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- PDB-10vm: Structure of human MAIT A-F7 TCR in complex with miniaturized MR1... -

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Basic information

Entry
Database: PDB / ID: 10vm
TitleStructure of human MAIT A-F7 TCR in complex with miniaturized MR1-5-OP-RU
Components
  • Human TCR alpha chain
  • Human TCR beta chain
  • Major histocompatibility complex class I-related protein 1
KeywordsIMMUNE SYSTEM / MR1 / MAIT / TCR
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
Chem-Q87 / Major histocompatibility complex class I-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsShinde, O. / Rotsides, P. / Sgourakis, N.G.
Funding support United Kingdom, United States, 3items
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, J.N. / Sgourakis, N.G.
History
DepositionFeb 10, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major histocompatibility complex class I-related protein 1
G: Human TCR alpha chain
H: Human TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4454
Polymers83,1153
Non-polymers3301
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Major histocompatibility complex class I-related protein 1 / MHC class I-related protein 1 / Class I histocompatibility antigen-like protein


Mass: 29602.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95460
#2: Protein Human TCR alpha chain


Mass: 22781.268 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein Human TCR beta chain


Mass: 30731.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-Q87 / 1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol


Mass: 330.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N4O7 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of human MAIT A-F7 TCR with miniaturized MR1-5-OP-RU
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.083 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTrisNH2C(CH2OH)31
2150 mMsodium chlorideNaCl1
30.145 mMFluorinated Octyl MaltosideC20H25F13O111
SpecimenConc.: 0.3 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
EM embeddingMaterial: vitrified ice
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX2.0_5885model refinement
3EPUimage acquisition
5cryoSPARCCTF correction
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1673666
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 287776 / Symmetry type: POINT
RefinementHighest resolution: 3.08 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035580
ELECTRON MICROSCOPYf_angle_d0.537577
ELECTRON MICROSCOPYf_dihedral_angle_d6.746782
ELECTRON MICROSCOPYf_chiral_restr0.04809
ELECTRON MICROSCOPYf_plane_restr0.004984

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