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- EMDB-54262: Cryo-EM structure of TCRpub/pMHC -

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Basic information

Entry
Database: EMDB / ID: EMD-54262
TitleCryo-EM structure of TCRpub/pMHC
Map data
Sample
  • Complex: Cryo-EM structure of TCRpub/pMHC
    • Protein or peptide: TCRpub alpha chain
    • Protein or peptide: TCRpub beta chain
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: ORF3a protein
Keywordscomplex / IMMUNE SYSTEM
Function / homology
Function and homology information


host cell lysosome / symbiont-mediated activation of host reticulophagy / Maturation of protein 3a / SARS-CoV-2 modulates autophagy / inorganic cation transmembrane transport / voltage-gated calcium channel complex / host cell endoplasmic reticulum / monoatomic ion channel activity / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / voltage-gated potassium channel complex ...host cell lysosome / symbiont-mediated activation of host reticulophagy / Maturation of protein 3a / SARS-CoV-2 modulates autophagy / inorganic cation transmembrane transport / voltage-gated calcium channel complex / host cell endoplasmic reticulum / monoatomic ion channel activity / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / voltage-gated potassium channel complex / molecular function activator activity / cytoplasmic side of plasma membrane / host cell endosome / Translation of Structural Proteins / Virion Assembly and Release / Induction of Cell-Cell Fusion / Attachment and Entry / host cell endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Protein 3a, betacoronavirus / 3a-like viroporin, transmembrane domain, alpha/betacoronavirus / 3a-like viroporin, cytosolic domain, alpha/betacoronavirus / Betacoronavirus viroporin / Coronavirus (CoV) 3a-like viroporin trans-membrane (TM) domain profile. / Coronavirus (CoV) 3a-like viroporin cytosolic (CD) domain profile. / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like ...Protein 3a, betacoronavirus / 3a-like viroporin, transmembrane domain, alpha/betacoronavirus / 3a-like viroporin, cytosolic domain, alpha/betacoronavirus / Betacoronavirus viroporin / Coronavirus (CoV) 3a-like viroporin trans-membrane (TM) domain profile. / Coronavirus (CoV) 3a-like viroporin cytosolic (CD) domain profile. / 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
MHC class I antigen / ORF3a protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 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
Authors: Akil C / Zhu Y / Hardenbrook N / Zhang P
History
DepositionJul 3, 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_54262.png

Downloads & links

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Map

FileDownload / File: emd_54262.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.)
0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.136
Minimum - Maximum-0.00180246 - 2.1268234
Average (Standard dev.)0.000621016 (±0.018381009)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54262_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_54262_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 : Cryo-EM structure of TCRpub/pMHC

EntireName: Cryo-EM structure of TCRpub/pMHC
Components
  • Complex: Cryo-EM structure of TCRpub/pMHC
    • Protein or peptide: TCRpub alpha chain
    • Protein or peptide: TCRpub beta chain
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: ORF3a protein

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Supramolecule #1: Cryo-EM structure of TCRpub/pMHC

SupramoleculeName: Cryo-EM structure of TCRpub/pMHC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: TCRpub alpha chain

MacromoleculeName: TCRpub alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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: TCRpub beta chain

MacromoleculeName: TCRpub beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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: MHC class I antigen

MacromoleculeName: MHC class I antigen / type: protein_or_peptide / ID: 3 / Number of copies: 1 / 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 #4: ORF3a protein

MacromoleculeName: ORF3a protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 1.199266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
FTSDYYQLY

UniProtKB: ORF3a protein

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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
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: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 103583
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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