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8VRW

Cryo-EM structure of human invariant chain in complex with HLA-DR15

Functional Information from GO Data
ChainGOidnamespacecontents
C0000139cellular_componentGolgi membrane
C0001516biological_processprostaglandin biosynthetic process
C0001540molecular_functionamyloid-beta binding
C0001934biological_processpositive regulation of protein phosphorylation
C0001961biological_processpositive regulation of cytokine-mediated signaling pathway
C0002250biological_processadaptive immune response
C0002286biological_processT cell activation involved in immune response
C0002606biological_processpositive regulation of dendritic cell antigen processing and presentation
C0002792biological_processnegative regulation of peptide secretion
C0002830biological_processpositive regulation of type 2 immune response
C0002906biological_processnegative regulation of mature B cell apoptotic process
C0004896molecular_functioncytokine receptor activity
C0005515molecular_functionprotein binding
C0005576cellular_componentextracellular region
C0005634cellular_componentnucleus
C0005737cellular_componentcytoplasm
C0005764cellular_componentlysosome
C0005765cellular_componentlysosomal membrane
C0005768cellular_componentendosome
C0005770cellular_componentlate endosome
C0005771cellular_componentmultivesicular body
C0005773cellular_componentvacuole
C0005783cellular_componentendoplasmic reticulum
C0005789cellular_componentendoplasmic reticulum membrane
C0005794cellular_componentGolgi apparatus
C0005886cellular_componentplasma membrane
C0006886biological_processintracellular protein transport
C0006952biological_processdefense response
C0009897cellular_componentexternal side of plasma membrane
C0009986cellular_componentcell surface
C0010628biological_processpositive regulation of gene expression
C0012507cellular_componentER to Golgi transport vesicle membrane
C0016020cellular_componentmembrane
C0016064biological_processimmunoglobulin mediated immune response
C0019882biological_processantigen processing and presentation
C0019883biological_processantigen processing and presentation of endogenous antigen
C0019886biological_processantigen processing and presentation of exogenous peptide antigen via MHC class II
C0019955molecular_functioncytokine binding
C0023026molecular_functionMHC class II protein complex binding
C0030336biological_processnegative regulation of cell migration
C0030658cellular_componenttransport vesicle membrane
C0030666cellular_componentendocytic vesicle membrane
C0030669cellular_componentclathrin-coated endocytic vesicle membrane
C0030890biological_processpositive regulation of B cell proliferation
C0031394biological_processpositive regulation of prostaglandin biosynthetic process
C0032588cellular_componenttrans-Golgi network membrane
C0032722biological_processpositive regulation of chemokine production
C0032755biological_processpositive regulation of interleukin-6 production
C0032757biological_processpositive regulation of interleukin-8 production
C0032991cellular_componentprotein-containing complex
C0033674biological_processpositive regulation of kinase activity
C0034341biological_processresponse to type II interferon
C0035691biological_processmacrophage migration inhibitory factor signaling pathway
C0035692cellular_componentmacrophage migration inhibitory factor receptor complex
C0035693cellular_componentNOS2-CD74 complex
C0035718molecular_functionmacrophage migration inhibitory factor binding
C0042289molecular_functionMHC class II protein binding
C0042609molecular_functionCD4 receptor binding
C0042613cellular_componentMHC class II protein complex
C0042658molecular_functionMHC class II protein binding, via antigen binding groove
C0042802molecular_functionidentical protein binding
C0043030biological_processregulation of macrophage activation
C0043066biological_processnegative regulation of apoptotic process
C0043123biological_processpositive regulation of canonical NF-kappaB signal transduction
C0043202cellular_componentlysosomal lumen
C0043410biological_processpositive regulation of MAPK cascade
C0043518biological_processnegative regulation of DNA damage response, signal transduction by p53 class mediator
C0044183molecular_functionprotein folding chaperone
C0045058biological_processT cell selection
C0045059biological_processpositive thymic T cell selection
C0045060biological_processnegative thymic T cell selection
C0045581biological_processnegative regulation of T cell differentiation
C0045582biological_processpositive regulation of T cell differentiation
C0045657biological_processpositive regulation of monocyte differentiation
C0045893biological_processpositive regulation of DNA-templated transcription
C0046598biological_processpositive regulation of viral entry into host cell
C0048146biological_processpositive regulation of fibroblast proliferation
C0050731biological_processpositive regulation of peptidyl-tyrosine phosphorylation
C0050998molecular_functionnitric-oxide synthase binding
C0051085biological_processchaperone cofactor-dependent protein refolding
C0060907biological_processpositive regulation of macrophage cytokine production
C0065003biological_processprotein-containing complex assembly
C0070062cellular_componentextracellular exosome
C0070374biological_processpositive regulation of ERK1 and ERK2 cascade
C0090023biological_processpositive regulation of neutrophil chemotaxis
C0098553cellular_componentlumenal side of endoplasmic reticulum membrane
C1902166biological_processnegative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
C2000343biological_processpositive regulation of chemokine (C-X-C motif) ligand 2 production
C2000448biological_processpositive regulation of macrophage migration inhibitory factor signaling pathway
F0000139cellular_componentGolgi membrane
F0001516biological_processprostaglandin biosynthetic process
F0001540molecular_functionamyloid-beta binding
F0001934biological_processpositive regulation of protein phosphorylation
F0001961biological_processpositive regulation of cytokine-mediated signaling pathway
F0002250biological_processadaptive immune response
F0002286biological_processT cell activation involved in immune response
F0002606biological_processpositive regulation of dendritic cell antigen processing and presentation
F0002792biological_processnegative regulation of peptide secretion
F0002830biological_processpositive regulation of type 2 immune response
F0002906biological_processnegative regulation of mature B cell apoptotic process
F0004896molecular_functioncytokine receptor activity
F0005515molecular_functionprotein binding
F0005576cellular_componentextracellular region
F0005634cellular_componentnucleus
F0005737cellular_componentcytoplasm
F0005764cellular_componentlysosome
F0005765cellular_componentlysosomal membrane
F0005768cellular_componentendosome
F0005770cellular_componentlate endosome
F0005771cellular_componentmultivesicular body
F0005773cellular_componentvacuole
F0005783cellular_componentendoplasmic reticulum
F0005789cellular_componentendoplasmic reticulum membrane
F0005794cellular_componentGolgi apparatus
F0005886cellular_componentplasma membrane
F0006886biological_processintracellular protein transport
F0006952biological_processdefense response
F0009897cellular_componentexternal side of plasma membrane
F0009986cellular_componentcell surface
F0010628biological_processpositive regulation of gene expression
F0012507cellular_componentER to Golgi transport vesicle membrane
F0016020cellular_componentmembrane
F0016064biological_processimmunoglobulin mediated immune response
F0019882biological_processantigen processing and presentation
F0019883biological_processantigen processing and presentation of endogenous antigen
F0019886biological_processantigen processing and presentation of exogenous peptide antigen via MHC class II
F0019955molecular_functioncytokine binding
F0023026molecular_functionMHC class II protein complex binding
F0030336biological_processnegative regulation of cell migration
F0030658cellular_componenttransport vesicle membrane
F0030666cellular_componentendocytic vesicle membrane
F0030669cellular_componentclathrin-coated endocytic vesicle membrane
F0030890biological_processpositive regulation of B cell proliferation
F0031394biological_processpositive regulation of prostaglandin biosynthetic process
F0032588cellular_componenttrans-Golgi network membrane
F0032722biological_processpositive regulation of chemokine production
F0032755biological_processpositive regulation of interleukin-6 production
F0032757biological_processpositive regulation of interleukin-8 production
F0032991cellular_componentprotein-containing complex
F0033674biological_processpositive regulation of kinase activity
F0034341biological_processresponse to type II interferon
F0035691biological_processmacrophage migration inhibitory factor signaling pathway
F0035692cellular_componentmacrophage migration inhibitory factor receptor complex
F0035693cellular_componentNOS2-CD74 complex
F0035718molecular_functionmacrophage migration inhibitory factor binding
F0042289molecular_functionMHC class II protein binding
F0042609molecular_functionCD4 receptor binding
F0042613cellular_componentMHC class II protein complex
F0042658molecular_functionMHC class II protein binding, via antigen binding groove
F0042802molecular_functionidentical protein binding
F0043030biological_processregulation of macrophage activation
F0043066biological_processnegative regulation of apoptotic process
F0043123biological_processpositive regulation of canonical NF-kappaB signal transduction
F0043202cellular_componentlysosomal lumen
F0043410biological_processpositive regulation of MAPK cascade
F0043518biological_processnegative regulation of DNA damage response, signal transduction by p53 class mediator
F0044183molecular_functionprotein folding chaperone
F0045058biological_processT cell selection
F0045059biological_processpositive thymic T cell selection
F0045060biological_processnegative thymic T cell selection
F0045581biological_processnegative regulation of T cell differentiation
F0045582biological_processpositive regulation of T cell differentiation
F0045657biological_processpositive regulation of monocyte differentiation
F0045893biological_processpositive regulation of DNA-templated transcription
F0046598biological_processpositive regulation of viral entry into host cell
F0048146biological_processpositive regulation of fibroblast proliferation
F0050731biological_processpositive regulation of peptidyl-tyrosine phosphorylation
F0050998molecular_functionnitric-oxide synthase binding
F0051085biological_processchaperone cofactor-dependent protein refolding
F0060907biological_processpositive regulation of macrophage cytokine production
F0065003biological_processprotein-containing complex assembly
F0070062cellular_componentextracellular exosome
F0070374biological_processpositive regulation of ERK1 and ERK2 cascade
F0090023biological_processpositive regulation of neutrophil chemotaxis
F0098553cellular_componentlumenal side of endoplasmic reticulum membrane
F1902166biological_processnegative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
F2000343biological_processpositive regulation of chemokine (C-X-C motif) ligand 2 production
F2000448biological_processpositive regulation of macrophage migration inhibitory factor signaling pathway
I0000139cellular_componentGolgi membrane
I0001516biological_processprostaglandin biosynthetic process
I0001540molecular_functionamyloid-beta binding
I0001934biological_processpositive regulation of protein phosphorylation
I0001961biological_processpositive regulation of cytokine-mediated signaling pathway
I0002250biological_processadaptive immune response
I0002286biological_processT cell activation involved in immune response
I0002606biological_processpositive regulation of dendritic cell antigen processing and presentation
I0002792biological_processnegative regulation of peptide secretion
I0002830biological_processpositive regulation of type 2 immune response
I0002906biological_processnegative regulation of mature B cell apoptotic process
I0004896molecular_functioncytokine receptor activity
I0005515molecular_functionprotein binding
I0005576cellular_componentextracellular region
I0005634cellular_componentnucleus
I0005737cellular_componentcytoplasm
I0005764cellular_componentlysosome
I0005765cellular_componentlysosomal membrane
I0005768cellular_componentendosome
I0005770cellular_componentlate endosome
I0005771cellular_componentmultivesicular body
I0005773cellular_componentvacuole
I0005783cellular_componentendoplasmic reticulum
I0005789cellular_componentendoplasmic reticulum membrane
I0005794cellular_componentGolgi apparatus
I0005886cellular_componentplasma membrane
I0006886biological_processintracellular protein transport
I0006952biological_processdefense response
I0009897cellular_componentexternal side of plasma membrane
I0009986cellular_componentcell surface
I0010628biological_processpositive regulation of gene expression
I0012507cellular_componentER to Golgi transport vesicle membrane
I0016020cellular_componentmembrane
I0016064biological_processimmunoglobulin mediated immune response
I0019882biological_processantigen processing and presentation
I0019883biological_processantigen processing and presentation of endogenous antigen
I0019886biological_processantigen processing and presentation of exogenous peptide antigen via MHC class II
I0019955molecular_functioncytokine binding
I0023026molecular_functionMHC class II protein complex binding
I0030336biological_processnegative regulation of cell migration
I0030658cellular_componenttransport vesicle membrane
I0030666cellular_componentendocytic vesicle membrane
I0030669cellular_componentclathrin-coated endocytic vesicle membrane
I0030890biological_processpositive regulation of B cell proliferation
I0031394biological_processpositive regulation of prostaglandin biosynthetic process
I0032588cellular_componenttrans-Golgi network membrane
I0032722biological_processpositive regulation of chemokine production
I0032755biological_processpositive regulation of interleukin-6 production
I0032757biological_processpositive regulation of interleukin-8 production
I0032991cellular_componentprotein-containing complex
I0033674biological_processpositive regulation of kinase activity
I0034341biological_processresponse to type II interferon
I0035691biological_processmacrophage migration inhibitory factor signaling pathway
I0035692cellular_componentmacrophage migration inhibitory factor receptor complex
I0035693cellular_componentNOS2-CD74 complex
I0035718molecular_functionmacrophage migration inhibitory factor binding
I0042289molecular_functionMHC class II protein binding
I0042609molecular_functionCD4 receptor binding
I0042613cellular_componentMHC class II protein complex
I0042658molecular_functionMHC class II protein binding, via antigen binding groove
I0042802molecular_functionidentical protein binding
I0043030biological_processregulation of macrophage activation
I0043066biological_processnegative regulation of apoptotic process
I0043123biological_processpositive regulation of canonical NF-kappaB signal transduction
I0043202cellular_componentlysosomal lumen
I0043410biological_processpositive regulation of MAPK cascade
I0043518biological_processnegative regulation of DNA damage response, signal transduction by p53 class mediator
I0044183molecular_functionprotein folding chaperone
I0045058biological_processT cell selection
I0045059biological_processpositive thymic T cell selection
I0045060biological_processnegative thymic T cell selection
I0045581biological_processnegative regulation of T cell differentiation
I0045582biological_processpositive regulation of T cell differentiation
I0045657biological_processpositive regulation of monocyte differentiation
I0045893biological_processpositive regulation of DNA-templated transcription
I0046598biological_processpositive regulation of viral entry into host cell
I0048146biological_processpositive regulation of fibroblast proliferation
I0050731biological_processpositive regulation of peptidyl-tyrosine phosphorylation
I0050998molecular_functionnitric-oxide synthase binding
I0051085biological_processchaperone cofactor-dependent protein refolding
I0060907biological_processpositive regulation of macrophage cytokine production
I0065003biological_processprotein-containing complex assembly
I0070062cellular_componentextracellular exosome
I0070374biological_processpositive regulation of ERK1 and ERK2 cascade
I0090023biological_processpositive regulation of neutrophil chemotaxis
I0098553cellular_componentlumenal side of endoplasmic reticulum membrane
I1902166biological_processnegative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
I2000343biological_processpositive regulation of chemokine (C-X-C motif) ligand 2 production
I2000448biological_processpositive regulation of macrophage migration inhibitory factor signaling pathway
Functional Information from PROSITE/UniProt
site_idPS00290
Number of Residues7
DetailsIG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YTCQVEH
ChainResidueDetails
BTYR171-HIS177
ATYR161-HIS167

site_idPS00484
Number of Residues30
DetailsTHYROGLOBULIN_1_1 Thyroglobulin type-1 repeat signature. FrpkCden.GnYlplQcygsigyc....WCVfpn.G
ChainResidueDetails
CPHE228-GLY257

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues75
DetailsTRANSMEM: Helical; Signal-anchor for type II membrane protein => ECO:0000255
ChainResidueDetails
CGLY47-TYR72
FGLY47-TYR72
IGLY47-TYR72

site_idSWS_FT_FI2
Number of Residues669
DetailsTOPO_DOM: Extracellular => ECO:0000255
ChainResidueDetails
CGLN73-MET296
FGLN73-MET296
IGLN73-MET296

site_idSWS_FT_FI3
Number of Residues3
DetailsSITE: Breakpoint for translocation to form a CD74-ROS1 fusion protein
ChainResidueDetails
CLYS208
FLYS208
ILYS208

site_idSWS_FT_FI4
Number of Residues3
DetailsMOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P04441
ChainResidueDetails
CSER25
HTRP61
HHIS81
HASN82
FSER25
ISER25
BASN82
EASP57
ETRP61
EHIS81
EASN82
HASP57

site_idSWS_FT_FI5
Number of Residues3
DetailsCARBOHYD: N-linked (GlcNAc...) asparagine
ChainResidueDetails
CASN130
FASN130
IASN130
DALA52
GGLY49
GALA52

site_idSWS_FT_FI6
Number of Residues3
DetailsCARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000269|PubMed:19159218
ChainResidueDetails
CASN136
FASN136
IASN136

site_idSWS_FT_FI7
Number of Residues3
DetailsCARBOHYD: O-linked (GalNAc...) threonine => ECO:0000269|PubMed:22171320, ECO:0000269|PubMed:23234360
ChainResidueDetails
CTHR203
FTHR203
ITHR203
HLYS225

site_idSWS_FT_FI8
Number of Residues3
DetailsCARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000269|PubMed:10022822
ChainResidueDetails
CASN256
FASN256
IASN256

site_idSWS_FT_FI9
Number of Residues3
DetailsCARBOHYD: O-linked (GalNAc...) serine => ECO:0000269|PubMed:23234360
ChainResidueDetails
CSER281
FSER281
ISER281

site_idSWS_FT_FI10
Number of Residues3
DetailsCARBOHYD: O-linked (Xyl...) (chondroitin sulfate) serine => ECO:0000269|PubMed:25326458, ECO:0000269|PubMed:32337544, ECO:0000269|PubMed:36213313, ECO:0000269|PubMed:37453717
ChainResidueDetails
CSER282
FSER282
ISER282

site_idSWS_FT_FI11
Number of Residues3
DetailsSITE: Self- and pathogen-derived peptide antigen => ECO:0000269|PubMed:17583734, ECO:0000269|PubMed:23260142, ECO:0000269|PubMed:31619516, ECO:0000269|PubMed:8145819, ECO:0007744|PDB:4FQX, ECO:0007744|PDB:4GBX
ChainResidueDetails
AARG76
DARG76
GARG76

site_idSWS_FT_FI12
Number of Residues6
DetailsCARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000269|PubMed:19159218, ECO:0000269|PubMed:7477400
ChainResidueDetails
AASN78
AASN118
DASN78
DASN118
GASN78
GASN118

site_idSWS_FT_FI13
Number of Residues6
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:19117940
ChainResidueDetails
ALYS219
DLYS219
GLYS219

222415

PDB entries from 2024-07-10

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