9N55 | pdb_00009n55

X-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer

PDB DOI: https://doi.org/10.2210/pdb9N55/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-02-03 Released: 2025-03-12
Deposition Author(s): San Felipe, C.J., Fraser, J.S.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.221 (Depositor), 0.222 (DCC)
R-Value Work:
0.198 (Depositor), 0.199 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

X-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer

San Felipe, C.J., Fraser, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 21.73 kDa
Atom Count: 1,396
Modelled Residue Count: 168
Deposited Residue Count: 194
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF9b protein	A, B	97	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: 9b
UniProt
Find proteins for P0DTD2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD2 Go to UniProtKB: P0DTD2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OCT (Subject of Investigation/LOI) Query on OCT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.221 (Depositor), 0.222 (DCC)
R-Value Work: 0.198 (Depositor), 0.199 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.85	α = 90
b = 64.23	β = 90
c = 73.57	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

San Felipe, C.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI171110

Revision History (Full details and data files)

Version 1.0: 2025-03-12
Type: Initial release

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.