[English] 日本語
Yorodumi
- PDB-9y0v: Crystal Structure of human MAIT A-F7 TCR-MR1*04 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9y0v
TitleCrystal Structure of human MAIT A-F7 TCR-MR1*04 complex
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related protein 1
  • TCR alpha chain
  • TCR beta chain
KeywordsIMMUNE SYSTEM / MAIT TCR / MR1 / metabolite presentation
Function / homology
Function and homology information


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / Interferon gamma signaling / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / MHC class II protein complex binding / T cell differentiation in thymus / DAP12 signaling / late endosome membrane / negative regulation of neuron projection development / protein refolding / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / external side of plasma membrane / innate immune response / lysosomal membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / : / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / 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, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / 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
Beta-2-microglobulin / Major histocompatibility complex class I-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLetoga, V. / Rossjohn, J. / Awad, W.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Allelic variation alters expression and antigen presentation of MR1 allomorphs.
Authors: Nelson, A.G. / Letoga, V. / Lee, C.Z.Q. / Samer, C. / Li, S. / Meehan, L.J. / McWilliam, H.E.G. / Gherardin, N.A. / Abendroth, A. / Villadangos, J.A. / Slobedman, B. / Corbett, A.J. / ...Authors: Nelson, A.G. / Letoga, V. / Lee, C.Z.Q. / Samer, C. / Li, S. / Meehan, L.J. / McWilliam, H.E.G. / Gherardin, N.A. / Abendroth, A. / Villadangos, J.A. / Slobedman, B. / Corbett, A.J. / McCluskey, J. / Rossjohn, J. / Chen, Z. / Souter, M.N.T. / Awad, W.
History
DepositionAug 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2026Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major histocompatibility complex class I-related protein 1
B: Beta-2-microglobulin
C: Major histocompatibility complex class I-related protein 1
D: TCR alpha chain
E: TCR beta chain
F: Beta-2-microglobulin
G: TCR alpha chain
H: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,37611
Polymers188,1008
Non-polymers2763
Water4,378243
1
A: Major histocompatibility complex class I-related protein 1
B: Beta-2-microglobulin
D: TCR alpha chain
E: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2346
Polymers94,0504
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-48 kcal/mol
Surface area35690 Å2
MethodPISA
2
C: Major histocompatibility complex class I-related protein 1
F: Beta-2-microglobulin
G: TCR alpha chain
H: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1425
Polymers94,0504
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-44 kcal/mol
Surface area35590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.389, 140.991, 114.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 4 types, 8 molecules ACBFDGEH

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


Mass: 31711.670 Da / Num. of mol.: 2
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 Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein TCR alpha chain


Mass: 22781.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Protein TCR beta chain


Mass: 27677.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 2 types, 246 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 6000, HEPES, Lithium Chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→46.72 Å / Num. obs: 39788 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 55.24 Å2 / CC1/2: 0.956 / Net I/σ(I): 6
Reflection shellResolution: 3→3.12 Å / Num. unique obs: 4483 / CC1/2: 0.478

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→43.5 Å / SU ML: 0.3626 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1203
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2436 1979 4.98 %
Rwork0.1948 37756 -
obs0.1971 39735 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.95 Å2
Refinement stepCycle: LAST / Resolution: 3→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12563 0 18 243 12824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001713035
X-RAY DIFFRACTIONf_angle_d0.466717780
X-RAY DIFFRACTIONf_chiral_restr0.04011924
X-RAY DIFFRACTIONf_plane_restr0.00322290
X-RAY DIFFRACTIONf_dihedral_angle_d13.70294578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.30941390.2662678X-RAY DIFFRACTION99.75
3.08-3.160.33831400.24732652X-RAY DIFFRACTION99.82
3.16-3.250.27431440.23562732X-RAY DIFFRACTION99.79
3.25-3.360.27521410.22492672X-RAY DIFFRACTION99.93
3.36-3.480.29131430.21122692X-RAY DIFFRACTION99.89
3.48-3.610.221460.20392705X-RAY DIFFRACTION99.89
3.62-3.780.25811400.18842659X-RAY DIFFRACTION99.89
3.78-3.980.23851410.18152700X-RAY DIFFRACTION99.79
3.98-4.230.19391380.16882703X-RAY DIFFRACTION99.93
4.23-4.550.19111350.15022704X-RAY DIFFRACTION100
4.55-5.010.20461440.15522698X-RAY DIFFRACTION99.75
5.01-5.730.23081400.19042716X-RAY DIFFRACTION99.86
5.74-7.220.26891380.2332712X-RAY DIFFRACTION99.86
7.22-43.50.26051500.19882733X-RAY DIFFRACTION99.07
Refinement TLS params.Method: refined / Origin x: -17.8791675768 Å / Origin y: 32.8872682623 Å / Origin z: 28.7724569869 Å
111213212223313233
T0.277587166934 Å2-0.0225554873572 Å2-0.0290078291284 Å2-0.234678691551 Å20.0139905372904 Å2--0.261084710865 Å2
L0.14712200125 °2-0.0822511118526 °2-0.163441164107 °2-0.166988175756 °20.13453457349 °2--0.328779958603 °2
S-0.0138279567901 Å °-0.0227914564643 Å °-0.000338150165265 Å °0.0329415055145 Å °0.0188421167076 Å °0.006454064527 Å °0.0173695363788 Å °0.0518160922971 Å °-0.00540017073618 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more