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- EMDB-41704: E. coli ExoVII(H238A) -

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Basic information

Entry
Database: EMDB / ID: EMD-41704
TitleE. coli ExoVII(H238A)
Map data
Sample
  • Complex: XseA4-XseB24 complex of ExoVII
    • Protein or peptide: Exodeoxyribonuclease 7 large subunit
    • Protein or peptide: Exodeoxyribonuclease 7 small subunit
KeywordsExonuclease / Endonuclease / DNA repair / DNA BINDING PROTEIN
Function / homology
Function and homology information


exodeoxyribonuclease VII / exodeoxyribonuclease VII activity / exodeoxyribonuclease VII complex / DNA catabolic process / mismatch repair / DNA binding / cytosol / cytoplasm
Similarity search - Function
Exonuclease VII, large subunit / Exonuclease VII, large subunit, C-terminal / OB-fold nucleic acid binding domain / Exonuclease VII, large subunit / OB-fold nucleic acid binding domain / Exonuclease VII, small subunit / Exonuclease VII, small subunit superfamily / Exonuclease VII small subunit
Similarity search - Domain/homology
Exodeoxyribonuclease 7 large subunit / Exodeoxyribonuclease 7 small subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLiu C / Berger JM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA263778 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structure of exonuclease VII.
Authors: Chuan Liu / Glenn Hauk / Qianyun Yan / James M Berger /
Abstract: Exonuclease VII (ExoVII) is a ubiquitous bacterial nuclease. Encoded by the and genes, ExoVII participates in multiple nucleic acid-dependent pathways including the processing of multicopy single- ...Exonuclease VII (ExoVII) is a ubiquitous bacterial nuclease. Encoded by the and genes, ExoVII participates in multiple nucleic acid-dependent pathways including the processing of multicopy single-stranded DNA and the repair of covalent DNA-protein crosslinks (DPCs). Although many biochemical properties of ExoVII have been defined, little is known about its structure/function relationships. Here, we use cryoelectron microscopy (cryoEM) to determine that ExoVII comprises a highly elongated XseA·XseB holo-complex. Each XseA subunit dimerizes through a central extended α-helical segment decorated by six XseB subunits and a C-terminal, domain-swapped β-barrel element; two XseA·XseB subcomplexes further associate using N-terminal OB (oligonucleotide/oligosaccharide-binding) folds and catalytic domains to form a spindle-shaped, catenated octaicosamer. The catalytic domains of XseA, which adopt a nuclease fold related to 3-dehydroquinate dehydratases, are sequestered in the center of the complex and accessible only through large pores formed between XseA tetramers. The architectural organization of ExoVII, combined with biochemical studies, indicate that substrate selectivity is controlled by steric access to its nuclease elements and that tetramer dissociation results from substrate DNA binding. Despite a lack of sequence and fold homology, the physical organization of ExoVII is reminiscent of Mre11·Rad50/SbcCD ATP (adenosine triphosphate)-dependent nucleases used in the repair of double-stranded DNA breaks, including those formed by DPCs through aberrant topoisomerase activity, suggesting that there may have been convergent evolutionary pressure to contend with such damage events.
History
DepositionAug 24, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41704.png

Downloads & links

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Map

FileDownload / File: emd_41704.map.gz / Format: CCP4 / Size: 590.7 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 Å/pix.
x 537 pix.
= 537. Å		1 Å/pix.
x 537 pix.
= 537. Å		1 Å/pix.
x 537 pix.
= 537. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-0.39137733 - 23.96565
Average (Standard dev.)-0.05543507 (±0.21382311)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions537537537
Spacing537537537
CellA=B=C: 537.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : XseA4-XseB24 complex of ExoVII

EntireName: XseA4-XseB24 complex of ExoVII
Components
  • Complex: XseA4-XseB24 complex of ExoVII
    • Protein or peptide: Exodeoxyribonuclease 7 large subunit
    • Protein or peptide: Exodeoxyribonuclease 7 small subunit

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Supramolecule #1: XseA4-XseB24 complex of ExoVII

SupramoleculeName: XseA4-XseB24 complex of ExoVII / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 420 KDa

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Macromolecule #1: Exodeoxyribonuclease 7 large subunit

MacromoleculeName: Exodeoxyribonuclease 7 large subunit / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 51.840141 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MLPSQSPAIF TVSRLNQTVR LLLEHEMGQV WISGEISNFT QPASGHWYFT LKDDTAQVRC AMFRNSNRRV TFRPQHGQQV LVRANITLY EPRGDYQIIV ESMQPAGEGL LQQKYEQLKA KLQAEGLFDQ QYKKPLPSPA HCVGVITSKT GAALHDILHV L KRRDPSLP ...String:
MLPSQSPAIF TVSRLNQTVR LLLEHEMGQV WISGEISNFT QPASGHWYFT LKDDTAQVRC AMFRNSNRRV TFRPQHGQQV LVRANITLY EPRGDYQIIV ESMQPAGEGL LQQKYEQLKA KLQAEGLFDQ QYKKPLPSPA HCVGVITSKT GAALHDILHV L KRRDPSLP VIIYPAAVQG DDAPGQIVRA IELANQRNEC DVLIVGRGGG SLEDLWSFND ERVARAIFTS RIPVVSAVGA ET DVTIADF VADLRAPTPS AAAEVVSRNQ QELLRQVQST RQRLEMAMDY YLANRTRRFT QIHHRLQQQH PQLRLARQQT MLE RLQKRM SFALENQLKR TGQQQQRLTQ RLNQQNPQPK IHRAQTRIQQ LEYRLAETLR AQLSATRERF GNAVTHLEAV SPLS TLARG YSVTTATDGN VLKKVKQVKA GEMLTTRLED GWIESEVKNI QPVKKSRKKV H

UniProtKB: Exodeoxyribonuclease 7 large subunit

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Macromolecule #2: Exodeoxyribonuclease 7 small subunit

MacromoleculeName: Exodeoxyribonuclease 7 small subunit / type: protein_or_peptide / ID: 2 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.959877 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MPKKNEAPAS FEKALSELEQ IVTRLESGDL PLEEALNEFE RGVQLARQGQ AKLQQAEQRV QILLSDNEDA SLTPFTPDNE

UniProtKB: Exodeoxyribonuclease 7 small subunit

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 497337
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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