentiation alpha-beta T cell activation	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex signaling receptor complex T cell receptor complex alpha-beta T cell receptor complex cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex signaling receptor complex T cell receptor complex alpha-beta T cell receptor complex 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
C [auth a], D [auth b]	T-cell surface glycoprotein CD3 zeta chain	protein heterodimerization activity protein binding binding protein dimerization activity protein-macromolecule adaptor activity molecular adaptor activity identical protein binding protein homodimerization activity protein tyrosine kinase binding kinase binding enzyme binding protein kinase binding molecular transducer activity transmembrane signaling receptor activity protein heterodimerization activity protein binding binding protein dimerization activity protein-macromolecule adaptor activity molecular adaptor activity identical protein binding protein homodimerization activity protein tyrosine kinase binding kinase binding enzyme binding protein kinase binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response biological regulation T cell receptor signaling pathway regulation of response to stimulus immune system process regulation of immune response antigen receptor-mediated signaling pathway activation of immune response adaptive immune response Fc receptor signaling pathway Fc-gamma receptor signaling pathway multicellular organismal process gamma-delta T cell activation T cell activation cell activation lymphocyte activation leukocyte activation alpha-beta T cell activation regulation of localization regulation of protein localization positive regulation of protein localization to cell surface localization protein localization to cell surface macromolecule localization positive regulation of protein localization regulation of protein localization to cell surface intracellular protein localization	protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex gamma-delta T cell receptor complex cell periphery cellular anatomical structure plasma membrane signaling receptor complex signaling receptor complex T cell receptor complex Fc-gamma receptor III complex Fc receptor complex intracellular anatomical structure protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex gamma-delta T cell receptor complex cell periphery cellular anatomical structure plasma membrane signaling receptor complex signaling receptor complex T cell receptor complex Fc-gamma receptor III complex Fc receptor complex intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system alpha-beta T cell receptor complex
B	4B1-H	-	-	-
A	4B1-L	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H [auth g]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
H [auth g]	IPR003598	Immunoglobulin subtype 2	Domain
H [auth g]	IPR032052	CD3 gamma/delta subunit, Ig-like domain	Domain
H [auth g]	IPR015484	CD3 protein, epsilon/gamma/delta subunit	Family
H [auth g]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
H [auth g]	IPR003110	Phosphorylated immunoreceptor signalling ITAM	Repeat
F [auth e], G [auth f]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
F [auth e], G [auth f]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
F [auth e], G [auth f]	IPR003110	Phosphorylated immunoreceptor signalling ITAM	Repeat
F [auth e], G [auth f]	IPR003598	Immunoglobulin subtype 2	Domain
F [auth e], G [auth f]	IPR015484	CD3 protein, epsilon/gamma/delta subunit	Family
E [auth d]	IPR032052	CD3 gamma/delta subunit, Ig-like domain	Domain
E [auth d]	IPR015484	CD3 protein, epsilon/gamma/delta subunit	Family
E [auth d]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
E [auth d]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
E [auth d]	IPR003110	Phosphorylated immunoreceptor signalling ITAM	Repeat
C [auth a], D [auth b]	IPR024128	T-cell surface glycoprotein CD3 zeta subunit	Family
C [auth a], D [auth b]	IPR003110	Phosphorylated immunoreceptor signalling ITAM	Repeat
C [auth a], D [auth b]	IPR021663	T-cell surface glycoprotein CD3 zeta subunit/High affinity IgE receptor gamma subunit	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
H [auth g]	: P09693	combined immunodeficiency due to CD3gamma deficiency lung carcinoma interstitial cystitis Pre B-cell acute lymphoblastic leukemia cutaneous lupus erythematosus lung adenocarcinoma psoriasis IgA glomerulonephritis lung cancer osteosarcoma
F [auth e], G [auth f]	: P07766	immunodeficiency 18 severe combined immunodeficiency rheumatoid arthritis gastrointestinal stromal tumor primary immunodeficiency disease Inflammation lung carcinoma psoriasis lung adenocarcinoma malignant glioma non-small cell lung carcinoma glioblastoma lung cancer Omenn syndrome cutaneous lupus erythematosus immunodeficiency 18 severe combined immunodeficiency rheumatoid arthritis gastrointestinal stromal tumor primary immunodeficiency disease Inflammation lung carcinoma psoriasis lung adenocarcinoma malignant glioma non-small cell lung carcinoma glioblastoma lung cancer Omenn syndrome cutaneous lupus erythematosus MHC class II deficiency ovarian cancer
E [auth d]	: P04234	immunodeficiency 19 severe combined immunodeficiency primary biliary cholangitis allergic contact dermatitis liver disease lung carcinoma lung adenocarcinoma Pre B-cell acute lymphoblastic leukemia lung cancer MHC class II deficiency osteosarcoma toxic encephalopathy cutaneous lupus erythematosus interstitial cystitis pancreatic intraductal papillary-mucinous neoplasm immunodeficiency 19 severe combined immunodeficiency primary biliary cholangitis allergic contact dermatitis liver disease lung carcinoma lung adenocarcinoma Pre B-cell acute lymphoblastic leukemia lung cancer MHC class II deficiency osteosarcoma toxic encephalopathy cutaneous lupus erythematosus interstitial cystitis pancreatic intraductal papillary-mucinous neoplasm psoriasis Sjogren syndrome invasive ductal breast carcinoma Omenn syndrome
C [auth a], D [auth b]	: P20963	systemic sclerosis immunodeficiency 25 oligoarticular juvenile idiopathic arthritis allergic rhinitis cutaneous lupus erythematosus hematologic disease interstitial cystitis lung carcinoma osteosarcoma Systemic Scleroderma asthma diffuse scleroderma hypothyroidism juvenile idiopathic arthritis lymphatic system disease systemic sclerosis immunodeficiency 25 oligoarticular juvenile idiopathic arthritis allergic rhinitis cutaneous lupus erythematosus hematologic disease interstitial cystitis lung carcinoma osteosarcoma Systemic Scleroderma asthma diffuse scleroderma hypothyroidism juvenile idiopathic arthritis lymphatic system disease psoriasis cancer Hashimoto thyroiditis lung cancer rheumatoid factor-negative juvenile idiopathic arthritis

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.