7N0D | pdb_00007n0d

Cryo-EM structure of the tetrameric form of SARS-CoV-2 nsp10-nsp14 (E191A)-RNA complex

PDB DOI: https://doi.org/10.2210/pdb7N0D/pdb
EM Map EMD-24104: EMDB EMDataResource
NAKB: 7N0D

Classification: VIRAL PROTEIN/RNA
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-05-25 Released: 2021-07-28
Deposition Author(s): Liu, C., Yang, Y.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme.

Liu, C., Shi, W., Becker, S.T., Schatz, D.G., Liu, B., Yang, Y.

(2021) Science 373: 1142-1146

PubMed: 34315827 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.abi9310
Primary Citation Related Structures:
7N0B, 7N0C, 7N0D

PubMed Abstract:
Coronavirus 3′-to-5′ exoribonuclease (ExoN), residing in the nonstructural protein (nsp) 10–nsp14 complex, boosts replication fidelity by proofreading RNA synthesis and is critical for the virus life cycle. ExoN also recognizes and excises nucleotide analog inhibitors incorporated into the nascent RNA, undermining the effectiveness of nucleotide analog–based antivirals. Here we present cryo–electron microscopy structures of both wild-type and mutant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nsp10-nsp14 in complex with an RNA substrate bearing a 3′-end mismatch at resolutions ranging from 2.5 to 3.9 angstroms. The structures reveal the molecular determinants of ExoN substrate specificity and offer insight into the molecular mechanisms of mismatch correction during coronavirus RNA synthesis. Our findings provide guidance for rational design of improved anticoronavirus therapies.

Organizational Affiliation

Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.

Macromolecule Content

Total Structure Weight: 335.49 kDa
Atom Count: 21,846
Modeled Residue Count: 2,648
Deposited Residue Count: 2,772
Unique protein chains: 2
Unique nucleic acid chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 10	A, C, H [auth E], J [auth G]	139	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proofreading exoribonuclease	B, D, I [auth F], K [auth H]	527	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 Gene Names: rep, 1a-1b EC: 3.1.13
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 3
RNA (5'-R(GPGPGPGPAPUPGPUPGPAPUPUPUPUPAPAPUPAP*G)-3')	E [auth T], L [auth I]	27	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 4
RNA (5'-R(CPUPAPUPUPAPAPAPAPUPCPAPCPC)-3')	F [auth K], M [auth L]	22	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 5
RNA (5'-R(CPCPCPCP*C)-3')	G [auth P], N [auth J]	5	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1N7 Query on 1N7 Download:Ideal Coordinates CCD File SDF format, chain LA [auth H] SDF format, chain BA [auth D] MOL2 format, chain LA [auth H] MOL2 format, chain BA [auth D] mmCIF format, chain LA [auth H] mmCIF format, chain BA [auth D]	BA [auth D], LA [auth H]	CHAPSO C₃₂ H₅₉ N₂ O₈ S GUQQBLRVXOUDTN-XOHPMCGNSA-O		Interactions Focus chain BA [auth D] Focus chain LA [auth H] Interactions & Density Focus chain BA [auth D] Focus chain LA [auth H]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain PA [auth H] SDF format, chain OA [auth H] SDF format, chain O [auth A] SDF format, chain NA [auth H] SDF format, chain KA [auth G] SDF format, chain JA [auth G] SDF format, chain IA [auth F] SDF format, chain HA [auth F] SDF format, chain GA [auth F] SDF format, chain DA [auth E] SDF format, chain CA [auth E] SDF format, chain AA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain PA [auth H] MOL2 format, chain OA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth H] MOL2 format, chain KA [auth G] MOL2 format, chain JA [auth G] MOL2 format, chain IA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain AA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain PA [auth H] mmCIF format, chain OA [auth H] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth H] mmCIF format, chain KA [auth G] mmCIF format, chain JA [auth G] mmCIF format, chain IA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain AA [auth D]	AA [auth D] CA [auth E] DA [auth E] GA [auth F] HA [auth F] AA [auth D], CA [auth E], DA [auth E], GA [auth F], HA [auth F], IA [auth F], JA [auth G], KA [auth G], NA [auth H], O [auth A], OA [auth H], P [auth A], PA [auth H], S [auth B], T [auth B], U [auth B], V [auth C], W [auth C], Y [auth D], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain NA [auth H] Focus chain O [auth A] Focus chain OA [auth H] Focus chain P [auth A] Focus chain PA [auth H] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain NA [auth H] Focus chain O [auth A] Focus chain OA [auth H] Focus chain P [auth A] Focus chain PA [auth H] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain FA [auth F] SDF format, chain X [auth D] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain MA [auth H] SDF format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain X [auth D] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain MA [auth H] MOL2 format, chain EA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain X [auth D] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain MA [auth H] mmCIF format, chain EA [auth F]	EA [auth F] FA [auth F] MA [auth H] Q [auth B] R [auth B] EA [auth F], FA [auth F], MA [auth H], Q [auth B], R [auth B], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth F] Focus chain FA [auth F] Focus chain MA [auth H] Focus chain Q [auth B] Focus chain R [auth B] Focus chain X [auth D] Interactions & Density Focus chain EA [auth F] Focus chain FA [auth F] Focus chain MA [auth H] Focus chain Q [auth B] Focus chain R [auth B] Focus chain X [auth D]