9X1P | pdb_00009x1p

The cryo-EM structure of HerA-NurA complex with ATPgammaS and dsDNA from Thermococcus kodakarensis (State 3)

PDB DOI: https://doi.org/10.2210/pdb9X1P/pdb
EM Map EMD-66466: EMDB EMDataResource

Classification: DNA BINDING PROTEIN
Organism(s): Thermococcus kodakarensis, DNA molecule
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-10-02 Released: 2026-02-04
Deposition Author(s): Uda, K., Numata, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

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

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Substrate specificity and mechanism of action of the HerA-NurA nuclease from the hyperthermophilic archaeon Thermococcus kodakarensis

Uda, K., Numata, T.

To be published.

Macromolecule Content

Total Structure Weight: 509.75 kDa
Atom Count: 34,280
Modeled Residue Count: 4,284
Deposited Residue Count: 4,464
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA helicase	A, B, C, D, E A, B, C, D, E, F	592	Thermococcus kodakarensis	Mutation(s): 0 Gene Names: TK2213 EC: 3.6.4.12
UniProt
Find proteins for Q5JHP7 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JHP7 Go to UniProtKB: Q5JHP7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JHP7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-3' nuclease, encoded next to Rad50 and Mre11 homologs	G, H	443	Thermococcus kodakarensis	Mutation(s): 1 Gene Names: TK2210
UniProt
Find proteins for Q5JHL5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JHL5 Go to UniProtKB: Q5JHL5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JHL5
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA	I	13	DNA molecule
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA	J	13	DNA molecule
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain M [auth B] SDF format, chain K [auth A] MOL2 format, chain T [auth F] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] mmCIF format, chain T [auth F] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A]	K [auth A], M [auth B], T [auth F]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain K [auth A] Focus chain M [auth B] Focus chain T [auth F] Interactions & Density Focus chain K [auth A] Focus chain M [auth B] Focus chain T [auth F]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E]	O [auth C], P [auth D], R [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain O [auth C] Focus chain P [auth D] Focus chain R [auth E] Interactions & Density Focus chain O [auth C] Focus chain P [auth D] Focus chain R [auth E]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain U [auth F] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain U [auth F]	L [auth A], N [auth B], Q [auth D], S [auth E], U [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain N [auth B] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Interactions & Density Focus chain L [auth A] Focus chain N [auth B] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.19.2_4158
MODEL REFINEMENT	Coot

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-02-04

Deposition Author(s):

Uda, K.

Numata, T.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP19K22289
Japan Society for the Promotion of Science (JSPS)	Japan	JP21K05394
Japan Society for the Promotion of Science (JSPS)	Japan	20H02916
Japan Society for the Promotion of Science (JSPS)	Japan	20K21281
Japan Society for the Promotion of Science (JSPS)	Japan	24H00505