[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.
Map dataMasked sharpened map
Sample
  • Complex: Klebsiella pneumoniae type II secretion system outer membrane complex. PulD, PulS and PulC HR domain.
    • Protein or peptide: Type II secretion system protein D
    • Protein or peptide: Pullulanase
    • Protein or peptide: Pectic enzymes secretion protein OutC
KeywordsType II secretion system / secretin / outer membrane channel / PROTEIN TRANSPORT
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / intracellular protein transport / cell outer membrane / identical protein binding / plasma membrane
Similarity search - Function
Type II secretion system protein GspC / Chaperone lipoprotein, PulS/OutS / Chaperone lipoprotein, PulS/OutS-like / PulS/OutS-like superfamily / Type II secretion system pilotin lipoprotein (PulS_OutS) / Bacterial type II secretion system protein C signature. / Type II secretion system protein GspC, N-terminal / Type II secretion system protein C / Type II secretion system protein GspD / : ...Type II secretion system protein GspC / Chaperone lipoprotein, PulS/OutS / Chaperone lipoprotein, PulS/OutS-like / PulS/OutS-like superfamily / Type II secretion system pilotin lipoprotein (PulS_OutS) / Bacterial type II secretion system protein C signature. / Type II secretion system protein GspC, N-terminal / Type II secretion system protein C / Type II secretion system protein GspD / : / GspD-like, N0 domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein / PDZ superfamily
Similarity search - Domain/homology
General secretion pathway protein C / Pullulanase D protein / Pullulanase-specific type II secretion system component C / Pullulanase secretion protein PulS / General secretion pathway protein D
Similarity search - Component
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.
History
DepositionAug 15, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseNov 27, 2019-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing 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)
AnnotationMasked sharpened map
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

-
Half map: half-map 1

Fileemd_0193_half_map_1.map
Annotationhalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_0193_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
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.
Components
  • Complex: Klebsiella pneumoniae type II secretion system outer membrane complex. PulD, PulS and PulC HR domain.
    • Protein or peptide: Type II secretion system protein D
    • Protein or peptide: Pullulanase
    • Protein or peptide: Pectic enzymes secretion protein OutC

-
Supramolecule #1: Klebsiella pneumoniae type II secretion system outer membrane com...

SupramoleculeName: Klebsiella pneumoniae type II secretion system outer membrane complex. PulD, PulS and PulC HR domain.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 1.3 MDa

-
Macromolecule #1: Type II secretion system protein D

MacromoleculeName: Type II secretion system protein D / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 70.328633 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSLRKMLPA LLILTPLLFS PAAAEEFSAS FKGTDIQEFI NTVSKNLNKT VIIDPSVRGT ITVRSYDMLN EEQYYQFFLS VLDVYGFAV INMNNGVLKV VRAKDAKTSA VPVASAAAPG EGDEVVTRVV PLTNVAARDL APLLRQLNDN AGAGSVVHYE P SNVLLMTG ...String:
MKSLRKMLPA LLILTPLLFS PAAAEEFSAS FKGTDIQEFI NTVSKNLNKT VIIDPSVRGT ITVRSYDMLN EEQYYQFFLS VLDVYGFAV INMNNGVLKV VRAKDAKTSA VPVASAAAPG EGDEVVTRVV PLTNVAARDL APLLRQLNDN AGAGSVVHYE P SNVLLMTG RAAVIKRLLT IVERVDNAGD RSVVTVPLSW ASAAEVVKLV TELNKDTSKS ALPGSMVANV VADERTNAVL VS GEPNSRQ RIIAMIKQLD RQQAVQGNTK VIYLKYAKAA DLVEVLTGIS SSLQSDKQSA RPVAAIDKNI IIKAHGQTNA LIV TAAPDV MNDLERVIAQ LDIRRPQVLV EAIIAEVQDA DGLNLGIQWA NKNAGMTQFT NSGLPISTAI AGANQYNKDG TISS SLASA LGSFNGIAAG FYQGNWAMLL TALSSSTKND ILATPSIVTL DNMQATFNVG QEVPVLTGSQ TTSGDNIFNT VERKT VGIK LKVKPQINEG DAVLLEIEQE VSSVADSASS TSSDLGATFN TRTVNNAVLV GSGETVVVGG LLDKTVTDTA DKVPLL GDI PVIGALFRSD SKKVSKRNLM LFIRPTIIRD RDEYRQASSG QYTAFNNAQT KQRGKESSEA SLSNDLLHIY PQQETQA FR QVSAAIDAFN LGGRP

UniProtKB: General secretion pathway protein D

-
Macromolecule #2: Pullulanase

MacromoleculeName: Pullulanase / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 15.872848 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIHYFDYSMM RIPLIFPLCM VALLSGCQQK PASTLSPAIS SQAQLEQLSS VAAGTRYLKN KCNRSDLPAD ETIYRAAVNV GKARGWGNI DVATLSQNSD RLYQQLLQDS TPEATQCSQF NRQLAPFIAS LRSDGSDYKD DDDK

-
Macromolecule #3: Pectic enzymes secretion protein OutC

MacromoleculeName: Pectic enzymes secretion protein OutC / type: protein_or_peptide / ID: 3 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 30.245924 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPVSVMRLTN INKGIIKLLP QIVTLIILIT AIPQLAKLTW RVVFPVSPED ISALPLTMPP AADPELKNVR PAFTLFGLAV KNSPTPTDA ASLNQVPVSS LKLRLAGLLA SSNPARSIAI IEKGNQQVSL STGDPLPGYD ARIAAILPDR IIVNYQGRKE A ILLFNDSR ...String:
MPVSVMRLTN INKGIIKLLP QIVTLIILIT AIPQLAKLTW RVVFPVSPED ISALPLTMPP AADPELKNVR PAFTLFGLAV KNSPTPTDA ASLNQVPVSS LKLRLAGLLA SSNPARSIAI IEKGNQQVSL STGDPLPGYD ARIAAILPDR IIVNYQGRKE A ILLFNDSR APSPPPTAAG NPPLVKRLRE QPQNILTYLS ISPVLSGDKL LGYRLNPGKD ASLFRQSGLQ ANDLAIALNG ID LRDQEQA QQALQNLADM TEITLTVERE GQRHDIAFAL GDE

UniProtKB: General secretion pathway protein C

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 0.3 sec. / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

1763

Final reconstructionApplied symmetry - Point group: C15 (15 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 7284
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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