[English] 日本語
Yorodumi
- EMDB-54366: Cryo-EM structure of TCRpriv/pMHC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54366
TitleCryo-EM structure of TCRpriv/pMHC
Map data
Sample
  • Complex: TCRpriv/pMHC complex
    • Protein or peptide: T cell receptor alpha chain
    • Protein or peptide: T cell receptor beta chain
    • Protein or peptide: SARS-CoV-2 ORF3a_207-215 epitope
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: Beta-2-microglobulin
Keywordscomplex / IMMUNE SYSTEM
Function / homology
Function and homology information


negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent ...negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / Modulation by Mtb of host immune system / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / ER-Phagosome pathway / negative regulation of neuron projection development / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / 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
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsAkil C / Zhu Y / Hardenbrook N / Zhang P
Funding support China, United Kingdom, 2 items
OrganizationGrant numberCountry
Chinese Academy of Sciences2024-I2M-2-001-1 China
Wellcome Trust203141/Z/16/Z United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of TCRpriv/pMHC
Authors: Akil C / Zhu Y / Hardenbrook N / Zhang P
History
DepositionJul 11, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54366.png

Downloads & links

-
Map

FileDownload / File: emd_54366.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 288 pix.
= 210.326 Å		0.73 Å/pix.
x 288 pix.
= 210.326 Å		0.73 Å/pix.
x 288 pix.
= 210.326 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7303 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0008
Minimum - Maximum-0.007802397 - 0.013112546
Average (Standard dev.)0.0000011632605 (±0.00034266463)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 210.3264 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_54366_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_54366_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : TCRpriv/pMHC complex

EntireName: TCRpriv/pMHC complex
Components
  • Complex: TCRpriv/pMHC complex
    • Protein or peptide: T cell receptor alpha chain
    • Protein or peptide: T cell receptor beta chain
    • Protein or peptide: SARS-CoV-2 ORF3a_207-215 epitope
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: Beta-2-microglobulin

-
Supramolecule #1: TCRpriv/pMHC complex

SupramoleculeName: TCRpriv/pMHC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: T cell receptor alpha chain

MacromoleculeName: T cell receptor alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.99048 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QQVMQIPQYQ HVQEGEDFTT YCNSSTTLSN IQWYKQRPGG HPVFLIQLVK SGEVKKQKRL TFQFGEAKKN SSLHITATQT TDVGTYFCA SDREGGSEKL VFGKGTKLTV NPYIQNPDPA VYQLRDSKSS DKSVCLFTDF DSQTNVSQSK DSDVYITDKC V LDMRSMDF ...String:
QQVMQIPQYQ HVQEGEDFTT YCNSSTTLSN IQWYKQRPGG HPVFLIQLVK SGEVKKQKRL TFQFGEAKKN SSLHITATQT TDVGTYFCA SDREGGSEKL VFGKGTKLTV NPYIQNPDPA VYQLRDSKSS DKSVCLFTDF DSQTNVSQSK DSDVYITDKC V LDMRSMDF KSNSAVAWSN KSDFACANAF NNSIIPEDTF FPSPESS

-
Macromolecule #2: T cell receptor beta chain

MacromoleculeName: T cell receptor beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.238217 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GVTQTPRYLI KTRGQQVTLS CSPISGHRSV SWYQQTPGQG LQFLFEYFSE TQRNKGNFPG RFSGRQFSNS RSEMNVSTLE LGDSALYLC ASSLWTGVGT EAFFGQGTRL TVVEDLKNVF PPEVAVFEPS EAEISHTQKA TLVCLATGFY PDHVELSWWV N GKEVHSGV ...String:
GVTQTPRYLI KTRGQQVTLS CSPISGHRSV SWYQQTPGQG LQFLFEYFSE TQRNKGNFPG RFSGRQFSNS RSEMNVSTLE LGDSALYLC ASSLWTGVGT EAFFGQGTRL TVVEDLKNVF PPEVAVFEPS EAEISHTQKA TLVCLATGFY PDHVELSWWV N GKEVHSGV CTDPQPLKEQ PALNDSRYAL SSRLRVSATF WQNPRNHFRC QVQFYGLSEN DEWTQDRAKP VTQIVSAEAW GR AD

-
Macromolecule #3: SARS-CoV-2 ORF3a_207-215 epitope

MacromoleculeName: SARS-CoV-2 ORF3a_207-215 epitope / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.199266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
FTSDYYQLY

-
Macromolecule #4: MHC class I antigen

MacromoleculeName: MHC class I antigen / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.49283 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HSMRYFFTSV SRPGRGEPRF IAVGYVDDTQ FVRFDSDAAS QKMEPRAPWI EQEGPEYWDQ ETRNMKAHSQ TDRANLGTLR GYYNQSEDG SHTIQIMYGC DVGPDGRFLR GYRQDAYDGK DYIALNEDLR SWTAADMAAQ ITKRKWEAVH AAEQRRVYLE G RCVDGLRR ...String:
HSMRYFFTSV SRPGRGEPRF IAVGYVDDTQ FVRFDSDAAS QKMEPRAPWI EQEGPEYWDQ ETRNMKAHSQ TDRANLGTLR GYYNQSEDG SHTIQIMYGC DVGPDGRFLR GYRQDAYDGK DYIALNEDLR SWTAADMAAQ ITKRKWEAVH AAEQRRVYLE G RCVDGLRR YLENGKETLQ RTDPPKTHMT HHPISDHEAT LRCWALGFYP AEITLTWQRD GEDQTQDTEL VETRPAGDGT FQ KWAAVVV PSGEEQRYTC HVQHEGLPKP LTLRW

UniProtKB: MHC class I antigen

-
Macromolecule #5: Beta-2-microglobulin

MacromoleculeName: Beta-2-microglobulin / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.74816 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IQRTPKIQVY SRHPAENGKS NFLNCYVSGF HPSDIEVDLL KNGERIEKVE HSDLSFSKDW SFYLLYYTEF TPTEKDEYAC RVNHVTLSQ PKIVKWDRDM

UniProtKB: Beta-2-microglobulin

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: 30 mM HEPES pH 7.4, 150 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Details: Titan Krios G4 (Thermo Fisher Scientific), equipped with a Selectris X
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 457735
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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