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- PDB-9ru5: Cryo-EM structure of TCRpub/pMHC -

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Basic information

Entry
Database: PDB / ID: 9ru5
TitleCryo-EM structure of TCRpub/pMHC
Components
  • MHC class I antigen
  • ORF3a protein
  • TCRpub alpha chain
  • TCRpub beta chain
KeywordsIMMUNE SYSTEM / complex
Function / homology
Function and homology information


host cell lysosome / symbiont-mediated activation of host reticulophagy / Maturation of protein 3a / SARS-CoV-2 modulates autophagy / : / 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 / : / 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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsAkil, C. / Zhu, Y. / Hardenbrook, N. / Zhang, P.
Funding support China, United Kingdom, 2items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TCRpub alpha chain
B: TCRpub beta chain
M: MHC class I antigen
P: ORF3a protein


Theoretical massNumber of molelcules
Total (without water)83,4354
Polymers83,4354
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein TCRpub alpha chain


Mass: 23175.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein TCRpub beta chain


Mass: 27151.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein MHC class I antigen


Mass: 31909.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Homo sapiens (human) / References: UniProt: F6IQR9
#4: Protein/peptide ORF3a protein / ORF3a / Accessory protein 3a / Protein 3a / Protein U274 / Protein X1


Mass: 1199.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: 3a / Production host: Homo sapiens (human) / References: UniProt: P0DTC3
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of TCRpub/pMHC / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4 / Details: 30 mM HEPES pH 7.4, 150 mM NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
Details: Titan Krios G4 (Thermo Fisher Scientific), equipped with a Selectris X

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Processing

EM software
IDNameVersionCategory
1cryoSPARCV4.4.1particle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103583 / Symmetry type: POINT
RefinementHighest resolution: 3.26 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034942
ELECTRON MICROSCOPYf_angle_d0.6086691
ELECTRON MICROSCOPYf_dihedral_angle_d5.032666
ELECTRON MICROSCOPYf_chiral_restr0.042700
ELECTRON MICROSCOPYf_plane_restr0.006881

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