9RTJ | pdb_00009rtj

Hydrid structure of the helix bundle domain of pRN1 primase in complex with DNA, ATP and dGTP

• PDB DOI: https://doi.org/10.2210/pdb9RTJ/pdb

• Classification: REPLICATION
• Organism(s): Saccharolobus islandicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-07-02 Released: 2026-03-25 
• Deposition Author(s): Wu, P., Damberger, F.F., Zehnder, J., Schroder, N., Lipps, G., Wiegand, T., Allain, F.H.-T.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

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• Method: SOLID-STATE NMR
• Conformers Calculated: 500 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Molecular Basis for Primer Synthesis Initiation by DNA Primase

Wu, P., Damberger, F.F., Zehnder, J., Schroder, N., Lipps, G., Wiegand, T., Allain, F.H.-T.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 17.62 kDa 
• Atom Count: 1,215 
• Modeled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SF3 helicase domain-containing protein	A [auth B]	118	Saccharolobus islandicus	Mutation(s): 0
UniProt
Find proteins for Q54324 (Saccharolobus islandicus) Explore Q54324  Go to UniProtKB:  Q54324

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3')	B [auth A]	9	Saccharolobus islandicus

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	D [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
DGT (Subject of Investigation/LOI)	C [auth B]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-N
MG (Subject of Investigation/LOI)	E [auth B], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

• Method: SOLID-STATE NMR
• Conformers Calculated: 500 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-03-25 
Deposition Author(s): Wu, P., Damberger, F.F., Zehnder, J., Schroder, N., Lipps, G., Wiegand, T., Allain, F.H.-T.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	163345
Swiss National Science Foundation	Switzerland	185252

Revision History  

• Version 1.0: 2026-03-25
  Type: Initial release