[English] 日本語
Yorodumi
- EMDB-1160: Double hexameric ring assembly of the type III protein translocas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1160
TitleDouble hexameric ring assembly of the type III protein translocase ATPase HrcN.
Map dataThis volume contains the 3D reconstruction of dodecameric HrcN. It is D6-symmetrized. A threshold of 0.61 is recommended for surface rendering.
Sample
  • Sample: HrcN
  • Protein or peptide: HrcN
Biological speciesPseudomonas syringae pv. phaseolicola (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 Å
AuthorsMuller SA / Poyidis C / Stone R / Meesters C / Chami M / Engel A / Economou A / Stahlberg H
CitationJournal: Mol Microbiol / Year: 2006
Title: Double hexameric ring assembly of the type III protein translocase ATPase HrcN.
Authors: Shirley A Müller / Charalambos Pozidis / Remington Stone / Christian Meesters / Mohamed Chami / Andreas Engel / Anastassios Economou / Henning Stahlberg /
Abstract: The specialized type III secretion (T3S) apparatus of pathogenic and symbiotic Gram-negative bacteria comprises a complex transmembrane organelle and an ATPase homologous to the F1-ATPase beta ...The specialized type III secretion (T3S) apparatus of pathogenic and symbiotic Gram-negative bacteria comprises a complex transmembrane organelle and an ATPase homologous to the F1-ATPase beta subunit. The T3S ATPase HrcN of Pseudomonas syringae associates with the inner membrane, and its ATP hydrolytic activity is stimulated by dodecamerization. The structure of dodecameric HrcN (HrcN12) determined to 1.6 nm by cryo-electron microscopy is presented. HrcN12 comprises two hexameric rings that are probably stacked face-to-face by the association of their C-terminal domains. It is 11.5 +/- 1.0 nm in diameter, 12.0 +/- 2.0 nm high and has a 2.0-3.8 nm wide inner channel. This structure is compared to a homology model based on the structure of the F1-beta-ATPase. A model for its incorporation within the T3S apparatus is presented.
History
DepositionSep 22, 2005-
Header (metadata) releaseSep 22, 2005-
Map releaseAug 7, 2006-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.61
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.61
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1160.gif

Downloads & links

-
Map

FileDownload / File: emd_1160.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis volume contains the 3D reconstruction of dodecameric HrcN. It is D6-symmetrized. A threshold of 0.61 is recommended for surface rendering.
Voxel sizeX=Y=Z: 4 Å
Density
Contour Level1: 0.802 / Movie #1: 0.61
Minimum - Maximum0.0 - 1.0
Average (Standard dev.)0.226394 (±0.22867)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 400 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z444
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z400.000400.000400.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean0.0001.0000.226

-
Supplemental data

-
Sample components

-
Entire : HrcN

EntireName: HrcN
Components
  • Sample: HrcN
  • Protein or peptide: HrcN

-
Supramolecule #1000: HrcN

SupramoleculeName: HrcN / type: sample / ID: 1000
Details: The sample had a tendency to aggregate rapidly. Images were usually highly crowded, or empty, from the same cryo-EM grid.
Oligomeric state: homododecamer / Number unique components: 1
Molecular weightExperimental: 601 KDa / Theoretical: 612 KDa / Method: STEM mass measurement

-
Macromolecule #1: HrcN

MacromoleculeName: HrcN / type: protein_or_peptide / ID: 1 / Name.synonym: HrcN / Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: Yes
Source (natural)Organism: Pseudomonas syringae pv. phaseolicola (bacteria) / synonym: Pseudomonas syringae pathovar phaseolicola
Molecular weightExperimental: 612 KDa / Theoretical: 601 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.0 mg/mL
BufferpH: 7.4 / Details: 50mM Tris-Cl, pH 7.4, 0.2M NaCl, 20% glycerol
GridDetails: Quantifoil 300 mesh
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Home-built

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Image recordingDigitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 5.0 µm / Number real images: 165 / Od range: 1 / Bits/pixel: 16
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

CTF correctionDetails: SPIDER
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 8742
Final two d classificationNumber classes: 352

+
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://pdbjlvh1.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