7F60

Crystal structure of auxiliary protein in complex with human nuclear protein

• PDB DOI: https://doi.org/10.2210/pdb7F60/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Insect cell expression vector pTIE1
• Mutation(s): No 


• Deposited: 2021-06-23 Released: 2022-09-14 
• Deposition Author(s): Gao, X., Cui, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.276 
• R-Value Work: 0.236 
• R-Value Observed: 0.238 

Starting Model: experimental

Literature

Structural basis for Sarbecovirus ORF6 mediated blockage of nucleocytoplasmic transport

Gao, X., Tian, H., Zhu, K., Li, Q., Hao, W., Wang, L., Qin, B., Deng, H., Cui, S.

(2022) Nat Commun 13: 4782

• DOI: https://doi.org/10.1038/s41467-022-32489-5

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 492.15 kDa 
• Atom Count: 6,151 
• Modelled Residue Count: 777 
• Deposited Residue Count: 4,492 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA export factor	A, B	368	Homo sapiens	Mutation(s): 0  Gene Names: RAE1, MRNP41
UniProt & NIH Common Fund Data Resources
Find proteins for P78406 (Homo sapiens) Explore P78406  Go to UniProtKB:  P78406
PHAROS:  P78406 GTEx:  ENSG00000101146

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear pore complex protein Nup98-Nup96	C, D	1,817	Homo sapiens	Mutation(s): 0  Gene Names: NUP98, ADAR2 EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for P52948 (Homo sapiens) Explore P52948  Go to UniProtKB:  P52948
PHAROS:  P52948 GTEx:  ENSG00000110713

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF6 protein	E, F	61	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC6 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC6  Go to UniProtKB:  P0DTC6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.276 
• R-Value Work: 0.236 
• R-Value Observed: 0.238 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.345	α = 90
b = 87.531	β = 93.68
c = 48.23	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Gao, X., Cui, S.

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description