4P5K | pdb_00004p5k

Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergy and Autoimmunity

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT 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)
C [auth D]	d4p5kd2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth D]	d4p5kd1	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4p5ka2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4p5ka1	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth E]	Cas_Cas5d	e4p5kE1	A: alpha bundles	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (develop294)
D [auth E]	L_protein_N	e4p5kE2	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: Restriction endonuclease-like	F: L_protein_N	ECOD (develop294)
B	Cas_Cas5d	e4p5kB2	A: alpha bundles	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (develop294)
B	L_protein_N	e4p5kB3	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: Restriction endonuclease-like	F: L_protein_N	ECOD (develop294)
C [auth D]	Cas_Cas5d	e4p5kD1	A: alpha bundles	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (develop294)
A	Cas_Cas5d	e4p5kA1	A: alpha bundles	X: Formyltransferase	H: Formyltransferase	T: Formyltransferase	F: Cas_Cas5d	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth E]	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
D [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth D]	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
C [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B, D [auth E]	MH2 HLA-DPA10103_PEPTIDE_HLA-DPB12602	PEPTIDE-II-BETA	Homo sapiens (human)	HLA-DPB13201, HLA-DPB14101, HLA-DPB14601, HLA-DPB18101, HLA-DPB11802, HLA-DPB12602	G-DOMAIN G-BETA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_PEPTIDE-BETA	IMGT (202610-0)
A, C [auth D]	MH2 HLA-DPA10103_PEPTIDE_HLA-DPB12602	II-ALPHA	Homo sapiens (human)	HLA-DPA1*0103	G-DOMAIN G-ALPHA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_PEPTIDE-BETA	IMGT (202610-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D [auth E]	PF00969	Class II histocompatibility antigen, beta domain (MHC_II_beta)	Class II histocompatibility antigen, beta domain		Domain
B, D [auth E]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
A, C [auth D]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
A, C [auth D]	PF00993	Class II histocompatibility antigen, alpha domain (MHC_II_alpha)	Class II histocompatibility antigen, alpha domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D [auth E]	RAS peptide,HLA class II histocompatibility antigen, DP beta 1 chain	binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding	regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process 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 cellular process antigen receptor-mediated signaling pathway activation of immune response adaptive immune response antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of peptide antigen antigen processing and presentation of exogenous antigen peptide antigen assembly with MHC class II protein complex protein-containing complex organization peptide antigen assembly with MHC protein complex MHC class II protein complex assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex assembly MHC protein complex assembly cellular component organization or biogenesis multicellular organismal process positive regulation of cell population proliferation regulation of leukocyte activation regulation of cell activation positive regulation of cell activation T cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of leukocyte proliferation cell population proliferation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation regulation of cell population proliferation mononuclear cell 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 lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of mononuclear cell proliferation regulation of multicellular organismal process 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 cell activation regulation of T cell activation regulation of T cell proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation regulation of type II interferon production type II interferon production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of type II interferon production regulation of gene expression biosynthetic process positive regulation of gene expression metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process	cellular anatomical structure 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 cellular anatomical structure 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 cell surface MHC protein complex cell periphery MHC class II protein complex protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex endosome membrane endosome late endosome membrane endomembrane system late endosome organelle subcompartment lumenal side of endoplasmic reticulum membrane side of membrane lumenal side of membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome Golgi membrane Golgi apparatus Golgi apparatus subcompartment trans-Golgi network membrane trans-Golgi network transport vesicle transport vesicle membrane COPII-coated ER to Golgi transport vesicle ER to Golgi transport vesicle membrane
A, C [auth D]	HLA class II histocompatibility antigen, DP alpha 1 chain	binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity MHC class II receptor activity immune receptor activity	regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process adaptive immune response antigen processing and presentation of exogenous peptide antigen via MHC class II regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process adaptive immune response antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of peptide antigen antigen processing and presentation of exogenous antigen peptide antigen assembly with MHC class II protein complex protein-containing complex organization peptide antigen assembly with MHC protein complex MHC class II protein complex assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex assembly cellular process MHC protein complex assembly cellular component organization or biogenesis biological process involved in interspecies interaction between organisms response to other organism defense response response to type II interferon response to cytokine defense response to symbiont response to external stimulus cellular response to type II interferon response to biotic stimulus response to peptide response to chemical defense response to other organism response to stress innate immune response cellular response to cytokine stimulus response to external biotic stimulus multicellular organismal process regulation of cellular process positive regulation of cell population proliferation regulation of leukocyte activation regulation of cell activation positive regulation of cell activation T cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of leukocyte proliferation cell population proliferation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation regulation of cell population proliferation mononuclear cell 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 lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of mononuclear cell proliferation regulation of multicellular organismal process 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 cell activation regulation of T cell activation regulation of T cell proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation regulation of type II interferon production type II interferon production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of type II interferon production regulation of gene expression biosynthetic process positive regulation of gene expression metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process	membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle cellular anatomical structure bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle cellular anatomical structure 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 membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane cell surface MHC protein complex cell periphery MHC class II protein complex protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex endosome membrane endosome late endosome membrane endomembrane system late endosome organelle subcompartment lumenal side of endoplasmic reticulum membrane side of membrane lumenal side of membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome Golgi membrane Golgi apparatus Golgi apparatus subcompartment trans-Golgi network membrane trans-Golgi network transport vesicle transport vesicle membrane COPII-coated ER to Golgi transport vesicle ER to Golgi transport vesicle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D [auth E]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, D [auth E]	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
B, D [auth E]	IPR003597	Immunoglobulin C1-set	Domain
B, D [auth E]	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
B, D [auth E]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B, D [auth E]	IPR000353	MHC class II, beta chain, N-terminal	Domain
B, D [auth E]	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
B, D [auth E]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, D [auth E]	IPR007110	Immunoglobulin-like domain	Domain
A, C [auth D]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, C [auth D]	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
A, C [auth D]	IPR003597	Immunoglobulin C1-set	Domain
A, C [auth D]	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
A, C [auth D]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A, C [auth D]	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
A, C [auth D]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, C [auth D]	IPR007110	Immunoglobulin-like domain	Domain
A, C [auth D]	IPR001003	MHC class II, alpha chain, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D [auth E]	Pharos: P04440	granulomatosis with polyangiitis rheumatoid arthritis angioedema sarcoidosis endometriosis asthma chronic beryllium disease myasthenia gravis cervical cancer celiac disease Drug Eruptions irritant dermatitis chronic hepatitis B virus infection urticaria juvenile idiopathic arthritis granulomatosis with polyangiitis rheumatoid arthritis angioedema sarcoidosis endometriosis asthma chronic beryllium disease myasthenia gravis cervical cancer celiac disease Drug Eruptions irritant dermatitis chronic hepatitis B virus infection urticaria juvenile idiopathic arthritis multiple sclerosis systemic sclerosis Hashimoto thyroiditis inflammatory bowel disease lung adenocarcinoma pulmonary hypertension schizophrenia dermatomyositis ulcerative colitis hepatitis B virus infection lung carcinoma allergic rhinitis breast carcinoma osteoarthritis Sjogren syndrome diabetes mellitus Graves disease IgA glomerulonephritis C1 inhibitor deficiency primary biliary cholangitis Crohn disease diffuse scleroderma
A, C [auth D]	Pharos: P20036	irritant dermatitis chronic hepatitis B virus infection hepatocellular carcinoma limb-girdle muscular dystrophy lymphoplasmacytic lymphoma malignant mesothelioma adrenal cortex carcinoma non-small cell lung carcinoma Becker muscular dystrophy pancreatic intraductal papillary-mucinous carcinoma chronic obstructive pulmonary disease pilocytic astrocytoma cystic fibrosis Sjogren syndrome diffuse scleroderma irritant dermatitis chronic hepatitis B virus infection hepatocellular carcinoma limb-girdle muscular dystrophy lymphoplasmacytic lymphoma malignant mesothelioma adrenal cortex carcinoma non-small cell lung carcinoma Becker muscular dystrophy pancreatic intraductal papillary-mucinous carcinoma chronic obstructive pulmonary disease pilocytic astrocytoma cystic fibrosis Sjogren syndrome diffuse scleroderma ulcerative colitis ductal breast carcinoma in situ glioblastoma interstitial cystitis juvenile dermatomyositis lung cancer malignant ependymoma malignant pancreatic neoplasm astrocytic tumor ovarian cancer breast carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia congestive heart failure plasma cell myeloma dermatomyositis subependymal giant cell astrocytoma Down syndrome esophageal adenocarcinoma head and neck cancer invasive ductal breast carcinoma large cell medulloblastoma lung carcinoma malignant glioma nephrosclerosis atypical teratoid rhabdoid tumor pancreatic ductal adenocarcinoma Pick disease Crohn disease psoriasis diabetes mellitus systemic sclerosis Duchenne muscular dystrophy exocrine pancreatic carcinoma

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.