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- EMDB-66462: The cryo-EM structure of HerA-NurA complex with AMPPNP from Therm... -

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Basic information

Entry
Database: EMDB / ID: EMD-66462
TitleThe cryo-EM structure of HerA-NurA complex with AMPPNP from Thermococcus kodakarensis
Map dataprimary map
Sample
  • Complex: Thermococcus kodakarensis HerA-NurA complex
    • Protein or peptide: DNA helicase
    • Protein or peptide: 5'-3' nuclease, encoded next to Rad50 and Mre11 homologs
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
KeywordsHerA / Helicase / NurA / Nuclease / TRANSLOCASE
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
5'-3' nuclease, encoded next to Rad50 and Mre11 homologs / Bipolar DNA helicase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsUda K / Numata T
Funding support Japan, 5 items
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, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66462.png

Downloads & links

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Map

FileDownload / File: emd_66462.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 500 pix.
= 400. Å		0.8 Å/pix.
x 500 pix.
= 400. Å		0.8 Å/pix.
x 500 pix.
= 400. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.080525964 - 0.17988269
Average (Standard dev.)-0.00009912271 (±0.0046495926)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 400.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66462_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharped map

Fileemd_66462_additional_1.map
Annotationsharped map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap B

Fileemd_66462_half_map_1.map
Annotationhalfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap A

Fileemd_66462_half_map_2.map
Annotationhalfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Thermococcus kodakarensis HerA-NurA complex

EntireName: Thermococcus kodakarensis HerA-NurA complex
Components
  • Complex: Thermococcus kodakarensis HerA-NurA complex
    • Protein or peptide: DNA helicase
    • Protein or peptide: 5'-3' nuclease, encoded next to Rad50 and Mre11 homologs
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: Thermococcus kodakarensis HerA-NurA complex

SupramoleculeName: Thermococcus kodakarensis HerA-NurA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: DNA helicase

MacromoleculeName: DNA helicase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 66.118117 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRIAEDINKP VGIVTGEATV SSFQFYAHPD TDLKFGDFVV ARLCKEAKDQ NCRWGENEEG VEWVIGTIRG LKNINWLLSE GKSTYTSLE LDIREYGESI GENEALIVTV HVLGKVQLNG EKAEVVPTRV PVPNGNRVYL ASSDLLRAIY YGGNGYIELG R LIIREDVP ...String:
MRIAEDINKP VGIVTGEATV SSFQFYAHPD TDLKFGDFVV ARLCKEAKDQ NCRWGENEEG VEWVIGTIRG LKNINWLLSE GKSTYTSLE LDIREYGESI GENEALIVTV HVLGKVQLNG EKAEVVPTRV PVPNGNRVYL ASSDLLRAIY YGGNGYIELG R LIIREDVP VYLNVNELVS RHFAILAVTG AGKSNTVSVM LWKLVEELGG TVIVLDPHGD YTKLSLPGTG REYVNLIEAK IR PEAMDGE ELADLMEIQS NASIQRSYLL RAWDTVLHEN QGIGGREAVK LVHDLLQRWA SEGGGTYWDP HAGQYRDLGE IKS AEKETI MRLTMKVSRF LRNYGHLLSS EDIVALIEPG KVNVIDLGPL DEGQMKLVVA KFLEKVFETR MDYEKARKRL DYLR TAYSS NISAVSDEIN ELEEFLRGVE KNYPALAEPV MVIVEEAHIF APHGEKGGAV RILGRIAREG RKFGVGLGLV SQRPS RLSE DVLSQTNTKI IMRIVNPNDQ QYVVRASEQV SGELMSDIAG LGKGEAVIVG QAISLPALVK IYNFKALGGN YGGEDI GAV ERWLERKRRE LEEKEKEEMY EEEGIEVDF

UniProtKB: Bipolar DNA helicase

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Macromolecule #2: 5'-3' nuclease, encoded next to Rad50 and Mre11 homologs

MacromoleculeName: 5'-3' nuclease, encoded next to Rad50 and Mre11 homologs
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 51.035672 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MYRLIDRRSV DRIKALLERG YREAESKLAE IEWKPLPKER KQTRVYAVDG SQGKQRLSGT IFYAVSSYAF GNGPAYRLVY TNAMLYNQG ISDQIIRLQM ETLENKLGYL SAKLGDVDYV MMDGTLTGSL TRPPVYPESV KGLTTIENAL GKGKLKELVK K FVSLLDEH ...String:
MYRLIDRRSV DRIKALLERG YREAESKLAE IEWKPLPKER KQTRVYAVDG SQGKQRLSGT IFYAVSSYAF GNGPAYRLVY TNAMLYNQG ISDQIIRLQM ETLENKLGYL SAKLGDVDYV MMDGTLTGSL TRPPVYPESV KGLTTIENAL GKGKLKELVK K FVSLLDEH YKELEDGLRE KGKINGNVIL ADEKLEEFEE FYKAMKGYKV RDFAGTTPRG IKISRATIDE YLKGRKSAEE IF QELLNEY GEERELSLDD ARNAVHVVLG YLEYLYSLEK LLRLNLVYVA KSFYNRKLTQ KLGIDIVDVP YLDAYLRKRF GEE IPGYFI ITQGGKAISH KMPKVLRETF PLVEHYIEHG VPMAYVRTMK GGVIYLLQSN REVDDDLLSE ILWHESNGYF RPLQ RAHEG VKIEKKAFEA ELKALLNIIK AESPELRVFL KYGRSPLE

UniProtKB: 5'-3' nuclease, encoded next to Rad50 and Mre11 homologs

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 6 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4 mg/mL
BufferpH: 7
Component:
ConcentrationName
100.0 mMsodium chloride
2.5 mMmanganese chloride
1.0 mMAMPPNP
0.001 %LMNG
50.0 mMTris-HCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 2 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.015 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4750 / Average exposure time: 2.5 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 60000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 204172
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9x1l:
The cryo-EM structure of HerA-NurA complex with AMPPNP from Thermococcus kodakarensis

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