6W4H

1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex from SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb6W4H/pdb

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


• Deposited: 2020-03-10 Released: 2020-03-18 
• Deposition Author(s): Minasov, G., Shuvalova, L., Rosas-Lemus, M., Kiryukhina, O., Wiersum, G., Godzik, A., Jaroszewski, L., Stogios, P.J., Skarina, T., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.163 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.79 kDa 
• Atom Count: 4,073 
• Modelled Residue Count: 415 
• Deposited Residue Count: 443 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2'-O-methyltransferase	A	301	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 2.1.1
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 10	B	142	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	D [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
BDF	G [auth A], J [auth B]	beta-D-fructopyranose C6 H12 O6 LKDRXBCSQODPBY-ARQDHWQXSA-N
SO3	C [auth A]	SULFITE ION O3 S LSNNMFCWUKXFEE-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)	H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	E [auth A], F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.163 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 
• Space Group: P 3₁ 2 1
• Diffraction Data: https://doi.org/10.18430/m36w4h

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.74	α = 90
b = 167.74	β = 90
c = 51.942	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Minasov, G., Shuvalova, L., Rosas-Lemus, M., Kiryukhina, O., Wiersum, G., Godzik, A., Jaroszewski, L., Stogios, P.J., Skarina, T., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2020-04-01
  Changes: Structure summary
• Version 1.2: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2021-01-27
  Changes: Database references, Structure summary
• Version 1.5: 2023-10-18
  Changes: Data collection, Database references, Refinement description