7RDX

SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - open class


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Ensemble cryo-electron microscopy reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex

Chen, J.Wang, Q.Malone, B.Llewellyn, E.Pechersky, Y.Maruthi, K.Eng, E.T.Perry, J.K.Campbell, E.A.Shaw, D.E.Darst, S.A.

(2021) Biorxiv 


Macromolecules

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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)
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)
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)
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)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
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Go to UniProtKB:  P0DTD1
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Entity ID: 5
MoleculeChainsLengthOrganismImage
Product RNAG [auth P]35synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
Template RNAH [auth T]55synthetic construct
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1N7 (Subject of Investigation/LOI)
Query on 1N7

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M [auth A], N [auth A], U [auth E]CHAPSO
C32 H59 N2 O8 S
GUQQBLRVXOUDTN-XOHPMCGNSA-O
 Ligand Interaction
ADP (Subject of Investigation/LOI)
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

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AA [auth F], T [auth E]ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

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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 
K [auth A], S [auth E], Z [auth F]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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: 2021-11-24
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references