8HQT

The complex structure of COPI cargo sorting module with SARS-CoV-2 Spike KxHxx sorting motif

• PDB DOI: https://doi.org/10.2210/pdb8HQT/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Saccharomyces cerevisiae YJM789, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-12-14 Released: 2023-12-20 
• Deposition Author(s): Ma, W.F., Nan, Y.N., Yang, M.R., Li, Y.Q.
• Funding Organization(s): Beijing University of Chinese Medicine (BUCM)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.225 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 

Literature

Tighter ER retention of SARS-CoV-2 Omicron spike caused by a constellation of folding disruptive mutations

Li, Y.Q., Yang, M.R., Nan, Y.N., Wang, J.M., Guo, J.J., He, P.F., Dai, W.X., Zhou, S.Q., Wang, S.J., Zhang, Y., Ma, W.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 35.06 kDa 
• Atom Count: 2,605 
• Modelled Residue Count: 301 
• Deposited Residue Count: 307 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coatomer subunit beta'	A	301	Saccharomyces cerevisiae YJM789	Mutation(s): 0  Gene Names: SEC27, SCY_1929
UniProt
Find proteins for P41811 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41811  Go to UniProtKB:  P41811

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV-2 Spike KxHxx motif	B	6	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.225 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.892	α = 90
b = 51.051	β = 101.62
c = 85.101	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Ma, W.F., Nan, Y.N., Yang, M.R., Li, Y.Q.

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Funding Organization	Location	Grant Number
Beijing University of Chinese Medicine (BUCM)	China	90011451310011, 1000061223476, ZYYCXTD-C-202006

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release