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- EMDB-31478: Reconstruction of the HerA-NurA complex from Deinococcus radiodurans -

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Basic information

Entry
Database: EMDB / ID: EMD-31478
TitleReconstruction of the HerA-NurA complex from Deinococcus radiodurans
Map data
Sample
  • Complex: Helicase-nuclease complex composed of HerA and NurA
    • Protein or peptide: NurA
    • Protein or peptide: HerA
Keywordsnuclease / helicase / end resection / DNA repair / HYDROLASE
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
NurA domain / NurA domain / NurA / : / Ribonuclease H-like superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Helicase HerA central domain-containing protein / NurA domain-containing protein
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsXu Y / Xu L
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
CitationJournal: Structure / Year: 2022
Title: Mechanisms of helicase activated DNA end resection in bacteria.
Authors: Ying Xu / Lingyi Xu / Chen Qin / Liangyan Wang / Jiangtao Guo / Yuejin Hua / Ye Zhao /
Abstract: DNA end resection mediated by the coordinated action of nuclease and helicase is a crucial step in initiating homologous recombination. The end-resection apparatus NurA nuclease and HerA helicase are ...DNA end resection mediated by the coordinated action of nuclease and helicase is a crucial step in initiating homologous recombination. The end-resection apparatus NurA nuclease and HerA helicase are present in both archaea and bacteria. Here, we report the cryo-electron microscopy structure of a bacterial HerA-NurA complex from Deinococcus radiodurans. The structure reveals a barrel-like hexameric HerA and a distinctive NurA dimer subcomplex, which has a unique extended N-terminal region (ENR) involved in bacterial NurA dimerization and activation. In addition to the long protruding linking loop and the C-terminal α helix of NurA, the flexible ENR is close to the HerA-NurA interface and divides the central channel of the DrNurA dimer into two halves, suggesting a possible mechanism of DNA end processing. In summary, this work provides new insights into the structure, assembly, and activation mechanisms of bacterial DNA end resection mediated by a minimal end-resection apparatus.
History
DepositionJun 25, 2021-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31478.png

Downloads & links

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Map

FileDownload / File: emd_31478.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 270 pix.
= 273.78 Å		1.01 Å/pix.
x 270 pix.
= 273.78 Å		1.01 Å/pix.
x 270 pix.
= 273.78 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0115
Minimum - Maximum-0.051733293 - 0.08395544
Average (Standard dev.)0.00029182958 (±0.0025866358)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 273.78003 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Helicase-nuclease complex composed of HerA and NurA

EntireName: Helicase-nuclease complex composed of HerA and NurA
Components
  • Complex: Helicase-nuclease complex composed of HerA and NurA
    • Protein or peptide: NurA
    • Protein or peptide: HerA

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Supramolecule #1: Helicase-nuclease complex composed of HerA and NurA

SupramoleculeName: Helicase-nuclease complex composed of HerA and NurA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Deinococcus radiodurans R1 (radioresistant)
Molecular weightTheoretical: 480 KDa

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Macromolecule #1: NurA

MacromoleculeName: NurA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Deinococcus radiodurans R1 (radioresistant) / Strain: R1
Molecular weightTheoretical: 40.482066 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MRIRLDPWPI DTFEGQLTLK PFAGLVFDVE TDRWEAIPTL GIPESVREVL VVDGKPRMEA RLLMDDDSG ELHLAAFGAY VVGAVSLCPH GTRQAELLDV RARRVLAYSS DAPLEPARLS PRNPHTGVLD YEPYAFSGRQ V EGPRAAVQ ...String:
MGSSHHHHHH SSGLVPRGSH MRIRLDPWPI DTFEGQLTLK PFAGLVFDVE TDRWEAIPTL GIPESVREVL VVDGKPRMEA RLLMDDDSG ELHLAAFGAY VVGAVSLCPH GTRQAELLDV RARRVLAYSS DAPLEPARLS PRNPHTGVLD YEPYAFSGRQ V EGPRAAVQ KLMLQDEQKL SRQLASPIAL EEGEADALPE SLVLQDGPVR LGGGGSAVVG YVKTLHTDYL GADRIGLLSS LK CGERTPI LRFRVGDRGG TFSEAEGREQ RFTWYVRLCD APFYQHPLAG IMRLEMHAPE DSSFVPAAVQ QIADLSGALL SKL GSKLHK DSRAPQNLIP TAALEQAMNR SMGNLELVTR RIRTHLVTQG VVA

UniProtKB: NurA domain-containing protein

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Macromolecule #2: HerA

MacromoleculeName: HerA / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Deinococcus radiodurans R1 (radioresistant) / Strain: R1
Molecular weightTheoretical: 67.452461 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MTGNDVQGAE KADAIGMVLG TEDVTPTVFW FAVSHGASVG LDDLVVVETR KPDGTPVRFY GLVDNVRKRH EGVTFESDVE DVVAGLLPA SVSYAARVLV TRVDPENFIP PQPGDHVRHA AGRELAMALS ADKMEEAAFP GGLLADGQPL PLNFRFINGE S GGHINISG ...String:
MTGNDVQGAE KADAIGMVLG TEDVTPTVFW FAVSHGASVG LDDLVVVETR KPDGTPVRFY GLVDNVRKRH EGVTFESDVE DVVAGLLPA SVSYAARVLV TRVDPENFIP PQPGDHVRHA AGRELAMALS ADKMEEAAFP GGLLADGQPL PLNFRFINGE S GGHINISG ISGVATKTSY ALFLLHSIFR SGVMDRTAQG SGGRQSGTAG GRALIFNVKG EDLLFLDKPN ARMVEKEDKV VR AKGLSAD RYALLGLPAE PFRDVQLLAP PRAGAAGTAI VPQTDQRSEG VTPFVFTIRE FCARRMLPYV FSDASASLNL GFV IGNIEE KLFRLAAAQT GKGTGLIVHD WQFEDSETPP ENLDFSELGG VNLQTFEQLI SYLEYKLLEE REGEGDPKWV LKQS PGTLR AFTRRLRGVQ KYLSPLIRGD LTPEQAEGYR PDPLRRGIQL TVVDIHALSA HAQMFVVGVL LREVFEYKER VGRQD TVFV VLDELNKYAP REGDSPIKDV LLDIAERGRS LGIILIGAQQ TASEVERRIV SNAAIRVVGR LDLAEAERPE YRFLPQ SFR GRAGILQPGT MLVSQPDVPN PVLVNYPFPA WATRRDEVDD LGGKAAAEVG AGLLR

UniProtKB: Helicase HerA central domain-containing protein

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1659937
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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