8HR0

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

• PDB DOI: https://doi.org/10.2210/pdb8HR0/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens, Human coronavirus OC43
• Expression System: Insect cell expression vector pTIE1, 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: 3.34 Å
• R-Value Free: 0.299 
• R-Value Work: 0.223 
• R-Value Observed: 0.229 

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 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 194.98 kDa 
• Atom Count: 12,401 
• Modelled Residue Count: 1,575 
• Deposited Residue Count: 1,725 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein transport protein Sec23A	A	765	Homo sapiens	Mutation(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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein transport protein Sec24A	B	751	Homo sapiens	Mutation(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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Vesicle-trafficking protein SEC22b	C	199	Homo sapiens	Mutation(s): 0  Gene Names: SEC22B, SEC22L1
UniProt & NIH Common Fund Data Resources
Find proteins for O75396 (Homo sapiens) Explore O75396  Go to UniProtKB:  O75396
PHAROS:  O75396 GTEx:  ENSG00000265808

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HCoV-OC43	D	10	Human coronavirus OC43	Mutation(s): 0
UniProt
Find proteins for P36334 (Human coronavirus OC43) Explore P36334  Go to UniProtKB:  P36334

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.34 Å
• R-Value Free: 0.299 
• R-Value Work: 0.223 
• R-Value Observed: 0.229 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.58	α = 90
b = 96.203	β = 90.01
c = 130.465	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