29QH | pdb_000029qh

Crystal structure of Parechovirus A1 RdRP in out/down conformation

• PDB DOI: https://doi.org/10.2210/pdb29QH/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Parechovirus ahumpari
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2026-03-30 Released: 2026-09-23 
• Deposition Author(s): Guryanov, S.G., Kajander, T., Mitchell, C., Butcher, S.J.
• Funding Organization(s): Jane and Aatos Erkko Foundation, Sigrid Juselius Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.211 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: in silico

Literature

Crystal structures of Parechovirus A1 3D pol reveal a mechanism of conformational stabilization in +ssRNA virus RNA-dependent RNA polymerase.

Guryanov, S.G., Mitchell, C., Kajander, T., Butcher, S.J.

(2026) J Struct Biol 218: 108370-108370

• PubMed: 42722143 
• DOI: https://doi.org/10.1016/j.jsb.2026.108370
• Primary Citation Related Structures: 
  29QG, 29QH, 29QI


• PubMed Abstract: 
  

  Parechovirus A1 (PeV A1) 3D ^pol is an RNA-dependent RNA polymerase responsible for replication of the virus genome. We solved crystal structures of PeV A1 3D ^pol structure in complex with GTP and in apo-state at 1.8-2.0 Å resolutions. In the 3D ^pol -GTP complex, the conformation of the conserved motif B loop was stabilized by zinc ion coordination by cysteine residues. Apo-state structures of PeV A1 3D ^pol showed significant conformational flexibility in the motif B loop, in the absence of zinc. While one of the conformational states of apo-3D ^pol was similar to the 3D ^pol -GTP complex structure, the alternative apo-3D ^pol conformation showed a 4.3 Å movement of the motif B loop out of the active site cavity relative to the complex of 3D ^pol with GTP. We propose that PeV A1 3D ^pol activity is regulated by conformational stabilization of the motif B loop by zinc coordination.

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Organizational Affiliation: 
• Department of Molecular and Integrative Biosciences, University of Helsinki, Helsinki, Finland; Institute of Biotechnology, University of Helsinki, Helsinki, Finland. Electronic address: [e-mail].
Department of Molecular and Integrative Biosciences, University of Helsinki, Helsinki, Finland; Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
Department of Molecular and Integrative Biosciences, University of Helsinki, Helsinki, Finland; Institute of Biotechnology, University of Helsinki, Helsinki, Finland. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.78 kDa 
• Atom Count: 4,175 
• Modeled Residue Count: 469 
• Deposited Residue Count: 469 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A	469	Parechovirus ahumpari	Mutation(s): 0
UniProt
Find proteins for Q66578 (Human parechovirus 1 (strain Harris)) Explore Q66578  Go to UniProtKB:  Q66578

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.211 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Diffraction Data: https://doi.org/10.15151/ESRF-ES-1058394277

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.114	α = 90
b = 103.918	β = 95.105
c = 104.441	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-23 
Deposition Author(s): Guryanov, S.G., Kajander, T., Mitchell, C., Butcher, S.J.

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Funding Organization	Location	Grant Number
Jane and Aatos Erkko Foundation	Finland	240002
Sigrid Juselius Foundation	Finland	95-7202-38
Sigrid Juselius Foundation	Finland	121-8570-56

Revision History  

• Version 1.0: 2026-09-23
  Type: Initial release