7JZ0 | pdb_00007jz0

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1) and S-Adenosyl-L-homocysteine (SAH).

PDB DOI: https://doi.org/10.2210/pdb7JZ0/pdb
NAKB: 7JZ0

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

Deposited: 2020-09-01 Released: 2020-09-16
Deposition Author(s): Minasov, G., Shuvalova, L., Rosas-Lemus, M., Kiryukhina, O., Brunzelle, J.S., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.198 (Depositor), 0.202 (DCC)
R-Value Work:
0.173 (Depositor), 0.179 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Mn2+ coordinates Cap-0-RNA to align substrates for efficient 2'-O-methyl transfer by SARS-CoV-2 nsp16

Minasov, G., Rosas-Lemus, M., Shuvalova, L., Inniss, N.L., Brunzelle, J.S., Daczkowski, C.M., Hoover, P., Mesecar, A.D., Satchell, K.J.F.

(2021) bioRxiv

DOI: https://doi.org/10.1101/2021.01.31.429023

Macromolecule Content

Total Structure Weight: 103.54 kDa
Atom Count: 7,305
Modeled Residue Count: 850
Deposited Residue Count: 896
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2'-O-methyltransferase	A, C	300	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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 10	B, D	141	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

Find similar nucleic acids by: Sequence

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-D((M7G))-R(P(A2M)PUPU)-3')	E, F	7	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain T [auth C] MOL2 format, chain G [auth A] MOL2 format, chain T [auth C] mmCIF format, chain G [auth A] mmCIF format, chain T [auth C]	G [auth A], T [auth C]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain G [auth A] Focus chain T [auth C] Interactions & Density Focus chain G [auth A] Focus chain T [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain EA [auth D] SDF format, chain DA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D]	DA [auth D], EA [auth D], O [auth B], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain O [auth B] Focus chain P [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain CA [auth C] SDF format, chain BA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C]	BA [auth C] CA [auth C] L [auth A] M [auth A] N [auth A] BA [auth C], CA [auth C], L [auth A], M [auth A], N [auth A], Q [auth B], R [auth B], S [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain K [auth A] SDF format, chain AA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth C]	AA [auth C] J [auth A] K [auth A] W [auth C] X [auth C] AA [auth C], J [auth A], K [auth A], W [auth C], X [auth C], Y [auth C], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain I [auth A]	H [auth A], I [auth A], U [auth C], V [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain U [auth C] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.198 (Depositor), 0.202 (DCC)
R-Value Work: 0.173 (Depositor), 0.179 (DCC)
R-Value Observed: 0.174 (Depositor)

Diffraction Data: https://doi.org/10.18430/m37jz0

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.238	α = 90
b = 167.238	β = 90
c = 98.867	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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-09-16

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2020-09-16
Type: Initial release
Version 1.1: 2021-12-15
Changes: Database references
Version 1.2: 2022-11-02
Changes: Database references
Version 1.3: 2023-10-18
Changes: Data collection, Refinement description
Version 2.0: 2024-03-06
Changes: Data collection, Non-polymer description, Structure summary
Version 2.1: 2026-04-01
Changes: Data collection, Database references, Structure summary