[English] 日本語
Yorodumi
- EMDB-28107: Structure of double homo-hexameric AAA+ ATPase RuvB motors -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28107
TitleStructure of double homo-hexameric AAA+ ATPase RuvB motors
Map data
Sample
  • Complex: Double homo-hexameric AAA+ ATPase RuvB motors
    • Protein or peptide: Holliday junction ATP-dependent DNA helicase RuvB
    • DNA: ssDNA
    • DNA: ssDNA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsHolliday Junction / AAA+ ATPase / RuvB / Homo-hexamer / DNA recombination / STRUCTURAL PROTEIN
Function / homology
Function and homology information


Holliday junction resolvase complex / four-way junction helicase activity / four-way junction DNA binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA recombination / DNA repair / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
DNA helicase, Holliday junction RuvB-type / RuvB C-terminal winged helix domain / RuvB-like P-loop domain / RuvB, AAA lid domain / RuvB C-terminal winged helix domain / Holliday junction DNA helicase RuvB P-loop domain / RuvB AAA lid domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities ...DNA helicase, Holliday junction RuvB-type / RuvB C-terminal winged helix domain / RuvB-like P-loop domain / RuvB, AAA lid domain / RuvB C-terminal winged helix domain / Holliday junction DNA helicase RuvB P-loop domain / RuvB AAA lid domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Holliday junction branch migration complex subunit RuvB
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsShen ZF / Rish AD / Fu TM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Molecular mechanisms of Holliday junction branch migration catalyzed by an asymmetric RuvB hexamer.
Authors: Anthony D Rish / Zhangfei Shen / Zhenhang Chen / Nan Zhang / Qingfei Zheng / Tian-Min Fu /
Abstract: The Holliday junction (HJ) is a DNA intermediate of homologous recombination, involved in many fundamental physiological processes. RuvB, an ATPase motor protein, drives branch migration of the ...The Holliday junction (HJ) is a DNA intermediate of homologous recombination, involved in many fundamental physiological processes. RuvB, an ATPase motor protein, drives branch migration of the Holliday junction with a mechanism that had yet to be elucidated. Here we report two cryo-EM structures of RuvB, providing a comprehensive understanding of HJ branch migration. RuvB assembles into a spiral staircase, ring-like hexamer, encircling dsDNA. Four protomers of RuvB contact the DNA backbone with a translocation step size of 2 nucleotides. The variation of nucleotide-binding states in RuvB supports a sequential model for ATP hydrolysis and nucleotide recycling, which occur at separate, singular positions. RuvB's asymmetric assembly also explains the 6:4 stoichiometry between the RuvB/RuvA complex, which coordinates HJ migration in bacteria. Taken together, we provide a mechanistic understanding of HJ branch migration facilitated by RuvB, which may be universally shared by prokaryotic and eukaryotic organisms.
History
DepositionSep 10, 2022-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28107.png

Downloads & links

-
Map

FileDownload / File: emd_28107.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 216 pix.
= 233.28 Å		1.08 Å/pix.
x 216 pix.
= 233.28 Å		1.08 Å/pix.
x 216 pix.
= 233.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.377
Minimum - Maximum-1.5659965 - 2.6353319
Average (Standard dev.)0.00875246 (±0.09180928)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 233.28001 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_28107_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_28107_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_28107_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Double homo-hexameric AAA+ ATPase RuvB motors

EntireName: Double homo-hexameric AAA+ ATPase RuvB motors
Components
  • Complex: Double homo-hexameric AAA+ ATPase RuvB motors
    • Protein or peptide: Holliday junction ATP-dependent DNA helicase RuvB
    • DNA: ssDNA
    • DNA: ssDNA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

-
Supramolecule #1: Double homo-hexameric AAA+ ATPase RuvB motors

SupramoleculeName: Double homo-hexameric AAA+ ATPase RuvB motors / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)

-
Macromolecule #1: Holliday junction ATP-dependent DNA helicase RuvB

MacromoleculeName: Holliday junction ATP-dependent DNA helicase RuvB / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: ATCC 27634 / DSM 579 / HB8
Molecular weightTheoretical: 36.024688 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEDLALRPKT LDEYIGQERL KQKLRVYLEA AKARKEPLEH LLLFGPPGLG KTTLAHVIAH ELGVNLRVTS GPAIEKPGDL AAILANSLE EGDILFIDEI HRLSRQAEEH LYPAMEDFVM DIVIGQGPAA RTIRLELPRF TLIGATTRPG LITAPLLSRF G IVEHLEYY ...String:
MEDLALRPKT LDEYIGQERL KQKLRVYLEA AKARKEPLEH LLLFGPPGLG KTTLAHVIAH ELGVNLRVTS GPAIEKPGDL AAILANSLE EGDILFIDEI HRLSRQAEEH LYPAMEDFVM DIVIGQGPAA RTIRLELPRF TLIGATTRPG LITAPLLSRF G IVEHLEYY TPEELAQGVM RDARLLGVRI TEEAALEIGR RSRGTMRVAK RLFRRVRDFA QVAGEEVITR ERALEALAAL GL DELGLEK RDREILEVLI LRFGGGPVGL ATLATALSED PGTLEEVHEP YLIRQGLLKR TPRGRVATEL AYRHLGYPPP VGP LLEP

UniProtKB: Holliday junction branch migration complex subunit RuvB

-
Macromolecule #2: ssDNA

MacromoleculeName: ssDNA / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 15.146732 KDa
SequenceString:
(DA)(DG)(DA)(DA)(DT)(DC)(DT)(DG)(DC)(DC) (DG)(DA)(DG)(DA)(DG)(DA)(DC)(DC)(DG)(DA) (DG)(DC)(DA)(DG)(DA)(DA)(DT)(DT)(DC) (DT)(DA)(DT)(DG)(DT)(DG)(DT)(DT)(DT)(DA) (DC) (DC)(DA)(DA)(DG)(DC)(DG)(DC)(DT) (DG)

-
Macromolecule #3: ssDNA

MacromoleculeName: ssDNA / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 15.69107 KDa
SequenceString:
(DC)(DA)(DG)(DC)(DG)(DC)(DT)(DT)(DG)(DG) (DT)(DA)(DA)(DA)(DC)(DA)(DC)(DA)(DT)(DA) (DG)(DA)(DA)(DT)(DT)(DC)(DT)(DG)(DC) (DT)(DC)(DT)(DC)(DG)(DG)(DT)(DC)(DT)(DG) (DA) (DG)(DC)(DC)(DG)(DT)(DC)(DT)(DA) (DA)(DG)(DA)

-
Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #6: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 6 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1hqc

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 326270
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

+
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