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- EMDB-54273: Cryo-EM structure of TCRpub/pMHC dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-54273
TitleCryo-EM structure of TCRpub/pMHC dimer
Map data
Sample
  • Complex: TCRpub/pMHC dimer
    • Protein or peptide: T cell receptor, alpha chain
    • Protein or peptide: T cell receptor, beta chain
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: ORF3a_207-215 epitope
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: 4.11 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 TCRpub/pMHC dimer
Authors: Akil C / Zhu Y / Hardenbrook N / Zhang P
History
DepositionJul 4, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54273.png

Downloads & links

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Map

FileDownload / File: emd_54273.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 233.696 Å		0.73 Å/pix.
x 320 pix.
= 233.696 Å		0.73 Å/pix.
x 320 pix.
= 233.696 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: 0.0746
Minimum - Maximum-0.001643049 - 2.3337426
Average (Standard dev.)0.0026930105 (±0.03812895)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 233.696 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54273_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_54273_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 : TCRpub/pMHC dimer

EntireName: TCRpub/pMHC dimer
Components
  • Complex: TCRpub/pMHC dimer
    • Protein or peptide: T cell receptor, alpha chain
    • Protein or peptide: T cell receptor, beta chain
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: ORF3a_207-215 epitope

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Supramolecule #1: TCRpub/pMHC dimer

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

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Macromolecule #1: T cell receptor, alpha chain

MacromoleculeName: T cell receptor, alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.175703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVAQPEDQV NVAEGNPLTV KCTYSVSGNP YLFWYVQYPN RGLQFLLKYI TGDNLVKGSY GFEAEFNKSQ TSFHLKKPSA LVSDSALYF CAVRVVTSGG SYIPTFGRGT SLIVHPYIQN PDPAVYQLRD SKSSDKSVCL FTDFDSQTNV SQSKDSDVYI T DKCVLDMR ...String:
QSVAQPEDQV NVAEGNPLTV KCTYSVSGNP YLFWYVQYPN RGLQFLLKYI TGDNLVKGSY GFEAEFNKSQ TSFHLKKPSA LVSDSALYF CAVRVVTSGG SYIPTFGRGT SLIVHPYIQN PDPAVYQLRD SKSSDKSVCL FTDFDSQTNV SQSKDSDVYI T DKCVLDMR SMDFKSNSAV AWSNKSDFAC ANAFNNSIIP EDTFFPSPES S

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Macromolecule #2: T cell receptor, beta chain

MacromoleculeName: T cell receptor, beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.151094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GVTQTPRYLI KTRGQQVTLS CSPISGHRSV SWYQQTPGQG LQFLFEYFSE TQRNKGNFPG RFSGRQFSNS RSEMNVSTLE LGDSALYLC ASSLAGDLGT EAFFGQGTRL TVVEDLKNVF PPEVAVFEPS EAEISHTQKA TLVCLATGFY PDHVELSWWV N GKEVHSGV ...String:
GVTQTPRYLI KTRGQQVTLS CSPISGHRSV SWYQQTPGQG LQFLFEYFSE TQRNKGNFPG RFSGRQFSNS RSEMNVSTLE LGDSALYLC ASSLAGDLGT EAFFGQGTRL TVVEDLKNVF PPEVAVFEPS EAEISHTQKA TLVCLATGFY PDHVELSWWV N GKEVHSGV CTDPQPLKEQ PALNDSRYAL SSRLRVSATF WQNPRNHFRC QVQFYGLSEN DEWTQDRAKP VTQIVSAEAW GR AD

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Macromolecule #3: Beta-2-microglobulin

MacromoleculeName: Beta-2-microglobulin / type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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

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Macromolecule #4: MHC class I antigen

MacromoleculeName: MHC class I antigen / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.909258 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 LTLRWELSS

UniProtKB: MHC class I antigen

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Macromolecule #5: ORF3a_207-215 epitope

MacromoleculeName: ORF3a_207-215 epitope / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.199266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
FTSDYYQLY

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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

BufferpH: 7.4 / Details: 30 mM HEPES pH 7.4, 150 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K

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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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 91648
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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