[English] 日本語
Yorodumi
- EMDB-2232: Full-length structure of the bacterial pKM101 type IV secretion s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2232
TitleFull-length structure of the bacterial pKM101 type IV secretion system core complexSecretion
Map dataReconstruction of the pKM101 type IV secretion system core complexSecretion
Sample
  • Sample: traN/traO/traF complex encoded by pKM101
  • Protein or peptide: traFTNF receptor associated factor
  • Protein or peptide: traO
  • Protein or peptide: traN
Keywordsbacterial secretion / type IV secretion / vir / tra
Function / homologyConjugal transfer, TrbG/VirB9/CagX / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily / Conjugal transfer protein / Type IV secretion system, VirB10 / TraB / TrbI / TraO protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.4 Å
AuthorsRivera-Calzada A / Fronzes R / Savva CG / Chandran V / Lian PW / Laeremans T / Pardon E / Steyaert J / Remaut H / Waksman G / Orlova EV
CitationJournal: Science / Year: 2009
Title: Structure of a type IV secretion system core complex.
Authors: Rémi Fronzes / Eva Schäfer / Luchun Wang / Helen R Saibil / Elena V Orlova / Gabriel Waksman /
Abstract: Type IV secretion systems (T4SSs) are important virulence factors used by Gram-negative bacterial pathogens to inject effectors into host cells or to spread plasmids harboring antibiotic resistance ...Type IV secretion systems (T4SSs) are important virulence factors used by Gram-negative bacterial pathogens to inject effectors into host cells or to spread plasmids harboring antibiotic resistance genes. We report the 15 angstrom resolution cryo-electron microscopy structure of the core complex of a T4SS. The core complex is composed of three proteins, each present in 14 copies and forming a approximately 1.1-megadalton two-chambered, double membrane-spanning channel. The structure is double-walled, with each component apparently spanning a large part of the channel. The complex is open on the cytoplasmic side and constricted on the extracellular side. Overall, the T4SS core complex structure is different in both architecture and composition from the other known double membrane-spanning secretion system that has been structurally characterized.
History
DepositionNov 1, 2012-
Header (metadata) releaseNov 14, 2012-
Map releaseApr 3, 2013-
UpdateApr 24, 2013-
Current statusApr 24, 2013Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2ypw
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2ypw
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2ypw
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2232_500...

Downloads & links

-
Map

FileDownload / File: emd_2232.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the pKM101 type IV secretion system core complex
Voxel sizeX=Y=Z: 2.22 Å
Density
Contour LevelBy AUTHOR: 0.45 / Movie #1: 0.45
Minimum - Maximum-3.12384415 - 13.97881508
Average (Standard dev.)0.03436751 (±0.32886896)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-79-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 355.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.222.222.22
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z355.200355.200355.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS-80-79-80
NC/NR/NS160160160
D min/max/mean-3.12413.9790.034

-
Supplemental data

-
Sample components

-
Entire : traN/traO/traF complex encoded by pKM101

EntireName: traN/traO/traF complex encoded by pKM101
Components
  • Sample: traN/traO/traF complex encoded by pKM101
  • Protein or peptide: traFTNF receptor associated factor
  • Protein or peptide: traO
  • Protein or peptide: traN

-
Supramolecule #1000: traN/traO/traF complex encoded by pKM101

SupramoleculeName: traN/traO/traF complex encoded by pKM101 / type: sample / ID: 1000 / Details: monodisperse / Oligomeric state: 14 / Number unique components: 3
Molecular weightExperimental: 1.1 MDa / Theoretical: 1.05 MDa / Method: gel filtration

-
Macromolecule #1: traF

MacromoleculeName: traF / type: protein_or_peptide / ID: 1 / Name.synonym: traF-virB10 / Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BL21 / Location in cell: inner and outer membrane
Molecular weightTheoretical: 40 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pASK-IBA3c
SequenceInterPro: Type IV secretion system, VirB10 / TraB / TrbI

-
Macromolecule #2: traO

MacromoleculeName: traO / type: protein_or_peptide / ID: 2 / Name.synonym: traO-virB9 / Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BL21 / Location in cell: outer membrane
Molecular weightTheoretical: 30 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pASK-IBA3c
SequenceInterPro: Conjugal transfer, TrbG/VirB9/CagX

-
Macromolecule #3: traN

MacromoleculeName: traN / type: protein_or_peptide / ID: 3 / Name.synonym: traN-virB7 / Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BL21 / Location in cell: outer membrane
Molecular weightTheoretical: 5 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pASK-IBA3c

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 8 / Details: 50 mM Tris-HCL, 200 mM NaCl, 10 mM LDAO
GridDetails: lacey carbon grids
VitrificationCryogen name: ETHANE / Chamber humidity: 60 % / Chamber temperature: 92 K / Instrument: OTHER / Method: blot 3 seconds before plunging

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 68100 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.1 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 66000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 95 K
Details4000x4000 CCD
DateJan 1, 2008
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN / Digitization - Sampling interval: 15 µm / Number real images: 420 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: phase flipping, each CCD image
Final two d classificationNumber classes: 800
Final reconstructionApplied symmetry - Point group: C14 (14 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: imagic / Details: final map were calculated from 3805 particles / Number images used: 3805
DetailsParticles picked with BOXER (EMAN)

-
Atomic model buiding 1

Initial modelPDB ID:

3jqo

SoftwareName: Chimera, Situs
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation
Output model

PDB-2ypw:
Atomic model for the N-terminus of TraO fitted in the full-length structure of the bacterial pKM101 type IV secretion system core complex

+
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