7MX9 | pdb_00007mx9

Crystal structure of the SARS-CoV-2 ORF8 accessory protein

PDB DOI: https://doi.org/10.2210/pdb7MX9/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2021-05-18 Released: 2023-01-25
Deposition Author(s): Bailey-Elkin, B.A., Stetefeld, J.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.297 (Depositor), 0.310 (DCC)
R-Value Work:
0.243 (Depositor), 0.250 (DCC)
R-Value Observed:
0.249 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

The unique ORF8 protein of SARS-CoV-2 binds to human dendritic cells and induces a cytokine storm

Hamdorf, M., Imhof, T., Theobald, S.J., Simonis, A., Di Cristanziano, V., Gieselmann, L., Dewald, F., Lehmann, C., Augustin, M., Klein, F., Alejandre Alcazar, M.A., Rongisch, R., Fabri, M., Cursiefen, C., Rybniker, J., Bailey-Elkin, B.A., Stetefeld, J., Koch, M., Bock, F.

To be published.

Macromolecule Content

Total Structure Weight: 12.91 kDa
Atom Count: 747
Modeled Residue Count: 88
Deposited Residue Count: 113
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF8 protein	A	113	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC8 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC8 Go to UniProtKB: P0DTC8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.297 (Depositor), 0.310 (DCC)
R-Value Work: 0.243 (Depositor), 0.250 (DCC)
R-Value Observed: 0.249 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.349	α = 90
b = 51.349	β = 90
c = 74.093	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-25

Deposition Author(s):

Bailey-Elkin, B.A.

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)		RGPIN-004954-2017
Canadian Institutes of Health Research (CIHR)		201610PJT-152935

Revision History (Full details and data files)

Version 1.0: 2023-01-25
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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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.