5YNO | pdb_00005yno

Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAH and m7GpppA

• PDB DOI: https://doi.org/10.2210/pdb5YNO/pdb

• Classification: TRANSFERASE
• Organism(s): Human betacoronavirus 2c EMC/2012
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-10-24 Released: 2018-12-05 
• Deposition Author(s): Wei, S.M., Yang, L., Ke, Z.H., Guo, D.Y., Fan, C.P.
• Funding Organization(s): NSFC

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.227 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the molecular mechanism of MERS Coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex

Wei, S.M., Yang, L., Ke, Z.H., Liu, Q.Y., Chen, Y., Guo, D.Y., Fan, C.P.

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: 49.94 kDa 
• Atom Count: 3,419 
• Modeled Residue Count: 412 
• Deposited Residue Count: 443 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nsp16 protein	A	303	Human betacoronavirus 2c EMC/2012	Mutation(s): 0  Gene Names: orf1ab
UniProt
Find proteins for K0BWD0 (Human betacoronavirus 2c (isolate EMC/2012)) Explore K0BWD0  Go to UniProtKB:  K0BWD0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nsp10 protein	B	140	Human betacoronavirus 2c EMC/2012	Mutation(s): 0  Gene Names: orf1ab
UniProt
Find proteins for K4LC41 (Human betacoronavirus 2c (isolate EMC/2012)) Explore K4LC41  Go to UniProtKB:  K4LC41

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTA	D [auth A]	P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE C21 H30 N10 O17 P3 QQOHNVHGNZYSBP-XPWFQUROSA-O
SAH	C [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN	E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.227 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.193	α = 90
b = 70.186	β = 90
c = 119.353	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-12-05 
Deposition Author(s): Wei, S.M., Yang, L., Ke, Z.H., Guo, D.Y., Fan, C.P.

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Funding Organization	Location	Grant Number
NSFC	China	31570762

Revision History  

• Version 1.0: 2018-12-05
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description