[English] 日本語
Yorodumi
- EMDB-2628: Structural similarity of secretins from Type II and Type III Secr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2628
TitleStructural similarity of secretins from Type II and Type III Secretion Systems
Map dataPulD
Sample
  • Sample: PulD
  • Protein or peptide: PulD
Keywordsbacterial secretion system / membrane protein / electron microscopy / Single Particle Analysis / secretin
Biological speciesKlebsiella oxytoca (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsTosi T / Estrozi LF / Job V / Guilvout I / Pugsley AP / Schoehn G / Dessen A
CitationJournal: Structure / Year: 2014
Title: Structural similarity of secretins from type II and type III secretion systems.
Authors: Tommaso Tosi / Leandro F Estrozi / Viviana Job / Ingrid Guilvout / Anthony P Pugsley / Guy Schoehn / Andréa Dessen /
Abstract: Secretins, the outer membrane components of several secretion systems in Gram-negative bacteria, assemble into channels that allow exoproteins to traverse the membrane. The membrane-inserted, ...Secretins, the outer membrane components of several secretion systems in Gram-negative bacteria, assemble into channels that allow exoproteins to traverse the membrane. The membrane-inserted, multimeric regions of PscC, the Pseudomonas aeruginosa type III secretion system secretin, and PulD, the Klebsiella oxytoca type II secretion system secretin, were purified after cell-free synthesis and their structures analyzed by single particle cryoelectron microscopy. Both homomultimeric, barrel-like structures display a "cup and saucer" architecture. The "saucer" region of both secretins is composed of two distinct rings, with that of PulD being less segmented than that of PscC. Both secretins have a central chamber that is occluded by a plug linked to the chamber walls through hairpin-like structures. Comparisons with published structures from other bacterial systems reveal that secretins have regions of local structural flexibility, probably reflecting their evolved functions in protein secretion and needle assembly.
History
DepositionApr 14, 2014-
Header (metadata) releaseApr 30, 2014-
Map releaseSep 3, 2014-
UpdateSep 17, 2014-
Current statusSep 17, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.41
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.41
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_2628.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPulD
Voxel sizeX=Y=Z: 1.3355 Å
Density
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.41
Minimum - Maximum-4.5924201 - 7.20779896
Average (Standard dev.)0.01434061 (±0.7908619)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 256.41602 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.33551.33551.3355
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z256.416256.416256.416
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-4.5927.2080.014

-
Supplemental data

-
Sample components

-
Entire : PulD

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

-
Supramolecule #1000: PulD

SupramoleculeName: PulD / type: sample / ID: 1000 / Oligomeric state: dodecamer / Number unique components: 1
Molecular weightExperimental: 468.6 KDa / Theoretical: 468.6 KDa

-
Macromolecule #1: PulD

MacromoleculeName: PulD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: dodecamer / Recombinant expression: Yes
Source (natural)Organism: Klebsiella oxytoca (bacteria)
Molecular weightExperimental: 468.6 KDa / Theoretical: 468.6 KDa
Recombinant expressionOrganism: Cell-free

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.0 mg/mL
GridDetails: 200 mesh coper quantifoil grid with thin carbon support
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 59000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateJan 1, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 1060 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Phase-flipping
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: OTHER / Software - Name: Imagic, RIco, bsoft, ctffind3, FPM / Number images used: 63500
DetailsThe particles were selected using an automatic selection program.

+
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