[English] 日本語
Yorodumi
- PDB-8vz9: Crystal structure of mouse MAIT M2A TCR-MR1-5-OP-RU complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vz9
TitleCrystal structure of mouse MAIT M2A TCR-MR1-5-OP-RU complex
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • Mouse MAIT MBV13-2A b-chain
  • Mouse MAIT TRAV1-TRAJ33 a-chain
KeywordsIMMUNE SYSTEM / Mouse MAIT TCR recognition of MR1
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 / antigen processing and presentation of peptide antigen via MHC class I / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / beta-2-microglobulin binding ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / antigen processing and presentation of peptide antigen via MHC class I / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / beta-2-microglobulin binding / cellular defense response / T cell receptor binding / Neutrophil degranulation / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / early endosome membrane / T cell differentiation in thymus / protein refolding / defense response to Gram-negative bacterium / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Golgi membrane / external side of plasma membrane / lysosomal membrane / innate immune response / endoplasmic reticulum membrane / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / 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
Chem-2LJ / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsCiacchi, L. / Rossjohn, J. / Awad, W.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE220101491 Australia
Australian Research Council (ARC)DP220102401 Australia
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Mouse mucosal-associated invariant T cell receptor recognition of MR1 presenting the vitamin B metabolite, 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil.
Authors: Ciacchi, L. / Mak, J.Y.W. / Le, J.P. / Fairlie, D.P. / McCluskey, J. / Corbett, A.J. / Rossjohn, J. / Awad, W.
History
DepositionFeb 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: Mouse MAIT TRAV1-TRAJ33 a-chain
D: Mouse MAIT MBV13-2A b-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8737
Polymers93,3724
Non-polymers5003
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.531, 84.259, 177.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

-
Protein , 4 types, 4 molecules ABCD

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


Mass: 31709.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mr1, Mr1a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8HWB0
#2: Protein Beta-2-microglobulin


Mass: 11731.427 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein Mouse MAIT TRAV1-TRAJ33 a-chain


Mass: 22650.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Protein Mouse MAIT MBV13-2A b-chain


Mass: 27281.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 2 types, 3 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-2LJ / 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol / 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil


Mass: 316.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O6 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris Propane (pH 7.5 - 8.5), 16-22% PEG 3350 and 0.2M sodium acetate
PH range: 7.5-8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 3.4→49.22 Å / Num. obs: 13899 / % possible obs: 99.8 % / Redundancy: 2 % / CC1/2: 0.995 / Net I/σ(I): 10.12
Reflection shellResolution: 3.4→3.52 Å / Num. unique obs: 1346 / CC1/2: 0.842

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
pointlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→49.22 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2633 1390 10.01 %
Rwork0.2424 --
obs0.2445 13893 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5887 0 35 0 5922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026090
X-RAY DIFFRACTIONf_angle_d0.5058336
X-RAY DIFFRACTIONf_dihedral_angle_d13.3632025
X-RAY DIFFRACTIONf_chiral_restr0.041933
X-RAY DIFFRACTIONf_plane_restr0.0051078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.520.30611340.27691210X-RAY DIFFRACTION99
3.52-3.660.27181370.26931221X-RAY DIFFRACTION100
3.66-3.830.27611370.24721238X-RAY DIFFRACTION100
3.83-4.030.26071360.25021220X-RAY DIFFRACTION100
4.03-4.280.24881380.22741245X-RAY DIFFRACTION100
4.28-4.610.23811380.22041241X-RAY DIFFRACTION100
4.62-5.080.22211370.21331235X-RAY DIFFRACTION100
5.08-5.810.29971400.23841256X-RAY DIFFRACTION100
5.81-7.320.25411420.28261284X-RAY DIFFRACTION100
7.32-49.220.27861510.23631353X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.9939 Å / Origin y: 21.179 Å / Origin z: 7.9074 Å
111213212223313233
T0.3601 Å2-0.0452 Å2-0.0155 Å2-0.306 Å20.0014 Å2--0.3382 Å2
L0.8739 °20.1585 °20.4893 °2--0.1193 °20.0275 °2--0.7695 °2
S0.1045 Å °-0.023 Å °0.0297 Å °-0.0258 Å °-0.0641 Å °0.04 Å °-0.0709 Å °0.0848 Å °0.0034 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