9F2G

Crystal structure of SARS-CoV-2 N-protein C-terminal domain (apo form)

PDB DOI: https://doi.org/10.2210/pdb9F2G/pdb

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

Deposited: 2024-04-23 Released: 2024-11-13
Deposition Author(s): Marquez-Monino, M.A., Gonzalez, B., Perez-Canadillas, J.M.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.229
R-Value Work: 0.189
R-Value Observed: 0.191

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The ALS drug riluzole binds to the C-terminal domain of SARS-CoV-2 nucleocapsid protein and has antiviral activity.

Marquez-Monino, M.A., Santiveri, C.M., de Leon, P., Camero, S., Campos-Olivas, R., Jimenez, M.A., Saiz, M., Gonzalez, B., Perez-Canadillas, J.M.

(2024) Structure

DOI: https://doi.org/10.1016/j.str.2024.10.025

Macromolecule Content

Total Structure Weight: 101.17 kDa
Atom Count: 8,310
Modelled Residue Count: 869
Deposited Residue Count: 888
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A, B, C, D, E A, B, C, D, E, F, G, H	111	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9 Go to UniProtKB: P0DTC9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain O [auth F] SDF format, chain J [auth D] SDF format, chain N [auth F] SDF format, chain P [auth F] SDF format, chain Q [auth F] MOL2 format, chain O [auth F] MOL2 format, chain J [auth D] MOL2 format, chain N [auth F] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth F] mmCIF format, chain O [auth F] mmCIF format, chain J [auth D] mmCIF format, chain N [auth F] mmCIF format, chain P [auth F] mmCIF format, chain Q [auth F]	J [auth D], N [auth F], O [auth F], P [auth F], Q [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth D] Focus chain N [auth F] Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth F] Interactions & Density Focus chain J [auth D] Focus chain N [auth F] Focus chain O [auth F] Focus chain P [auth F] Focus chain Q [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain R [auth G] SDF format, chain K [auth D] MOL2 format, chain I [auth A] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain R [auth G] MOL2 format, chain K [auth D] mmCIF format, chain I [auth A] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain R [auth G] mmCIF format, chain K [auth D]	I [auth A], K [auth D], L [auth D], M [auth E], R [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth E] Focus chain R [auth G] Interactions & Density Focus chain I [auth A] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth E] Focus chain R [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.229
R-Value Work: 0.189
R-Value Observed: 0.191
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.704	α = 90
b = 45.14	β = 93.96
c = 109.061	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing
BUCCANEER	model building
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-13

Deposition Author(s):

Marquez-Monino, M.A.

Gonzalez, B.

Perez-Canadillas, J.M.

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2020-117400GB-100
Spanish Ministry of Science, Innovation, and Universities	Spain	MCIN/AEI/10.13039/501100011033

Revision History (Full details and data files)

Version 1.0: 2024-11-13
Type: Initial release

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Help and Resources

9F2G

Crystal structure of SARS-CoV-2 N-protein C-terminal domain (apo form)

The ALS drug riluzole binds to the C-terminal domain of SARS-CoV-2 nucleocapsid protein and has antiviral activity.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)