6WL4

preTCRbeta-pMHC complex crystal structure

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	MHC antigen-recognition domain	8036210	3000521	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MHC antigen-recognition domain	8036210	3000521	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	MHC antigen-recognition domain	8036210	3000521	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	PF00129	e6wl4A1	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: PF00129	ECOD (1.6)
D	PF00129	e6wl4D1	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: PF00129	ECOD (1.6)
G	PF00129	e6wl4G1	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: PF00129	ECOD (1.6)
C	PF07654	e6wl4C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C	PF07686	e6wl4C2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
F	PF07654	e6wl4F1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
F	PF07686	e6wl4F2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
I	PF07654	e6wl4I1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
I	PF07686	e6wl4I2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

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, G	H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN,B, E, H	G-ALPHA1-ALPHA2	-	MH1-K1b	G-DOMAIN G-ALPHA1, G-DOMAIN G-ALPHA2	MH	(G-ALPHA1-ALPHA2)	IMGT (202417-0)
C, F, I	H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN,B, E, H	TR-BETA-1	-	TRBV12-101, TRBJ2-701, TRBJ2-702, TRBC101, TRBC201, TRBC203	V-DOMAIN V-BETA, C-DOMAIN C-BETA-1	MH	(G-ALPHA1-ALPHA2)	IMGT (202417-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G	PF00129	Class I Histocompatibility antigen, domains alpha 1 and 2 (MHC_I)	Class I Histocompatibility antigen, domains alpha 1 and 2	-	Domain
B, E, H	PF00945	Rhabdovirus nucleocapsid protein (Rhabdo_ncap)	Rhabdovirus nucleocapsid protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, G	H-2 class I histocompatibility antigen, K-B alpha chain	binding antigen binding peptide antigen binding peptide binding protein binding protein-folding chaperone binding TAP1 binding TAP binding 14-3-3 protein binding natural killer cell lectin-like receptor binding signaling receptor binding protein-containing complex binding TAP complex binding beta-2-microglobulin binding binding antigen binding peptide antigen binding peptide binding protein binding protein-folding chaperone binding TAP1 binding TAP binding 14-3-3 protein binding natural killer cell lectin-like receptor binding signaling receptor binding protein-containing complex binding TAP complex binding beta-2-microglobulin binding T cell receptor binding identical protein binding CD8 receptor binding protein homodimerization activity protein dimerization activity MHC class I protein binding MHC protein binding TAP2 binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity T cell mediated cytotoxicity T cell mediated immunity response to tumor cell T cell mediated cytotoxicity directed against tumor cell target response to stimulus immune response immune response to tumor cell leukocyte mediated cytotoxicity adaptive immune response response to biotic stimulus immune effector process T cell mediated immune response to tumor cell immune system process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity T cell mediated cytotoxicity T cell mediated immunity response to tumor cell T cell mediated cytotoxicity directed against tumor cell target response to stimulus immune response immune response to tumor cell leukocyte mediated cytotoxicity adaptive immune response response to biotic stimulus immune effector process T cell mediated immune response to tumor cell immune system process leukocyte mediated immunity cellular process cell killing regulation of defense response regulation of immune effector process positive regulation of response to biotic stimulus regulation of response to biotic stimulus positive regulation of leukocyte mediated immunity biological process involved in interspecies interaction between organisms regulation of response to external stimulus positive regulation of lymphocyte mediated immunity positive regulation of biological process positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of immune response response to stress regulation of response to stress positive regulation of natural killer cell mediated immunity innate immune response regulation of immune system process positive regulation of immune effector process response to external biotic stimulus natural killer cell mediated immunity positive regulation of immune system process regulation of biological process regulation of natural killer cell mediated immunity positive regulation of innate immune response response to other organism defense response regulation of innate immune response biological regulation defense response to symbiont response to external stimulus regulation of leukocyte mediated immunity regulation of lymphocyte mediated immunity regulation of response to stimulus defense response to other organism positive regulation of defense response regulation of immune response multicellular organismal process regulation of cellular process regulation of leukocyte activation negative regulation of biological process regulation of cell activation lymphocyte activation negative regulation of lymphocyte activation negative regulation of natural killer cell activation leukocyte activation negative regulation of cellular process regulation of multicellular organismal process regulation of natural killer cell activation cell activation natural killer cell activation negative regulation of cell activation negative regulation of immune system process negative regulation of multicellular organismal process negative regulation of leukocyte activation regulation of lymphocyte activation positive regulation of cell population proliferation CD8-positive, alpha-beta T cell activation regulation of alpha-beta T cell activation CD8-positive, alpha-beta T cell proliferation positive regulation of alpha-beta T cell proliferation positive regulation of CD8-positive, alpha-beta T cell activation positive regulation of cell activation T cell activation alpha-beta T cell proliferation lymphocyte proliferation positive regulation of leukocyte activation positive regulation of CD8-positive, alpha-beta T cell proliferation alpha-beta T cell activation regulation of leukocyte proliferation positive regulation of T cell activation cell population proliferation regulation of CD8-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 mononuclear cell proliferation regulation of cell population proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation positive regulation of multicellular organismal process positive regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion leukocyte proliferation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation regulation of alpha-beta T cell proliferation cell adhesion cell-cell adhesion positive regulation of mononuclear cell proliferation regulation of cell-cell adhesion positive regulation of cellular process T cell proliferation regulation of lymphocyte proliferation positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation regulation of T cell proliferation regulation of mononuclear cell proliferation regulation of CD8-positive, alpha-beta T cell activation T cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process cytokine production organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of adaptive immune response positive regulation of T cell cytokine production regulation of T cell mediated immunity regulation of cytokine production involved in immune response regulation of adaptive immune response cellular metabolic process regulation of cellular metabolic process regulation of gene expression biosynthetic process positive regulation of production of molecular mediator of immune response 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 cellular biosynthetic process positive regulation of cellular metabolic process regulation of T cell cytokine production organic substance metabolic process 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 cytokine production involved in immune response production of molecular mediator of immune response regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process positive regulation of gene expression positive regulation of T cell mediated immunity positive regulation of cytokine production involved in immune response positive regulation of cellular biosynthetic process interleukin-13 production positive regulation of interleukin-13 production regulation of interleukin-13 production developmental process ear development sensory organ development inner ear development animal organ development anatomical structure development humoral immune response antibacterial humoral response antimicrobial humoral response defense response to bacterium response to bacterium detection of external biotic stimulus detection of biotic stimulus detection of bacterium detection of stimulus detection of other organism negative regulation of lymphocyte proliferation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of cell-cell adhesion negative regulation of mononuclear cell proliferation negative regulation of cell population proliferation antigen processing and presentation antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway antigen processing and presentation of endogenous peptide antigen antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent antigen processing and presentation of peptide antigen antigen processing and presentation of endogenous antigen antigen processing and presentation of endogenous peptide antigen via MHC class I negative regulation of lymphocyte mediated immunity negative regulation of natural killer cell mediated immunity negative regulation of immune response negative regulation of immune effector process negative regulation of response to external stimulus negative regulation of defense response natural killer cell mediated cytotoxicity regulation of cell killing negative regulation of natural killer cell mediated cytotoxicity regulation of natural killer cell mediated cytotoxicity negative regulation of response to biotic stimulus protection from natural killer cell mediated cytotoxicity negative regulation of leukocyte mediated cytotoxicity negative regulation of cell killing negative regulation of response to stimulus regulation of leukocyte mediated cytotoxicity negative regulation of leukocyte mediated immunity negative regulation of innate immune response regulation of neuron projection development regulation of cellular component organization cellular developmental process cell projection organization cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation cell differentiation cellular component organization or biogenesis negative regulation of cell projection organization system development plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization nervous system development negative regulation of neuron projection development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization immunoglobulin production positive regulation of immunoglobulin production regulation of immunoglobulin production positive regulation of memory T cell activation regulation of memory T cell activation memory T cell activation positive regulation of natural killer cell activation antigen processing and presentation of exogenous peptide antigen via MHC class I antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of exogenous antigen immune system development natural killer cell tolerance induction tolerance induction antigen processing and presentation of peptide antigen via MHC class Ib antigen processing and presentation via MHC class Ib antigen processing and presentation of exogenous peptide antigen via MHC class Ib positive regulation of leukocyte mediated cytotoxicity positive regulation of T cell mediated cytotoxicity regulation of T cell mediated cytotoxicity positive regulation of cell killing positive regulation of natural killer cell mediated cytotoxicity regulation of natural killer cell cytokine production natural killer cell cytokine production positive regulation of natural killer cell cytokine production cellular response to stimulus immune response-regulating cell surface receptor signaling pathway signaling cell communication immune response-activating signaling pathway immune response-regulating signaling pathway signal transduction cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway T cell receptor signaling pathway antigen receptor-mediated signaling pathway activation of immune response antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent positive regulation of natural killer cell proliferation natural killer cell proliferation regulation of natural killer cell proliferation antigen processing and presentation of endogenous peptide antigen via MHC class Ib regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production regulation of interleukin-4 production positive regulation of interleukin-4 production interleukin-4 production positive regulation of TRAIL production TRAIL production regulation of TRAIL production regulation of type II interferon production type II interferon production positive regulation of type II interferon production defense response to Gram-positive bacterium positive regulation of acute inflammatory response to antigenic stimulus regulation of myeloid leukocyte mediated immunity regulation of acute inflammatory response to antigenic stimulus regulation of type IIa hypersensitivity myeloid leukocyte mediated immunity inflammatory response to antigenic stimulus positive regulation of hypersensitivity positive regulation of inflammatory response positive regulation of antibody-dependent cellular cytotoxicity antibody-dependent cellular cytotoxicity regulation of type II hypersensitivity positive regulation of immunoglobulin mediated immune response hypersensitivity regulation of inflammatory response regulation of B cell mediated immunity type II hypersensitivity positive regulation of myeloid leukocyte mediated immunity B cell mediated immunity type IIa hypersensitivity regulation of acute inflammatory response inflammatory response positive regulation of acute inflammatory response positive regulation of B cell mediated immunity regulation of immunoglobulin mediated immune response acute inflammatory response regulation of hypersensitivity regulation of inflammatory response to antigenic stimulus acute inflammatory response to antigenic stimulus positive regulation of inflammatory response to antigenic stimulus immunoglobulin mediated immune response positive regulation of type IIa hypersensitivity positive regulation of type II hypersensitivity regulation of antibody-dependent cellular cytotoxicity	membrane-bounded organelle intracellular anatomical structure cis-Golgi network membrane Golgi apparatus membrane intracellular membrane-bounded organelle cellular anatomical entity endomembrane system intracellular organelle bounding membrane of organelle cis-Golgi network organelle cytoplasm organelle membrane membrane-bounded organelle intracellular anatomical structure cis-Golgi network membrane Golgi apparatus membrane intracellular membrane-bounded organelle cellular anatomical entity endomembrane system intracellular organelle bounding membrane of organelle cis-Golgi network organelle cytoplasm organelle membrane cell periphery cell surface plasma membrane external side of plasma membrane side of membrane MHC class I protein complex MHC protein complex protein-containing complex plasma membrane protein complex membrane protein complex endoplasmic reticulum exit site endoplasmic reticulum MHC class Ib protein complex intracellular vesicle phagocytic vesicle phagocytic vesicle membrane cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane endocytic vesicle membrane vesicle endocytic vesicle vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome Golgi membrane MHC class I peptide loading complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane extracellular region extracellular space Golgi apparatus subcompartment Golgi cisterna Golgi stack Golgi medial cisterna early endosome endosome lumenal side of endoplasmic reticulum membrane lumenal side of membrane endosome membrane early endosome membrane
B, E, H	ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU	RNA binding binding organic cyclic compound binding nucleic acid binding	viral gene expression viral process viral transcription nucleobase-containing compound metabolic process organic cyclic compound metabolic process RNA replication organic substance metabolic process RNA metabolic process metabolic process primary metabolic process macromolecule metabolic process nucleic acid metabolic process	protein-containing complex ribonucleoprotein complex viral nucleocapsid viral capsid virion component host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region cellular anatomical entity helical viral capsid
C, F, I	N15 preTCR beta	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, D, G	IPR010579	MHC class I, alpha chain, C-terminal	Domain
A, D, G	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
A, D, G	IPR001039	MHC class I alpha chain, alpha1 alpha2 domains	Domain
A, D, G	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A, D, G	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, D, G	IPR007110	Immunoglobulin-like domain	Domain
A, D, G	IPR003597	Immunoglobulin C1-set	Domain
A, D, G	IPR011161	MHC class I-like antigen recognition-like	Domain
A, D, G	IPR037055	MHC class I-like antigen recognition-like superfamily	Homologous Superfamily
B, E, H	IPR035961	Rhabdovirus nucleoprotein-like	Homologous Superfamily
B, E, H	IPR000448	Rhabdovirus nucleocapsid	Domain
B, E, H	IPR023330	Rhabdovirus nucleocapsid, N-terminal	Homologous Superfamily
B, E, H	IPR023331	Rhabdovirus nucleocapsid, C-terminal	Homologous Superfamily

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 R01GM133198.