Journal: J Biol Chem / Year: 2012 Title: The hexameric structure of a conjugative VirB4 protein ATPase provides new insights for a functional and phylogenetic relationship with DNA translocases. Authors: Alejandro Peña / Inmaculada Matilla / Jaime Martín-Benito / José M Valpuesta / José L Carrascosa / Fernando de la Cruz / Elena Cabezón / Ignacio Arechaga / Abstract: VirB4 proteins are ATPases essential for pilus biogenesis and protein transport in type IV secretion systems. These proteins contain a motor domain that shares structural similarities with the motor ...VirB4 proteins are ATPases essential for pilus biogenesis and protein transport in type IV secretion systems. These proteins contain a motor domain that shares structural similarities with the motor domains of DNA translocases, such as the VirD4/TrwB conjugative coupling proteins and the chromosome segregation pump FtsK. Here, we report the three-dimensional structure of full-length TrwK, the VirB4 homologue in the conjugative plasmid R388, determined by single-particle electron microscopy. The structure consists of a hexameric double ring with a barrel-shaped structure. The C-terminal half of VirB4 proteins shares a striking structural similarity with the DNA translocase TrwB. Docking the atomic coordinates of the crystal structures of TrwB and FtsK into the EM map revealed a better fit for FtsK. Interestingly, we have found that like TrwB, TrwK is able to bind DNA with a higher affinity for G4 quadruplex structures than for single-stranded DNA. Furthermore, TrwK exerts a dominant negative effect on the ATPase activity of TrwB, which reflects an interaction between the two proteins. Our studies provide new insights into the structure-function relationship and the evolution of these DNA and protein translocases.
History
Deposition
Sep 28, 2012
-
Header (metadata) release
Oct 10, 2012
-
Map release
Oct 24, 2012
-
Update
Nov 28, 2012
-
Current status
Nov 28, 2012
Processing site: RCSB / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Macromolecule #1: VirB4 component of type IV transporter system
Macromolecule
Name: VirB4 component of type IV transporter system / type: protein_or_peptide / ID: 1 / Name.synonym: VirB4 / Oligomeric state: Hexamer / Recombinant expression: Yes
Source (natural)
Organism: Escherichia coli (E. coli)
Molecular weight
Theoretical: 540 KDa
Recombinant expression
Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET
Sequence
GO: ATP binding InterPro: CagE, TrbE, VirB component of type IV transporter system
-
Experimental details
-
Structure determination
Method
negative staining
Processing
single particle reconstruction
Aggregation state
particle
-
Sample preparation
Concentration
0.1 mg/mL
Buffer
pH: 6.45 Details: 50 mM PIPES-NaOH, 75 mM potassium acetate, 5% (w/v) glycerol, 10 mM magnesium acetate, 0.1 mM EDTA, and 0.5 mM phenylmethylsulfonyl fluoride.
Staining
Type: NEGATIVE Details: Samples were negatively stained with 2% (w/v) uranyl acetate
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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