7NH7 | pdb_00007nh7

OC43 coronavirus methyltransferase

• PDB DOI: https://doi.org/10.2210/pdb7NH7/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human coronavirus OC43
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-02-10 Released: 2021-06-23 
• Deposition Author(s): Dostalik, P., Krafcikova, P., Boura, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.211 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

OC43 coronavirus methyltransferase

Dostalik, P., Krafcikova, P., Boura, E.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.06 kDa 
• Atom Count: 3,513 
• Modeled Residue Count: 415 
• Deposited Residue Count: 421 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A	299	Human coronavirus OC43	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 3.4.22 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.1.1 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for P0C6X6 (Human coronavirus OC43) Explore P0C6X6  Go to UniProtKB:  P0C6X6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1a	B	122	Human coronavirus OC43	Mutation(s): 0  Gene Names: 1a EC: 3.4.19.12 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0C6U7 (Human coronavirus OC43) Explore P0C6U7  Go to UniProtKB:  P0C6U7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SFG	C [auth A]	SINEFUNGIN C15 H23 N7 O5 LMXOHSDXUQEUSF-YECHIGJVSA-N
ZN	D [auth B], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.211 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.945	α = 90
b = 61.945	β = 90
c = 109.717	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-23 
Deposition Author(s): Dostalik, P., Krafcikova, P., Boura, E.

Revision History  

• Version 1.0: 2021-06-23
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description