[English] 日本語
Yorodumi
- PDB-9x1p: The cryo-EM structure of HerA-NurA complex with ATPgammaS and dsD... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9x1p
TitleThe cryo-EM structure of HerA-NurA complex with ATPgammaS and dsDNA from Thermococcus kodakarensis (State 3)
Components
  • (DNA) x 2
  • 5'-3' nuclease, encoded next to Rad50 and Mre11 homologs
  • DNA helicase
KeywordsDNA BINDING PROTEIN / HerA / Helicase / NurA / Nuclease
Function / homology
Function and homology information


3'-5' DNA helicase activity / 5'-3' DNA helicase activity / metal ion binding
Similarity search - Function
: / Helicase HerA, barrel domain / HAS barrel domain / DNA double-strand break repair nuclease NurA-like / : / NurA domain / NurA domain / NurA / Helicase HerA-like / Helicase HerA, central domain ...: / Helicase HerA, barrel domain / HAS barrel domain / DNA double-strand break repair nuclease NurA-like / : / NurA domain / NurA domain / NurA / Helicase HerA-like / Helicase HerA, central domain / Helicase HerA, central domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / : / DNA / DNA (> 10) / 5'-3' nuclease, encoded next to Rad50 and Mre11 homologs / Bipolar DNA helicase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
DNA molecule (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsUda, K. / Numata, T.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19K22289 Japan
Japan Society for the Promotion of Science (JSPS)JP21K05394 Japan
Japan Society for the Promotion of Science (JSPS)20H02916 Japan
Japan Society for the Promotion of Science (JSPS)20K21281 Japan
Japan Society for the Promotion of Science (JSPS)24H00505 Japan
CitationJournal: To Be Published
Title: Substrate specificity and mechanism of action of the HerA-NurA nuclease from the hyperthermophilic archaeon Thermococcus kodakarensis
Authors: Uda, K. / Numata, T.
History
DepositionOct 2, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA helicase
B: DNA helicase
C: DNA helicase
D: DNA helicase
E: DNA helicase
F: DNA helicase
G: 5'-3' nuclease, encoded next to Rad50 and Mre11 homologs
H: 5'-3' nuclease, encoded next to Rad50 and Mre11 homologs
I: DNA
J: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)509,75421
Polymers506,62810
Non-polymers3,12611
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
DNA helicase


Mass: 66118.117 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK2213 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold CodonPlus RIL / References: UniProt: Q5JHP7, DNA helicase
#2: Protein 5'-3' nuclease, encoded next to Rad50 and Mre11 homologs


Mass: 50991.660 Da / Num. of mol.: 2 / Mutation: D49A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK2210 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold CodonPlus RIL / References: UniProt: Q5JHL5

-
DNA chain , 2 types, 2 molecules IJ

#3: DNA chain DNA


Mass: 4026.731 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#4: DNA chain DNA


Mass: 3909.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)

-
Non-polymers , 3 types, 11 molecules

#5: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Thermococcus kodakarensis HerA-NurA complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.5 MDa / Experimental value: NO
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: Gold CodonPlus RIL / Plasmid: pET21a, pET24a
Buffer solutionpH: 7
Buffer component
IDConc.NameBuffer-ID
1100 mMsodium chloride1
22.5 mMmanganese chloride1
31 mMATPgammaS1
40.01 %LMNG1
550 mMTris-HCl1
612 uMdsDNA1
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

-
Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10350
EM imaging opticsEnergyfilter name: In-column Omega Filter

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
8UCSF ChimeraXmodel fitting
9PHENIXmodel fitting
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
13cryoSPARCclassification
14cryoSPARC3D reconstruction
15PHENIX1.19.2_4158model refinement
16Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96354 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00234928
ELECTRON MICROSCOPYf_angle_d0.47247318
ELECTRON MICROSCOPYf_dihedral_angle_d11.6213230
ELECTRON MICROSCOPYf_chiral_restr0.045268
ELECTRON MICROSCOPYf_plane_restr0.0036004

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more