[English] 日本語
Yorodumi
- EMDB-5505: Hexameric structure of the conjugative VirB4 ATPase TrwK: new ins... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5505
TitleHexameric structure of the conjugative VirB4 ATPase TrwK: new insights into a functional and phylogenetic relationship with DNA translocases
Map dataReconstruction of hexameric TrwK
Sample
  • Sample: Hexameric TrwK
  • Protein or peptide: VirB4 component of type IV transporter system
Keywordsbacterial secretion systems / conjugation
Function / homologyCagE, TrbE, VirB component of type IV transporter system / ATP binding
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsPena A / Matilla I / Martin-Benito J / Valpuesta JM / Carrascosa JL / De la Cruz F / Cabezon E / Arechaga I
CitationJournal: 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
DepositionSep 28, 2012-
Header (metadata) releaseOct 10, 2012-
Map releaseOct 24, 2012-
UpdateNov 28, 2012-
Current statusNov 28, 2012Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5505.tif

Downloads & links

-
Map

FileDownload / File: emd_5505.map.gz / Format: CCP4 / Size: 602.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of hexameric TrwK
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.66 Å/pix.
x 54 pix.
= 251.64 Å		4.66 Å/pix.
x 54 pix.
= 251.64 Å		4.66 Å/pix.
x 54 pix.
= 251.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.07715909 - 0.11468405
Average (Standard dev.)0.00622329 (±0.02549224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions545454
Spacing545454
CellA=B=C: 251.63998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.664.664.66
M x/y/z545454
origin x/y/z0.0000.0000.000
length x/y/z251.640251.640251.640
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS545454
D min/max/mean-0.0770.1150.006

-
Supplemental data

-
Sample components

-
Entire : Hexameric TrwK

EntireName: Hexameric TrwK
Components
  • Sample: Hexameric TrwK
  • Protein or peptide: VirB4 component of type IV transporter system

-
Supramolecule #1000: Hexameric TrwK

SupramoleculeName: Hexameric TrwK / type: sample / ID: 1000 / Oligomeric state: hexameric / Number unique components: 1
Molecular weightTheoretical: 540 KDa

-
Macromolecule #1: VirB4 component of type IV transporter system

MacromoleculeName: 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 weightTheoretical: 540 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET
SequenceGO: ATP binding
InterPro: CagE, TrbE, VirB component of type IV transporter system

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 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.
StainingType: NEGATIVE
Details: Samples were negatively stained with 2% (w/v) uranyl acetate
GridDetails: freshly glow-discharged carbon-coated grids
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeJEOL 1200EXII
DateDec 11, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 5.6 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL

-
Image processing

CTF correctionDetails: Yes
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: XMIPP / Number images used: 1179

+
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