[English] 日本語
Yorodumi
- EMDB-0193: Klebsiella pneumoniae type II secretion system outer membrane com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0193
TitleKlebsiella pneumoniae type II secretion system outer membrane complex. PulD, PulS and PulC HR domain.Type II secretion system
Map dataType II secretion system
SampleKlebsiella pneumoniae type II secretion system outer membrane complex. PulD, PulS and PulC HR domain.Type II secretion system
  • Type II secretion system protein DType II secretion system
  • Pullulanase
  • Pectic enzymes secretion protein OutC
Function / homology
Function and homology information


type II protein secretion system complex / protein secretion by the type II secretion system / cell outer membrane
Type II secretion system protein C / GspD/PilQ family / Type II secretion system GspD, conserved site / Type II/III secretion system / NolW-like / Type II secretion system GspD / Type II secretion system protein C, N-terminal / PDZ superfamily / NolW-like superfamily
General secretion pathway protein C / Type II secretion system protein D
Biological speciesKlebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsChernyatina AA / Low HH
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust200074/Z/15/Z United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Core architecture of a bacterial type II secretion system.
Authors: Anastasia A Chernyatina / Harry H Low /
Abstract: Bacterial type II secretion systems (T2SSs) translocate virulence factors, toxins and enzymes across the cell outer membrane. Here we use negative stain and cryo-electron microscopy to reveal the ...Bacterial type II secretion systems (T2SSs) translocate virulence factors, toxins and enzymes across the cell outer membrane. Here we use negative stain and cryo-electron microscopy to reveal the core architecture of an assembled T2SS from the pathogen Klebsiella pneumoniae. We show that 7 proteins form a ~2.4 MDa complex that spans the cell envelope. The outer membrane complex includes the secretin PulD, with all domains modelled, and the pilotin PulS. The inner membrane assembly platform components PulC, PulE, PulL, PulM and PulN have a relative stoichiometric ratio of 2:1:1:1:1. The PulE ATPase, PulL and PulM combine to form a flexible hexameric hub. Symmetry mismatch between the outer membrane complex and assembly platform is overcome by PulC linkers spanning the periplasm, with PulC HR domains binding independently at the secretin base. Our results show that the T2SS has a highly dynamic modular architecture, with implication for pseudo-pilus assembly and substrate loading.
Validation ReportPDB-ID: 6hcg

SummaryFull reportAbout validation report
History
DepositionAug 15, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseNov 27, 2019-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6hcg
  • Surface level: 4.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0193.png

Downloads & links

-
Map

FileDownload / File: emd_0193.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.78 Å/pix.
x 230 pix.
= 409.4 Å		1.78 Å/pix.
x 230 pix.
= 409.4 Å		1.78 Å/pix.
x 230 pix.
= 409.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.3 / Movie #1: 4.3
Minimum - Maximum-13.503257 - 23.618986
Average (Standard dev.)0.124008186 (±0.8839676)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230230230
Spacing230230230
CellA=B=C: 409.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.781.781.78
M x/y/z230230230
origin x/y/z0.0000.0000.000
length x/y/z409.400409.400409.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS230230230
D min/max/mean-13.50323.6190.124

-
Supplemental data

-
Sample components

-
Entire Klebsiella pneumoniae type II secretion system outer membrane com...

EntireName: Klebsiella pneumoniae type II secretion system outer membrane complex. PulD, PulS and PulC HR domain.Type II secretion system
Number of components: 4

-
Component #1: protein, Klebsiella pneumoniae type II secretion system outer mem...

ProteinName: Klebsiella pneumoniae type II secretion system outer membrane complex. PulD, PulS and PulC HR domain.Type II secretion system
Recombinant expression: No
MassTheoretical: 1.3 MDa
SourceSpecies: Klebsiella pneumoniae (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

-
Component #2: protein, Type II secretion system protein D

ProteinName: Type II secretion system protein DType II secretion system
Number of Copies: 15 / Recombinant expression: No
MassTheoretical: 70.328633 kDa
SourceSpecies: Klebsiella pneumoniae (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

-
Component #3: protein, Pullulanase

ProteinName: Pullulanase / Number of Copies: 15 / Recombinant expression: No
MassTheoretical: 15.872848 kDa
SourceSpecies: Klebsiella pneumoniae (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

-
Component #4: protein, Pectic enzymes secretion protein OutC

ProteinName: Pectic enzymes secretion protein OutC / Number of Copies: 15 / Recombinant expression: No
MassTheoretical: 30.245924 kDa
SourceSpecies: Klebsiella pneumoniae (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C15 (15 fold cyclic) / Number of projections: 7284
3D reconstructionSoftware: RELION / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

6hcg

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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