7X7Q

CryoEM structure of RuvA-RuvB-Holliday junction complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of the RuvAB-Holliday junction intermediate complex from Pseudomonas aeruginosa.

Zhang, X.Zhou, Z.Dai, L.Chao, Y.Liu, Z.Huang, M.Qu, Q.Lin, Z.

(2023) Front Plant Sci 14: 1139106-1139106

  • DOI: https://doi.org/10.3389/fpls.2023.1139106
  • Primary Citation of Related Structures:  
    7X5A, 7X5B, 7X7P, 7X7Q

  • PubMed Abstract: 

    Holliday junction (HJ) is a four-way structured DNA intermediate in homologous recombination. In bacteria, the HJ-specific binding protein RuvA and the motor protein RuvB together form the RuvAB complex to catalyze HJ branch migration. Pseudomonas aeruginosa ( P. aeruginosa , Pa) is a ubiquitous opportunistic bacterial pathogen that can cause serious infection in a variety of host species, including vertebrate animals, insects and plants. Here, we describe the cryo-Electron Microscopy (cryo-EM) structure of the RuvAB-HJ intermediate complex from P. aeruginosa . The structure shows that two RuvA tetramers sandwich HJ at the junction center and disrupt base pairs at the branch points of RuvB-free HJ arms. Eight RuvB subunits are recruited by the RuvA octameric core and form two open-rings to encircle two opposite HJ arms. Each RuvB subunit individually binds a RuvA domain III. The four RuvB subunits within the ring display distinct subdomain conformations, and two of them engage the central DNA duplex at both strands with their C-terminal β-hairpins. Together with the biochemical analyses, our structure implicates a potential mechanism of RuvB motor assembly onto HJ DNA.


  • Organizational Affiliation

    College of Chemistry, Fuzhou University, Fuzhou, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Holliday junction ATP-dependent DNA helicase RuvA
A, B, C, D, E
A, B, C, D, E, F, G, H
201Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: ruvAPA0966
EC: 3.6.4.12
UniProt
Find proteins for Q51425 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q51425 
Go to UniProtKB:  Q51425
Entity Groups  
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UniProt GroupQ51425
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Holliday junction ATP-dependent DNA helicase RuvBI [auth M],
J [auth N],
K [auth O],
L [auth P]
352Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: ruvBPA0967
EC: 3.6.4.12
UniProt
Find proteins for Q51426 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q51426 
Go to UniProtKB:  Q51426
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UniProt GroupQ51426
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (40-MER)M [auth I]40synthetic construct
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (40-MER)N [auth K]40synthetic construct
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (26-MER)O [auth J]26synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (26-MER)P [auth L]26synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31971222
National Natural Science Foundation of China (NSFC)China32171194

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references