8GW1 | pdb_00008gw1

A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors

PDB DOI: https://doi.org/10.2210/pdb8GW1/pdb
EM Map EMD-34302: EMDB EMDataResource
NAKB: 8GW1

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-09-16 Released: 2023-10-25
Deposition Author(s): Yan, L., Rao, Z., Lou, Z.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.31 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors.

Yan, L., Huang, Y., Ge, J., Liu, Z., Lu, P., Huang, B., Gao, S., Wang, J., Tan, L., Ye, S., Yu, F., Lan, W., Xu, S., Zhou, F., Shi, L., Guddat, L.W., Gao, Y., Rao, Z., Lou, Z.

(2022) Cell 185: 4347-4360.e17

PubMed: 36335936 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2022.09.037
Primary Citation Related Structures:
8GW1, 8GWB, 8GWE, 8GWF, 8GWG, 8GWI, 8GWK, 8GWM, 8GWN, 8GWO

PubMed Abstract:
Decoration of cap on viral RNA plays essential roles in SARS-CoV-2 proliferation. Here, we report a mechanism for SARS-CoV-2 RNA capping and document structural details at atomic resolution. The NiRAN domain in polymerase catalyzes the covalent link of RNA 5' end to the first residue of nsp9 (termed as RNAylation), thus being an intermediate to form cap core (GpppA) with GTP catalyzed again by NiRAN. We also reveal that triphosphorylated nucleotide analog inhibitors can be bonded to nsp9 and fit into a previously unknown "Nuc-pocket" in NiRAN, thus inhibiting nsp9 RNAylation and formation of GpppA. S-loop (residues 50-KTN-52) in NiRAN presents a remarkable conformational shift observed in RTC bound with sofosbuvir monophosphate, reasoning an "induce-and-lock" mechanism to design inhibitors. These findings not only improve the understanding of SARS-CoV-2 RNA capping and the mode of action of NAIs but also provide a strategy to design antiviral drugs.

Organizational Affiliation

MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China.

MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.

MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; Innovation Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China.

MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.

Division of Biosciences, University College London, London, UK.

Beijing StoneWise Technology Co Ltd., Beijing, China.

Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.

Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.

Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. Electronic address: gaoyan@shanghaitech.edu.cn.

MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; Innovation Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. Electronic address: raozh@tsinghua.edu.cn.

MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China. Electronic address: louzy@mail.tsinghua.edu.cn.

Macromolecule Content

Total Structure Weight: 324.81 kDa
Atom Count: 21,843
Modeled Residue Count: 2,707
Deposited Residue Count: 2,787
Unique protein chains: 5
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A	942	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1 Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (PDB Primary Data)
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
Non-structural protein 8	B, D	198	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	C	83	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1 Go to UniProtKB: P0DTC1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase	G [auth E], H [auth F]	601	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
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: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 9	I [auth G]	113	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
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

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 4
RNA (25-MER)	E [auth I]	25	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 5
Template	F [auth J]	26	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
U5P Query on U5P Download:Ideal Coordinates CCD File SDF format, chain T [auth G] MOL2 format, chain T [auth G] mmCIF format, chain T [auth G]	T [auth G]	URIDINE-5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₉ P DJJCXFVJDGTHFX-XVFCMESISA-N		Interactions Focus chain T [auth G] Interactions & Density Focus chain T [auth G]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth E] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain R [auth F] SDF format, chain S [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] MOL2 format, chain S [auth F] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth E] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth F] mmCIF format, chain S [auth F]	J [auth A] K [auth A] N [auth E] O [auth E] P [auth E] J [auth A], K [auth A], N [auth E], O [auth E], P [auth E], Q [auth F], R [auth F], S [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth F] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth F]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	L [auth A], M [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.31 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-10-25

Deposition Author(s):

Yan, L.

Rao, Z.

Lou, Z.

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2020YFA0707500
Ministry of Science and Technology (MoST, China)	China	2017YFC0840300

Revision History (Full details and data files)

Version 1.0: 2023-10-25
Type: Initial release
Version 2.0: 2024-01-24
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2024-11-06
Changes: Data collection, Structure summary
Version 2.2: 2025-06-25
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

8GW1 | pdb_00008gw1

A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors

Literature

A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

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Entity ID: 3

UniProt

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Sequence Annotations

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Entity ID: 6

UniProt

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Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

Sequence Annotations

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Entity ID: 5

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)