8GWM

SARS-CoV-2 E-RTC bound with MMP-nsp9 and GMPPNP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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

  • DOI: https://doi.org/10.1016/j.cell.2022.09.037
  • Primary Citation of 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase932Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 8
B, D
198Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 783Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Helicase
E, F
601Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 9113Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
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Explore P0DTD1 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
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  • Reference Sequence

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Entity ID: 6
MoleculeChains LengthOrganismImage
RNA (25-MER)H [auth I]25Severe acute respiratory syndrome coronavirus 2
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Entity ID: 7
MoleculeChains LengthOrganismImage
RNA (26-MER)I [auth J]26Severe acute respiratory syndrome coronavirus 2
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
Query on GNP

Download Ideal Coordinates CCD File 
L [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
6GS (Subject of Investigation/LOI)
Query on 6GS

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S [auth G]2'-deoxy-2'-fluoro-2'-methyluridine 5'-(trihydrogen diphosphate)
C10 H15 F N2 O11 P2
VPPLCOBQDZAMRD-VPCXQMTMSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
M [auth E]
N [auth E]
O [auth E]
J [auth A],
K [auth A],
M [auth E],
N [auth E],
O [auth E],
P [auth F],
Q [auth F],
R [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2020YFA0707500
Ministry of Science and Technology (MoST, China)China2017YFC0840300

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release