7F60 | pdb_00007f60

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.276 (Depositor), 0.278 (DCC)
R-Value Work:
0.236 (Depositor), 0.235 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78406
Sequence Annotations Expand
Reference Sequence

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52948
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.276 (Depositor), 0.278 (DCC)
R-Value Work: 0.236 (Depositor), 0.235 (DCC)
R-Value Observed: 0.238 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2022-09-14

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.