8HR0 | pdb_00008hr0

The complex structure of COPII coat with HCoV-OC43 DD sorting motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.34 Å
  • R-Value Free: 
    0.299 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

SARS-CoV-2 spike host cell surface exposure promoted by a COPI sorting inhibitor.

Li, Y.Yang, M.Nan, Y.Wang, J.Wang, S.Cui, D.Guo, J.He, P.Dai, W.Zhou, S.Zhang, Y.Ma, W.

(2023) Acta Pharm Sin B 13: 3043-3053

  • DOI: https://doi.org/10.1016/j.apsb.2023.04.007
  • Primary Citation of Related Structures:  
    8HQT, 8HQV, 8HQW, 8HQX, 8HR0

  • PubMed Abstract: 

    Via an insufficient coat protein complex I (COPI) retrieval signal, the majority of SARS-CoV-2 spike (S) is resident in host early secretory organelles and a tiny amount is leaked out in cell surface. Only surface-exposed S can be recognized by B cell receptor (BCR) or anti-S therapeutic monoclonal antibodies (mAbs) that is the trigger step for B cell activation after S mRNA vaccination or infected cell clearance by S mAbs. Now, a drug strategy to promote S host surface exposure is absent. Here, we first combined structural and biochemical analysis to characterize S COPI sorting signals. A potent S COPI sorting inhibitor was then invented, evidently capable of promoting S surface exposure and facilitating infected cell clearance by S antibody-dependent cellular cytotoxicity (ADCC). Importantly, with the inhibitor as a probe, we revealed Omicron BA.1 S is less cell surface exposed than prototypes because of a constellation of S folding mutations, possibly corresponding to its ER chaperone association. Our findings not only suggest COPI is a druggable target against COVID-19, but also highlight SARS-CoV-2 evolution mechanism driven by S folding and trafficking mutations.


  • Organizational Affiliation

    School of Life Science, Beijing University of Chinese Medicine, Beijing 102488, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec23A765Homo sapiensMutation(s): 0 
Gene Names: SEC23A
UniProt & NIH Common Fund Data Resources
Find proteins for Q15436 (Homo sapiens)
Explore Q15436 
Go to UniProtKB:  Q15436
PHAROS:  Q15436
GTEx:  ENSG00000100934 
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UniProt GroupQ15436
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec24A751Homo sapiensMutation(s): 0 
Gene Names: SEC24A
UniProt & NIH Common Fund Data Resources
Find proteins for O95486 (Homo sapiens)
Explore O95486 
Go to UniProtKB:  O95486
PHAROS:  O95486
GTEx:  ENSG00000113615 
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UniProt GroupO95486
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Vesicle-trafficking protein SEC22b199Homo sapiensMutation(s): 0 
Gene Names: SEC22BSEC22L1
UniProt & NIH Common Fund Data Resources
Find proteins for O75396 (Homo sapiens)
Explore O75396 
Go to UniProtKB:  O75396
PHAROS:  O75396
GTEx:  ENSG00000265808 
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UniProt GroupO75396
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
HCoV-OC4310Human coronavirus OC43Mutation(s): 0 
UniProt
Find proteins for P36334 (Human coronavirus OC43)
Explore P36334 
Go to UniProtKB:  P36334
Entity Groups  
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UniProt GroupP36334
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.34 Å
  • R-Value Free:  0.299 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.58α = 90
b = 96.203β = 90.01
c = 130.465γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Beijing University of Chinese Medicine (BUCM)China90011451310011, 1000061223476, ZYYCXTD-C-202006

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2025-01-29
    Changes: Database references, Structure summary