8C0G | pdb_00008c0g

SARS-CoV nsp16-nsp10 complexed with N7-GTP

• PDB DOI: https://doi.org/10.2210/pdb8C0G/pdb

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


• Deposited: 2022-12-16 Released: 2023-12-27 
• Deposition Author(s): Ferron, F., Debarnot, C., Coutard, B., Canard, B., Marseilles Structural Genomics Program @ AFMB (MSGP)
• Funding Organization(s): European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.263 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Observation of N7-GTP in nsp16-nsp10 Sars-CoV

Ferron, F., Canard, B., Debarnot, C., Coutard, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 46.82 kDa 
• Atom Count: 3,442 
• Modeled Residue Count: 409 
• Deposited Residue Count: 414 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	A	292	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7  Go to UniProtKB:  P0C6X7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	B	122	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7  Go to UniProtKB:  P0C6X7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SRC (Subject of Investigation/LOI)	D [auth A]	[[(2~{R},3~{S},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate C11 H20 N5 O14 P3 BUJQMJUTTBGELS-UHTZMRCNSA-N
PEG	C [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.263 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.232	α = 90
b = 185.042	β = 90
c = 128.577	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Ferron, F., Debarnot, C., Coutard, B., Canard, B., Marseilles Structural Genomics Program @ AFMB (MSGP)

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	VIZIER integrated project (LSHG-CT-2004-511960)
European Union (EU)	European Union	European FP7 Capacities Project no 228292

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release