8HQV

The complex structure of COPI cargo sorting module with HCoV-OC43 Spike KTSHxx sorting motif

• PDB DOI: https://doi.org/10.2210/pdb8HQV/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Saccharomyces cerevisiae YJM789, Human coronavirus OC43
• 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): Other government

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.208 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 

Starting Model: experimental

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 35.45 kDa 
• Atom Count: 2,770 
• Modelled Residue Count: 307 
• Deposited Residue Count: 311 
• 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
HCoV-OC43 Spike KTSHxx sorting motif	B	10	Human coronavirus OC43	Mutation(s): 0
UniProt
Find proteins for P36334 (Human coronavirus OC43) Explore P36334  Go to UniProtKB:  P36334

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.208 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.93	α = 90
b = 51.273	β = 101.61
c = 85.256	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
XSCALE	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.

---

Funding Organization	Location	Grant Number
Other government	China	--

Revision History  

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