9BLF | pdb_00009blf

SARS-CoV-2 core polymerase complex inhibited by araCTP


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9BLF

This is version 2.1 of the entry. See complete history

Literature

Incorporation of arabinose-CTP and arabinose-UTP inhibits viral polymerases by inducing long pauses.

Xiao, Z.Das, A.Jain, A.Anderson, T.K.Cameron, C.E.Arnold, J.J.Dulin, D.Kirchdoerfer, R.N.

(2026) J Biological Chem 302: 111027-111027

  • DOI: https://doi.org/10.1016/j.jbc.2025.111027
  • Primary Citation Related Structures: 
    9BLF

  • PubMed Abstract: 

    Key to supporting human health in the face of evolving viruses is the development of novel antiviral drug scaffolds with the potential for broad inhibition of viral families. Nucleoside analogs are a key class of drugs that have demonstrated potential for the inhibition of several viral species. Here, we evaluate arabinose nucleotides (ara-NTP) as inhibitors of the severe acute respiratory syndrome coronavirus 2 and poliovirus polymerases using biochemistry, biophysics, and structural biology. Ara-NTPs compete poorly with their natural counterparts for incorporation into RNA by viral polymerases. However, upon incorporation, ara-NMPs induce long polymerase pausing during both severe acute respiratory syndrome coronavirus 2 and poliovirus polymerase RNA elongation. Our studies suggest that following ara-NMP incorporation, additional nucleotide incorporation is inhibited at the catalytic step.


  • Organizational Affiliation
    • Institute for Molecular Virology, Center for Quantitative Cell Imaging, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.

Macromolecule Content 

  • Total Structure Weight: 186.91 kDa 
  • Atom Count: 12,360 
  • Modeled Residue Count: 1,439 
  • Deposited Residue Count: 1,515 
  • Unique protein chains: 3
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase nsp12964Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Non-structural protein 8
B, D
199Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Non-structural protein 784Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC1 
Go to UniProtKB:  P0DTC1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC1
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 4
MoleculeChains LengthOrganismImage
Primer RNAE [auth P]31Severe acute respiratory syndrome coronavirus 2
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 5
MoleculeChains LengthOrganismImage
Template RNAF [auth T]38synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HF4
(Subject of Investigation/LOI)

Query on HF4



Download:Ideal Coordinates CCD File
J [auth A],
L [auth A]
4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-CCXZUQQUSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
I [auth A],
K [auth A],
M [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARCv4.4.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI123498
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI158463
United States Department of Agriculture (USDA)United StatesWIS03099

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 2.0: 2025-11-19
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2026-05-27
    Changes: Data collection, Database references