Annotations: 9WC3

Crystal structure of HLA-A*02:01-YL9 complexed with C4 TCR

External Resource: Annotation

Domain Annotation: SCOP2 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)
D	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8003766	3000071	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E	Wilms tumor protein	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding protein binding C2H2 zinc finger domain binding protein domain specific binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding protein binding C2H2 zinc finger domain binding protein domain specific binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity hemi-methylated DNA-binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity double-stranded methylated DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding RNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development animal gross anatomical part developmental process system development heart development circulatory system development tissue development extracellular matrix organization renal system development glomerular basement membrane development cellular component organization glomerulus development cellular process cellular component organization or biogenesis nephron development kidney development extracellular structure organization external encapsulating structure organization regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological 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 positive regulation of cellular process renal filtration cell differentiation kidney epithelium development cellular developmental process glomerular epithelial cell differentiation epithelial cell differentiation cell differentiation nephron epithelium development epithelial cell differentiation involved in kidney development epithelium development glomerular epithelium development cell differentiation involved in kidney development podocyte differentiation positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death regulation of developmental process regulation of gonad development regulation of reproductive process positive regulation of developmental process positive regulation of male gonad development regulation of multicellular organismal process regulation of male gonad development positive regulation of reproductive process positive regulation of gonad development positive regulation of multicellular organismal process regulation of growth regulation of cellular component organization negative regulation of biological process growth negative regulation of cell growth regulation of cell growth cell growth negative regulation of growth negative regulation of cellular process genitalia development male genitalia development cellular response to stimulus response to stimulus cellular response to gonadotropin stimulus response to endogenous stimulus response to gonadotropin cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical cellular response to hormone stimulus RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process sex determination diaphragm development muscle structure development skeletal muscle organ development respiratory system development muscle organ development metanephric epithelium development metanephros development positive regulation of DNA-templated transcription positive regulation of miRNA transcription positive regulation of miRNA metabolic process regulation of primary metabolic process regulation of RNA metabolic process miRNA transcription regulation of miRNA metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process regulation of RNA biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription regulation of miRNA transcription adrenal cortex development endocrine system development gland development adrenal cortex formation anatomical structure morphogenesis adrenal gland development anatomical structure formation involved in morphogenesis RNA splicing RNA processing cardiac muscle cell fate commitment muscle cell fate commitment muscle cell differentiation striated muscle tissue development cardiac cell fate commitment muscle tissue development cardiac muscle tissue development cardiac muscle cell differentiation cardiocyte differentiation striated muscle cell differentiation cell fate commitment developmental growth organ growth regulation of organ growth regulation of heart growth positive regulation of developmental growth positive regulation of heart growth heart growth regulation of multicellular organismal development regulation of developmental growth positive regulation of organ growth positive regulation of growth negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process mesonephric epithelium development nephron morphogenesis branching morphogenesis of an epithelial tube nephron tubule morphogenesis nephron epithelium morphogenesis nephron tubule development ureteric bud morphogenesis tube morphogenesis branching involved in ureteric bud morphogenesis renal tubule development animal organ morphogenesis epithelial tube morphogenesis ureteric bud development tube development mesonephros development morphogenesis of an epithelium tissue morphogenesis kidney morphogenesis morphogenesis of a branching structure mesonephric tubule morphogenesis mesonephric tubule development renal tubule morphogenesis morphogenesis of a branching epithelium positive regulation of transcription by RNA polymerase II negative regulation of gonad development development of primary female sexual characteristics regulation of female gonad development negative regulation of female gonad development negative regulation of developmental process female gonad development female sex differentiation negative regulation of reproductive process negative regulation of multicellular organismal process protein biosynthetic process post-transcriptional regulation of gene expression negative regulation of translation protein metabolic process negative regulation of protein metabolic process regulation of protein metabolic process translation negative regulation of gene expression regulation of translation negative regulation of gene expression via chromosomal CpG island methylation chromatin organization chromatin remodeling epigenetic regulation of gene expression negative regulation of gene expression, epigenetic regulation of kidney development metanephros morphogenesis positive regulation of metanephric ureteric bud development metanephric part of ureteric bud development regulation of metanephric ureteric bud development regulation of metanephros development posterior mesonephric tubule development sexual reproduction multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism gamete generation germ cell development sensory organ development eye development visual system development camera-type eye development sensory system development visceral serous pericardium development pericardium development negative regulation of programmed cell death negative regulation of apoptotic process regulation of animal organ morphogenesis regulation of animal organ formation animal organ formation regulation of anatomical structure morphogenesis cellular response to nitrogen compound response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP cellular response to oxygen-containing compound cellular response to cAMP blastoderm segmentation zygotic determination of anterior/posterior axis, embryo embryonic pattern specification anterior/posterior pattern specification anterior/posterior axis specification, embryo segmentation pattern specification process embryo development regionalization tripartite regional subdivision embryonic axis specification anterior/posterior axis specification thorax and anterior abdomen determination axis specification blood vessel morphogenesis vasculogenesis vasculature development blood vessel development negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation metanephric glomerulus vasculature development connective tissue development metanephric glomerulus development kidney vasculature development negative regulation of cell proliferation involved in kidney development renal system vasculature development regulation of glomerular mesangial cell proliferation metanephric glomerular mesangial cell proliferation involved in metanephros development negative regulation of glomerular mesangial cell proliferation metanephric nephron development regulation of metanephric glomerular mesangial cell proliferation negative regulation of metanephric glomerular mesangial cell proliferation cell proliferation involved in kidney development glomerular mesangium development metanephric glomerular mesangium development cell proliferation involved in metanephros development glomerular mesangial cell proliferation glomerulus vasculature development metanephric mesenchyme development mesenchyme development kidney mesenchyme development mesenchymal to epithelial transition metanephric nephron morphogenesis S-shaped body morphogenesis metanephric S-shaped body morphogenesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen cytoplasm cytosol nucleolus
D	Beta-2-microglobulin	binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding identical protein binding protein binding protein homodimerization activity protein dimerization activity structural molecule activity	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis 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 intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis 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 cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of 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 immune response regulation of adaptive immune response immune effector process regulation of gene expression regulation of leukocyte mediated immunity biosynthetic process regulation of response to stimulus positive regulation of production of molecular mediator of immune response positive regulation of multicellular organismal process regulation 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 positive regulation of lymphocyte mediated immunity positive regulation of biological process positive regulation of response to stimulus regulation of 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 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 cellular response to stimulus cellular response to iron ion cellular response to metal ion cellular response to chemical stimulus response to metal ion response to iron ion response to chemical regulation of localization import into cell regulation of cellular component organization transport negative regulation of biological process negative regulation of transport negative regulation of endocytosis vesicle-mediated transport cellular component organization localization negative regulation of cellular process cellular component organization or biogenesis regulation of endocytosis negative regulation of cellular component organization negative regulation of receptor-mediated endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization endocytosis receptor-mediated endocytosis positive regulation of cellular component organization positive regulation of endocytosis positive regulation of receptor-mediated endocytosis positive regulation of transport peptide antigen assembly with MHC class I protein complex protein-containing complex organization peptide antigen assembly with MHC protein complex MHC class I protein complex assembly cellular component biogenesis antigen processing and presentation cellular component assembly protein-containing complex assembly antigen processing and presentation of peptide antigen via MHC class I MHC protein complex assembly antigen processing and presentation of peptide antigen regulation of developmental process cellular developmental process cell development regulation of cell differentiation regulation of neurogenesis regulation of cell development regulation of nervous system development negative regulation of neurogenesis multicellular organism development neurogenesis cell differentiation anatomical structure development negative regulation of nervous system development negative regulation of cell differentiation system development developmental process regulation of multicellular organismal development negative regulation of developmental process nervous system development negative regulation of cell development negative regulation of multicellular organismal process animal gross anatomical part developmental process regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus response to biotic stimulus response to stress regulation of response to stress innate immune response response to external biotic stimulus natural killer cell mediated immunity regulation of natural killer cell mediated immunity response to other organism defense response regulation of innate immune response defense response to symbiont response to external stimulus defense response to other organism 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 antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of exogenous antigen negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation establishment of protein localization iron ion transport metal ion transport protein transport macromolecule localization transferrin transport transition metal ion transport monoatomic ion transport intracellular protein localization monoatomic cation transport system process sensory perception of chemical stimulus sensory perception nervous system process sensory perception of smell primary metabolic process protein metabolic process supramolecular fiber organization amyloid fibril formation protein homotetramerization protein complex oligomerization protein tetramerization protein homooligomerization antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II peptide antigen assembly with MHC class II protein complex MHC class II protein complex assembly cellular response to nicotine response to nicotine regulation of cellular senescence cellular senescence positive regulation of cellular senescence cellular response to stress antigen processing and presentation of endogenous peptide antigen antigen processing and presentation of endogenous antigen antigen processing and presentation of endogenous peptide antigen via MHC class I behavior learning or memory cognition negative regulation of monoatomic ion transport regulation of monoatomic ion transport regulation of iron ion transport regulation of metal ion transport negative regulation of iron ion transport regulation of leukocyte activation regulation of cell activation 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 positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of cell-cell adhesion positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of leukocyte cell-cell adhesion regulation of lymphocyte activation negative regulation of forebrain neuron differentiation forebrain development regulation of forebrain neuron differentiation central nervous system neuron differentiation neuron differentiation head development forebrain generation of neurons animal organ development brain development generation of neurons central nervous system development forebrain neuron differentiation negative regulation of neuron differentiation regulation of neuron differentiation	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex signaling receptor complex HFE-transferrin receptor complex MHC class I protein complex MHC protein complex endosome membrane intracellular anatomical structure endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane late endosome cytoplasm organelle membrane phagocytic vesicle phagocytic vesicle membrane endocytic vesicle membrane endocytic vesicle vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome Golgi apparatus membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen organelle lumen endoplasmic reticulum 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 vesicle lumen cytoplasmic vesicle lumen secretory granule lumen specific granule lumen secretory granule secretory vesicle specific granule anchoring junction cell junction focal adhesion cell-substrate junction MHC class II protein complex early endosome endosome lumen early endosome lumen recycling endosome recycling endosome membrane tertiary granule lumen tertiary granule early endosome membrane transport vesicle transport vesicle membrane coated vesicle membrane COPII-coated ER to Golgi transport vesicle ER to Golgi transport vesicle membrane coated vesicle
C	HLA-A 0201	-	-	-
B	C4 TCR beta chain	-	-	-
A	C4 TCR alpha chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E	IPR013087	Zinc finger C2H2-type	Domain
E	IPR000976	Wilm's tumour protein, N-terminal	Domain
E	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D	IPR007110	Immunoglobulin-like domain	Domain
D	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
D	IPR003597	Immunoglobulin C1-set	Domain
D	IPR015707	Beta-2-Microglobulin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E	: P19544	Denys-Drash syndrome Frasier syndrome WAGR syndrome kidney Wilms tumor malignant mesothelioma desmoplastic small round cell tumor schwannoma aniridia chronic myelogenous leukemia, BCR-ABL1 positive congenital diaphragmatic hernia nephrotic syndrome, type 4 glioblastoma glomerulonephritis acute myeloid leukemia giant cell glioblastoma Denys-Drash syndrome Frasier syndrome WAGR syndrome kidney Wilms tumor malignant mesothelioma desmoplastic small round cell tumor schwannoma aniridia chronic myelogenous leukemia, BCR-ABL1 positive congenital diaphragmatic hernia nephrotic syndrome, type 4 glioblastoma glomerulonephritis acute myeloid leukemia giant cell glioblastoma leukemia breast carcinoma primary ovarian failure Wilms tumor 1 malignant colon neoplasm malignant peripheral nerve sheath tumor Meacham syndrome osteosarcoma acute promyelocytic leukemia breast cancer cancer Congenital hernia of foramen of Morgagni endometrial carcinoma ovarian cancer peritoneal neoplasm Perlman syndrome 46,XY complete gonadal dysgenesis hereditary Wilms tumor intellectual disability malignant pancreatic neoplasm familial nephrotic syndrome pancreatic intraductal papillary-mucinous neoplasm heart disease 46,XY partial gonadal dysgenesis kidney disease aniridia 1 lung benign neoplasm colonic neoplasm pancreatic neoplasm hematologic disease prostate cancer uterine corpus leiomyoma benign colon neoplasm lung cancer congenital anemia
D	: P61769	familial visceral amyloidosis hypoproteinemia, hypercatabolic diffuse large B-cell lymphoma MHC class I deficiency esophageal squamous cell carcinoma kidney disease amyloidosis mature T-cell and NK-cell non-Hodgkin lymphoma autoimmune disease variant ABeta2M amyloidosis Hypergammaglobulinemia prostate cancer heart disease interstitial cystitis lung carcinoma familial visceral amyloidosis hypoproteinemia, hypercatabolic diffuse large B-cell lymphoma MHC class I deficiency esophageal squamous cell carcinoma kidney disease amyloidosis mature T-cell and NK-cell non-Hodgkin lymphoma autoimmune disease variant ABeta2M amyloidosis Hypergammaglobulinemia prostate cancer heart disease interstitial cystitis lung carcinoma acquired metabolic disease ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pilocytic astrocytoma psoriasis Sjogren syndrome glioblastoma juvenile dermatomyositis lung adenocarcinoma lymphatic system disease acute kidney failure pancreatic intraductal papillary-mucinous carcinoma periodic fever syndrome bone marrow disease rheumatoid arthritis Down syndrome subependymal giant cell astrocytoma lung cancer lymphoplasmacytic lymphoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm cancer schizophrenia ulcerative colitis

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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.