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- EMDB-43501: Cryo-EM structure of human invariant chain in complex with HLA-DQ -

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Entry
Database: EMDB / ID: EMD-43501
TitleCryo-EM structure of human invariant chain in complex with HLA-DQ
Map data
Sample
  • Complex: Trimeric complex of invariant chain associated with HLA-DQ alpha and beta
    • Protein or peptide: HLA class II histocompatibility antigen, DQ alpha 1 chain
    • Protein or peptide: HLA class II histocompatibility antigen, DQ beta 1 chain
    • Protein or peptide: HLA class II histocompatibility antigen gamma chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAntigen presentation / membrane protein / trimeric complex / IMMUNE SYSTEM
Function / homology
Function and homology information


negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / macrophage migration inhibitory factor binding / negative regulation of T cell differentiation / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization ...negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / macrophage migration inhibitory factor binding / negative regulation of T cell differentiation / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization / macrophage migration inhibitory factor receptor complex / positive regulation of cytokine-mediated signaling pathway / positive regulation of prostaglandin biosynthetic process / T cell activation involved in immune response / T cell selection / positive regulation of type 2 immune response / MHC class II receptor activity / host-mediated suppression of symbiont invasion / negative thymic T cell selection / MHC class II protein binding / negative regulation of mature B cell apoptotic process / positive regulation of kinase activity / positive regulation of monocyte differentiation / positive thymic T cell selection / vacuole / CD4 receptor binding / cytokine receptor activity / positive regulation of neutrophil chemotaxis / positive regulation of chemokine (C-X-C motif) ligand 2 production / prostaglandin biosynthetic process / positive regulation of macrophage cytokine production / positive regulation of T cell differentiation / transport vesicle membrane / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of macrophage activation / antigen processing and presentation / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / cytokine binding / nitric-oxide synthase binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / : / immunoglobulin mediated immune response / humoral immune response / Generation of second messenger molecules / Co-inhibition by PD-1 / response to type II interferon / positive regulation of chemokine production / positive regulation of B cell proliferation / multivesicular body / protein folding chaperone / MHC class II antigen presentation / lysosomal lumen / negative regulation of cell migration / trans-Golgi network membrane / Cell surface interactions at the vascular wall / positive regulation of interleukin-8 production / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / intracellular protein transport / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / positive regulation of interleukin-6 production / positive regulation of protein phosphorylation / positive regulation of fibroblast proliferation / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / late endosome / T cell receptor signaling pathway / amyloid-beta binding / protein-containing complex assembly / adaptive immune response / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / protein stabilization / immune response / Golgi membrane / lysosomal membrane / external side of plasma membrane / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / protein-containing complex / extracellular exosome / identical protein binding / nucleus / membrane / plasma membrane
Similarity search - Function
MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / : / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 ...MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / : / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DQ alpha 1 chain / HLA class II histocompatibility antigen, DQ beta 1 chain / HLA class II histocompatibility antigen gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsWang N / Caveney NA / Jude KM / Garcia KC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH R01 AI103867 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structural insights into human MHC-II association with invariant chain.
Authors: Nan Wang / Deepa Waghray / Nathanael A Caveney / Kevin M Jude / K Christopher Garcia /
Abstract: The loading of processed peptides on to major histocompatibility complex II (MHC-II) molecules for recognition by T cells is vital to cell-mediated adaptive immunity. As part of this process, MHC-II ...The loading of processed peptides on to major histocompatibility complex II (MHC-II) molecules for recognition by T cells is vital to cell-mediated adaptive immunity. As part of this process, MHC-II associates with the invariant chain (Ii) during biosynthesis in the endoplasmic reticulum to prevent premature peptide loading and to serve as a scaffold for subsequent proteolytic processing into MHC-II-CLIP. Cryo-electron microscopy structures of full-length Human Leukocyte Antigen-DR (HLA-DR) and HLA-DQ complexes associated with Ii, resolved at 3.0 to 3.1 Å, elucidate the trimeric assembly of the HLA/Ii complex and define atomic-level interactions between HLA, Ii transmembrane domains, loop domains, and class II-associated invariant chain peptides (CLIP). Together with previous structures of MHC-II peptide loading intermediates DO and DM, our findings complete the structural path governing class II antigen presentation.
History
DepositionJan 24, 2024-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43501.png

Downloads & links

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Map

FileDownload / File: emd_43501.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 240 pix.
= 302.04 Å		1.26 Å/pix.
x 240 pix.
= 302.04 Å		1.26 Å/pix.
x 240 pix.
= 302.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2585 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00402
Minimum - Maximum-0.041426066 - 1.6262422
Average (Standard dev.)0.00094482664 (±0.02104436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 302.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43501_msk_1.map
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Half map: #2

Fileemd_43501_half_map_1.map
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Half map: #1

Fileemd_43501_half_map_2.map
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Sample components

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Entire : Trimeric complex of invariant chain associated with HLA-DQ alpha ...

EntireName: Trimeric complex of invariant chain associated with HLA-DQ alpha and beta
Components
  • Complex: Trimeric complex of invariant chain associated with HLA-DQ alpha and beta
    • Protein or peptide: HLA class II histocompatibility antigen, DQ alpha 1 chain
    • Protein or peptide: HLA class II histocompatibility antigen, DQ beta 1 chain
    • Protein or peptide: HLA class II histocompatibility antigen gamma chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Trimeric complex of invariant chain associated with HLA-DQ alpha ...

SupramoleculeName: Trimeric complex of invariant chain associated with HLA-DQ alpha and beta
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 330 KDa

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Macromolecule #1: HLA class II histocompatibility antigen, DQ alpha 1 chain

MacromoleculeName: HLA class II histocompatibility antigen, DQ alpha 1 chain
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.599943 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: MILNKALMLG ALALTTVMSP CGGEDIVADH VASYGVNLYQ SYGPSGQYTH EFDGDEQFYV DLGRKETVWC LPVLRQFRFD PQFALTNIA VLKHNLNSLI KRSNSTAATN EVPEVTVFSK SPVTLGQPNI LICLVDNIFP PVVNITWLSN GHSVTEGVSE T SFLSKSDH ...String:
MILNKALMLG ALALTTVMSP CGGEDIVADH VASYGVNLYQ SYGPSGQYTH EFDGDEQFYV DLGRKETVWC LPVLRQFRFD PQFALTNIA VLKHNLNSLI KRSNSTAATN EVPEVTVFSK SPVTLGQPNI LICLVDNIFP PVVNITWLSN GHSVTEGVSE T SFLSKSDH SFFKISYLTL LPSAEESYDC KVEHWGLDKP LLKHWEPEIP APMSELTETV VCALGLSVGL VGIVVGTVFI IR GLRSVGA SRHQGPLAAA LEVLFQGPGA AEDQVDPRLI DGKHHHHHHH H

UniProtKB: HLA class II histocompatibility antigen, DQ alpha 1 chain

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Macromolecule #2: HLA class II histocompatibility antigen, DQ beta 1 chain

MacromoleculeName: HLA class II histocompatibility antigen, DQ beta 1 chain
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.798309 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: MSWKKALRIP GGLRAATVTL MLAMLSTPVA EGRDSPEDFV YQFKAMCYFT NGTERVRYVT RYIYNREEYA RFDSDVEVYR AVTPLGPPD AEYWNSQKEV LERTRAELDT VCRHNYQLEL RTTLQRRVEP TVTISPSRTE ALNHHNLLVC SVTDFYPAQI K VRWFRNDQ ...String:
MSWKKALRIP GGLRAATVTL MLAMLSTPVA EGRDSPEDFV YQFKAMCYFT NGTERVRYVT RYIYNREEYA RFDSDVEVYR AVTPLGPPD AEYWNSQKEV LERTRAELDT VCRHNYQLEL RTTLQRRVEP TVTISPSRTE ALNHHNLLVC SVTDFYPAQI K VRWFRNDQ EETTGVVSTP LIRNGDWTFQ ILVMLEMTPQ HGDVYTCHVE HPSLQNPITV EWRAQSESAQ SKMLSGIGGF VL GLIFLGL GLIIHHRSQK GLLHAAALEV LFQGPGAAED QVDPRLIDGK HHHHHHHH

UniProtKB: HLA class II histocompatibility antigen, DQ beta 1 chain

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Macromolecule #3: HLA class II histocompatibility antigen gamma chain

MacromoleculeName: HLA class II histocompatibility antigen gamma chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.901906 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: MDYKDDDDAG TSRHRRRSRS CREDQKPVMD DQRDLISNNE QLPMLGRRPG APESKCSRGA LYTGFSILVT LLLAGQATTA YFLYQQQGR LDKLTVTSQN LQLENLRMKL PKPPKPVSKM RMATPLLMQA LPMGALPQGP MQNATKYGNM TEDHVMHLLQ N ADPLKVYP ...String:
MDYKDDDDAG TSRHRRRSRS CREDQKPVMD DQRDLISNNE QLPMLGRRPG APESKCSRGA LYTGFSILVT LLLAGQATTA YFLYQQQGR LDKLTVTSQN LQLENLRMKL PKPPKPVSKM RMATPLLMQA LPMGALPQGP MQNATKYGNM TEDHVMHLLQ N ADPLKVYP PLKGSFPENL RHLKNTMETI DWKVFESWMH HWLLFEMSRH SLEQKPTDAP PKVLTKCQEE VSHIPAVHPG SF RPKCDEN GNYLPLQCYG SIGYCWCVFP NGTEVPNTRS RGHHNCSESL ELEDPSSGLG VTKQDLGPVP M

UniProtKB: HLA class II histocompatibility antigen gamma chain

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3pdo

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 421582
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8vsp:
Cryo-EM structure of human invariant chain in complex with HLA-DQ

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