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- EMDB-75491: Structure of human MAIT A-F7 TCR in complex with miniaturized MR1... -

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Basic information

Entry
Database: EMDB / ID: EMD-75491
TitleStructure of human MAIT A-F7 TCR in complex with miniaturized MR1-5-OP-RU
Map data
Sample
  • Complex: Complex of human MAIT A-F7 TCR with miniaturized MR1-5-OP-RU
    • Protein or peptide: Major histocompatibility complex class I-related protein 1
    • Protein or peptide: Human TCR alpha chain
    • Protein or peptide: Human TCR beta chain
  • Ligand: 1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol
KeywordsMR1 / MAIT / TCR / IMMUNE SYSTEM
Function / homology
Function and homology information


antigen processing and presentation of exogenous antigen / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / MHC class I receptor activity / T cell differentiation in thymus / beta-2-microglobulin binding / T cell receptor binding / late endosome membrane / early endosome membrane / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium ...antigen processing and presentation of exogenous antigen / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / MHC class I receptor activity / T cell differentiation in thymus / beta-2-microglobulin binding / T cell receptor binding / late endosome membrane / early endosome membrane / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / extracellular region / plasma membrane
Similarity search - Function
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 ...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
Major histocompatibility complex class I-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsShinde O / Rotsides P / Sgourakis NG
Funding support United Kingdom, United States, 3 items
OrganizationGrant numberCountry
Cancer Research UKCGCATF-2023/100004 United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)OT2CA297575 United States
The Mark Foundation United States
CitationJournal: Elife / Year: 2026
Title: A miniaturized MR1 metabolite display system with native-like protein features
Authors: Rotsides P / Shinde O / Danon JN / Sgourakis NG
History
DepositionFeb 10, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75491.png

Downloads & links

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Map

FileDownload / File: emd_75491.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.7 Å/pix.
x 384 pix.
= 267.84 Å		0.7 Å/pix.
x 384 pix.
= 267.84 Å		0.7 Å/pix.
x 384 pix.
= 267.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6975 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085
Minimum - Maximum-0.9198338 - 1.1705815
Average (Standard dev.)-0.000003473002 (±0.01658536)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 267.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75491_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75491_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of human MAIT A-F7 TCR with miniaturized MR1-5-OP-RU

EntireName: Complex of human MAIT A-F7 TCR with miniaturized MR1-5-OP-RU
Components
  • Complex: Complex of human MAIT A-F7 TCR with miniaturized MR1-5-OP-RU
    • Protein or peptide: Major histocompatibility complex class I-related protein 1
    • Protein or peptide: Human TCR alpha chain
    • Protein or peptide: Human TCR beta chain
  • Ligand: 1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol

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Supramolecule #1: Complex of human MAIT A-F7 TCR with miniaturized MR1-5-OP-RU

SupramoleculeName: Complex of human MAIT A-F7 TCR with miniaturized MR1-5-OP-RU
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83 KDa

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Macromolecule #1: Major histocompatibility complex class I-related protein 1

MacromoleculeName: Major histocompatibility complex class I-related protein 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.602254 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSGDREDVER LLRSVEWAIK AGDPYSARIL VELAREDAEK IGDERLRREV EELLRELEEL EEELARLPKL PPDRTHSLRY FRLGVSDPI HGVPEFISVG YVDSHPITTY DSVTRQKEPR APWMAENLAP DHWERYTQLL RGWQQMFKVE LKRLQRHYNH S GSHTYQRM ...String:
MSGDREDVER LLRSVEWAIK AGDPYSARIL VELAREDAEK IGDERLRREV EELLRELEEL EEELARLPKL PPDRTHSLRY FRLGVSDPI HGVPEFISVG YVDSHPITTY DSVTRQKEPR APWMAENLAP DHWERYTQLL RGWQQMFKVE LKRLQRHYNH S GSHTYQRM IGCELLEDGS TTGFLQYAYD GQDFLIFNKD TLSWLAVDNV AHTIKQAWEA NQHELLYQKN WLEEECIAWL KR FLEYGKD TLQ

UniProtKB: Major histocompatibility complex class I-related protein 1

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Macromolecule #2: Human TCR alpha chain

MacromoleculeName: Human TCR alpha chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.781268 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGQNIDQPTE MTATEGAIVQ INCTYQTSGF NGLFWYQQHA GEAPTFLSYN VLDGLEEKGR FSSFLSRSKG YSYLLLKELQ MKDSASYLC AVKDSNYQLI WGAGTKLIIK PDIQNPDPAV YQLRDSKSSD KSVCLFTDFD SQTNVSQSKD SDVYITDKCV L DMRSMDFK ...String:
MGQNIDQPTE MTATEGAIVQ INCTYQTSGF NGLFWYQQHA GEAPTFLSYN VLDGLEEKGR FSSFLSRSKG YSYLLLKELQ MKDSASYLC AVKDSNYQLI WGAGTKLIIK PDIQNPDPAV YQLRDSKSSD KSVCLFTDFD SQTNVSQSKD SDVYITDKCV L DMRSMDFK SNSAVAWSNK SDFACANAFN NSIIPEDTFF PSPESS

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Macromolecule #3: Human TCR beta chain

MacromoleculeName: Human TCR beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.731123 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGVTQTPKF QVLKTGQSMT LQCAQDMNHN SMYWYRQDPG MGLRLIYYSA SEGTTDKGEV PNGYNVSRLN KREFSLRLES AAPSQTSVY FCASSVWTGE GSGELFFGEG SRLTVLEDLK NVFPPEVAVF EPSEAEISHT QKATLVCLAT GFYPDHVELS W WVNGKEVH ...String:
MAGVTQTPKF QVLKTGQSMT LQCAQDMNHN SMYWYRQDPG MGLRLIYYSA SEGTTDKGEV PNGYNVSRLN KREFSLRLES AAPSQTSVY FCASSVWTGE GSGELFFGEG SRLTVLEDLK NVFPPEVAVF EPSEAEISHT QKATLVCLAT GFYPDHVELS W WVNGKEVH SGVCTDPQPL KEQPALNDSR YALSSRLRVS ATFWQNPRNH FRCQVQFYGL SENDEWTQDR AKPVTQIVSA EA WGRADLE GGLEVLFQGP GGGLNDIFEA QKIEWHE

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Macromolecule #4: 1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tet...

MacromoleculeName: 1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol
type: ligand / ID: 4 / Number of copies: 1 / Formula: Q87
Molecular weightTheoretical: 330.294 Da
Chemical component information

ChemComp-Q87:
1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol

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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

Concentration0.3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMNH2C(CH2OH)3Tris
150.0 mMNaClsodium chloride
0.145 mMC20H25F13O11Fluorinated Octyl Maltoside
Sugar embeddingMaterial: vitrified ice
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000

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Image processing

Particle selectionNumber selected: 1673666
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 287776
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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