6XEZ

Structure of SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.3 of the entry. See complete history


Literature

Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex.

Chen, J.Malone, B.Llewellyn, E.Grasso, M.Shelton, P.M.M.Olinares, P.D.B.Maruthi, K.Eng, E.T.Vatandaslar, H.Chait, B.T.Kapoor, T.M.Darst, S.A.Campbell, E.A.

(2020) Cell 182: 1560-1573.e13

  • DOI: 10.1016/j.cell.2020.07.033
  • Primary Citation of Related Structures:  
    6XEZ

  • PubMed Abstract: 
  • SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated and transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp8 2 /nsp12) along with a cast of accessory factors. One of these factors is the nsp13 helicase ...

    SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated and transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp8 2 /nsp12) along with a cast of accessory factors. One of these factors is the nsp13 helicase. Both the holo-RdRp and nsp13 are essential for viral replication and are targets for treating the disease COVID-19. Here we present cryoelectron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template product in complex with two molecules of the nsp13 helicase. The Nidovirales order-specific N-terminal domains of each nsp13 interact with the N-terminal extension of each copy of nsp8. One nsp13 also contacts the nsp12 thumb. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. We also observe ADP-Mg 2+ bound in the nsp12 N-terminal nidovirus RdRp-associated nucleotidyltransferase domain, detailing a new pocket for anti-viral therapy development.


    Related Citations: 
    • Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex.
      Chen, J., Malone, B., Llewellyn, E., Grasso, M., Shelton, P.M.M., Olinares, P.D.B., Maruthi, K., Eng, E.T., Vatandaslar, H., Chait, B., Kapoor, T., Darst, S.A., Campbell, E.A.
      (2020) Biorxiv --: --
    • Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex.
      Chen, J., Malone, B., Llewellyn, E., Grasso, M., Shelton, P.M.M., Olinares, P.D.B., Maruthi, K., Eng, E.T., Vatandaslar, H., Chait, B., Kapoor, T., Darst, S.A., Campbell, E.A.
      (2020) Biorxiv --: --

    Organizational Affiliation

    Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA. Electronic address: campbee@rockefeller.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymeraseA932Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 2.7.7.48 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 8B, D199Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 7C88Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HelicaseE, F605Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
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Entity ID: 5
MoleculeChainsLengthOrganismImage
Product RNAG [auth P]35Severe acute respiratory syndrome coronavirus 2
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Entity ID: 6
MoleculeChainsLengthOrganismImage
Template RNAH [auth T]55Severe acute respiratory syndrome coronavirus 2
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1N7
Query on 1N7

Download Ideal Coordinates CCD File 
M [auth A], N [auth A], U [auth E]CHAPSO
C32 H59 N2 O8 S
GUQQBLRVXOUDTN-XOHPMCGNSA-O
 Ligand Interaction
ADP
Query on ADP

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L [auth A], R [auth E], Y [auth F]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
AF3
Query on AF3

Download Ideal Coordinates CCD File 
S [auth E], Z [auth F]ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], O [auth E], P [auth E], Q [auth E], V [auth F], W [auth F], X [auth F]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth F], K [auth A], T [auth E]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references
  • Version 1.2: 2020-09-30
    Changes: Database references
  • Version 1.3: 2021-01-27
    Changes: Structure summary