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
BMRB: 35007
NAKB: 9RTJ

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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9RTJ

This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q54324
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	B [auth A]	9	Saccharolobus islandicus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain D [auth B]
DGT (Subject of Investigation/LOI) Query on DGT Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ HAAZLUGHYHWQIW-KVQBGUIXSA-N		Interactions Focus chain C [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B]	E [auth B], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B]

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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-25

Deposition Author(s):

Damberger, F.F.

Allain, F.H.-T.

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.