7C2I

Crystal structure of nsp16-nsp10 heterodimer from SARS-CoV-2 in complex with SAM (with additional SAM during crystallization)

PDB DOI: https://doi.org/10.2210/pdb7C2I/pdb

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

Deposited: 2020-05-07 Released: 2020-05-27
Deposition Author(s): Lin, S., Chen, H., Ye, F., Chen, Z.M., Yang, F.L., Zheng, Y., Cao, Y., Qiao, J.X., Yang, S.Y., Lu, G.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.209
R-Value Work: 0.174
R-Value Observed: 0.176

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of SARS-CoV-2 nsp10/nsp16 2'-O-methylase and its implication on antiviral drug design.

Lin, S., Chen, H., Ye, F., Chen, Z., Yang, F., Zheng, Y., Cao, Y., Qiao, J., Yang, S., Lu, G.

(2020) Signal Transduct Target Ther 5: 131-131

PubMed: 32728018 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41392-020-00241-4
Primary Citation of Related Structures:
7C2I, 7C2J

Organizational Affiliation

West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and Collaborative Innovation Center of Biotherapy, Sichuan University, 610041, Chengdu, Sichuan, China.

Macromolecule Content

Total Structure Weight: 50.06 kDa
Atom Count: 3,389
Modelled Residue Count: 414
Deposited Residue Count: 449
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2'-O-methyltransferase	A	305	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 10	B	144	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM (Subject of Investigation/LOI) Query on SAM Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B]	D [auth B], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.209
R-Value Work: 0.174
R-Value Observed: 0.176
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.817	α = 90
b = 167.817	β = 90
c = 51.571	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-05-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-05-27
Type: Initial release
Version 1.1: 2020-06-10
Changes: Structure summary
Version 1.2: 2020-09-02
Changes: Database references
Version 1.3: 2021-03-10
Changes: Structure summary
Version 1.4: 2023-11-29
Changes: Data collection, Database references, Refinement description