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- EMDB-28573: CryoEM structure of HLA-A2 bound to MAGEA4 (230-239) peptide -

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Basic information

Entry
Database: EMDB / ID: EMD-28573
TitleCryoEM structure of HLA-A2 bound to MAGEA4 (230-239) peptide
Map data
Sample
  • Complex: Single chain disulfide stabilized trimer of HLA-A2, Beta-2-microglobulin, MAGE-A4 peptide in complex with anti-Beta-2-microglobulin Fab 2M2
    • Protein or peptide: Beta-2-microglobulin,HLA class I antigen,MAGE-A4 peptide chimera
KeywordsHLA / MHC / IMMUNE SYSTEM
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / ER to Golgi transport vesicle membrane / MHC class I protein complex / phagocytic vesicle membrane / recycling endosome membrane / early endosome membrane / immune response / cell surface / metal ion binding
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSaotome K / Franklin MC
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2023
Title: Structural analysis of cancer-relevant TCR-CD3 and peptide-MHC complexes by cryoEM.
Authors: Kei Saotome / Drew Dudgeon / Kiersten Colotti / Michael J Moore / Jennifer Jones / Yi Zhou / Ashique Rafique / George D Yancopoulos / Andrew J Murphy / John C Lin / William C Olson / Matthew C Franklin /
Abstract: The recognition of antigenic peptide-MHC (pMHC) molecules by T-cell receptors (TCR) initiates the T-cell mediated immune response. Structural characterization is key for understanding the specificity ...The recognition of antigenic peptide-MHC (pMHC) molecules by T-cell receptors (TCR) initiates the T-cell mediated immune response. Structural characterization is key for understanding the specificity of TCR-pMHC interactions and informing the development of therapeutics. Despite the rapid rise of single particle cryoelectron microscopy (cryoEM), x-ray crystallography has remained the preferred method for structure determination of TCR-pMHC complexes. Here, we report cryoEM structures of two distinct full-length α/β TCR-CD3 complexes bound to their pMHC ligand, the cancer-testis antigen HLA-A2/MAGEA4 (230-239). We also determined cryoEM structures of pMHCs containing MAGEA4 (230-239) peptide and the closely related MAGEA8 (232-241) peptide in the absence of TCR, which provided a structural explanation for the MAGEA4 preference displayed by the TCRs. These findings provide insights into the TCR recognition of a clinically relevant cancer antigen and demonstrate the utility of cryoEM for high-resolution structural analysis of TCR-pMHC interactions.
History
DepositionOct 13, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28573.png

Downloads & links

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Map

FileDownload / File: emd_28573.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 12.0
Minimum - Maximum-58.082740000000001 - 80.70523
Average (Standard dev.)-0.000000000003776 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28573_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28573_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Single chain disulfide stabilized trimer of HLA-A2, Beta-2-microg...

EntireName: Single chain disulfide stabilized trimer of HLA-A2, Beta-2-microglobulin, MAGE-A4 peptide in complex with anti-Beta-2-microglobulin Fab 2M2
Components
  • Complex: Single chain disulfide stabilized trimer of HLA-A2, Beta-2-microglobulin, MAGE-A4 peptide in complex with anti-Beta-2-microglobulin Fab 2M2
    • Protein or peptide: Beta-2-microglobulin,HLA class I antigen,MAGE-A4 peptide chimera

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Supramolecule #1: Single chain disulfide stabilized trimer of HLA-A2, Beta-2-microg...

SupramoleculeName: Single chain disulfide stabilized trimer of HLA-A2, Beta-2-microglobulin, MAGE-A4 peptide in complex with anti-Beta-2-microglobulin Fab 2M2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Beta-2-microglobulin,HLA class I antigen,MAGE-A4 peptide chimera

MacromoleculeName: Beta-2-microglobulin,HLA class I antigen,MAGE-A4 peptide chimera
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.306184 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: GVYDGREHTV GCGGSGGGGS GGGGSIQRTP KIQVYSRHPA ENGKSNFLNC YVSGFHPSDI EVDLLKNGER IEKVEHSDLS FSKDWSFYL LYYTEFTPTE KDEYACRVNH VTLSQPKIVK WDRDMGGGGS GGGGSGGGGS GGGGSGSHSM RYFFTSVSRP G RGEPRFIA ...String:
GVYDGREHTV GCGGSGGGGS GGGGSIQRTP KIQVYSRHPA ENGKSNFLNC YVSGFHPSDI EVDLLKNGER IEKVEHSDLS FSKDWSFYL LYYTEFTPTE KDEYACRVNH VTLSQPKIVK WDRDMGGGGS GGGGSGGGGS GGGGSGSHSM RYFFTSVSRP G RGEPRFIA VGYVDDTQFV RFDSDAASQR MEPRAPWIEQ EGPEYWDGET RKVKAHSQTH RVDLGTLRGC YNQSEAGSHT VQ RMYGCDV GSDWRFLRGY HQYAYDGKDY IALKEDLRSW TAADMAAQTT KHKWEAAHVA EQLRAYLEGT CVEWLRRYLE NGK ETLQRT DAPKTHMTHH AVSDHEATLR CWALSFYPAE ITLTWQRDGE DQTQDTELVE TRPAGDGTFQ KWAAVVVPSG QEQR YTCHV QHEGLPKPLT LRWEPEQKLI SEEDLGGEQK LISEEDLHHH HHH

UniProtKB: HLA class I antigen

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76433
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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