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- EMDB-40036: RuvA Holliday junction DNA complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-40036
TitleRuvA Holliday junction DNA complex
Map data
Sample
  • Complex: RuvA DNA binding protein complexed with Holliday Junction DNA
    • Complex: Tetrameric RuvA binding protein
      • Complex: Holliday Junction DNA adapted from PDB 2HOI
        • DNA: DNA (34-MER)
        • DNA: DNA (34-MER)
      • Protein or peptide: Holliday junction branch migration complex subunit RuvA
Function / homology
Function and homology information


Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / four-way junction DNA binding / DNA recombination / DNA repair / ATP binding / cytoplasm
Similarity search - Function
Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvA N terminal domain / RuvA, C-terminal domain / Bacterial DNA recombination protein RuvA / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Holliday junction branch migration complex subunit RuvA
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria) / Punavirus P1 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsRish AD / Fu T
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118291-05 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM144293-01 United States
CitationJournal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
History
DepositionMar 9, 2023-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateMay 10, 2023-
Current statusMay 10, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40036.png

Downloads & links

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Map

FileDownload / File: emd_40036.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.95 Å
Density
Contour LevelBy AUTHOR: 0.222
Minimum - Maximum-3.5528626 - 4.7079887
Average (Standard dev.)0.0010096945 (±0.06306138)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 243.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_40036_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40036_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RuvA DNA binding protein complexed with Holliday Junction DNA

EntireName: RuvA DNA binding protein complexed with Holliday Junction DNA
Components
  • Complex: RuvA DNA binding protein complexed with Holliday Junction DNA
    • Complex: Tetrameric RuvA binding protein
      • Complex: Holliday Junction DNA adapted from PDB 2HOI
        • DNA: DNA (34-MER)
        • DNA: DNA (34-MER)
      • Protein or peptide: Holliday junction branch migration complex subunit RuvA

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Supramolecule #1: RuvA DNA binding protein complexed with Holliday Junction DNA

SupramoleculeName: RuvA DNA binding protein complexed with Holliday Junction DNA
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)

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Supramolecule #2: Tetrameric RuvA binding protein

SupramoleculeName: Tetrameric RuvA binding protein / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)

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Supramolecule #3: Holliday Junction DNA adapted from PDB 2HOI

SupramoleculeName: Holliday Junction DNA adapted from PDB 2HOI / type: complex / ID: 3 / Chimera: Yes / Parent: 2 / Macromolecule list: #2-#3
Source (natural)Organism: Punavirus P1

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Macromolecule #1: Holliday junction branch migration complex subunit RuvA

MacromoleculeName: Holliday junction branch migration complex subunit RuvA
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 14.933622 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MIRYLRGLVL KKEAGGFVLL AGGVGFFLQA PTPFLQALEE GKEVGVHTHL LLKEEGLSLY GFPDEENLAL FELLLSVSGV GPKVALALL SALPPRLLAR ALLEGDARLL TSASGVGRRL AERIALELKG KVPPHLLAGE K

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Macromolecule #2: DNA (34-MER)

MacromoleculeName: DNA (34-MER) / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.399752 KDa
SequenceString:
(DA)(DT)(DA)(DA)(DC)(DT)(DT)(DC)(DG)(DT) (DA)(DT)(DA)(DG)(DC)(DA)(DT)(DA)(DC)(DA) (DT)(DT)(DA)(DT)(DA)(DC)(DG)(DA)(DA) (DC)(DT)(DT)(DA)(DT)

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Macromolecule #3: DNA (34-MER)

MacromoleculeName: DNA (34-MER) / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.51081 KDa
SequenceString:
(DA)(DT)(DA)(DA)(DG)(DT)(DT)(DC)(DG)(DT) (DA)(DT)(DA)(DA)(DT)(DG)(DT)(DA)(DT)(DG) (DC)(DT)(DA)(DT)(DA)(DC)(DG)(DA)(DA) (DG)(DT)(DT)(DA)(DT)

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130426
FSC plot (resolution estimation)

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