[English] 日本語
Yorodumi
- EMDB-8812: Structure of the PulG pseudopilus -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8812
TitleStructure of the PulG pseudopilus
Map datamap of PulG filament
SamplePulG pseudopilus:
General secretion pathway protein G / ligand
Function / homologyBacterial general secretion pathway protein G-type pilin / General secretion pathway protein G / Prokaryotic N-terminal methylation site / Type II secretion system protein G / Prokaryotic N-terminal methylation motif / Type II secretion system (T2SS), protein G / Prokaryotic N-terminal methylation site. / type II protein secretion system complex / protein secretion by the type II secretion system / protein transporter activity ...Bacterial general secretion pathway protein G-type pilin / General secretion pathway protein G / Prokaryotic N-terminal methylation site / Type II secretion system protein G / Prokaryotic N-terminal methylation motif / Type II secretion system (T2SS), protein G / Prokaryotic N-terminal methylation site. / type II protein secretion system complex / protein secretion by the type II secretion system / protein transporter activity / integral component of membrane / General secretion pathway protein GspG
Function and homology information
SourceKlebsiella oxytoca (bacteria)
Methodhelical reconstruction / cryo EM / 5 Å resolution
AuthorsLopez-Castilla A / Thomassin JL
CitationJournal: Nat Microbiol / Year: 2017
Title: Structure of the calcium-dependent type 2 secretion pseudopilus.
Authors: Aracelys López-Castilla / Jenny-Lee Thomassin / Benjamin Bardiaux / Weili Zheng / Mangayarkarasi Nivaskumar / Xiong Yu / Michael Nilges / Edward H Egelman / Nadia Izadi-Pruneyre / Olivera Francetic
Validation ReportPDB-ID: 5wda

SummaryFull reportAbout validation report
DateDeposition: Jul 4, 2017 / Header (metadata) release: Aug 9, 2017 / Map release: Oct 25, 2017 / Last update: Dec 13, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.056
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.056
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5wda
  • Surface level: 0.056
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5wda
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_8812.map.gz (map file in CCP4 format, 8468 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.05 Å/pix.
= 315. Å
84 pix
1.05 Å/pix.
= 88.2 Å
84 pix
1.05 Å/pix.
= 88.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour Level:0.056 (by author), 0.056 (movie #1):
Minimum - Maximum-0.044437073 - 0.11336735
Average (Standard dev.)0.012011195 (0.02283012)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions8484300
Origin-42-42-150
Limit4141149
Spacing8484300
CellA: 88.2 Å / B: 88.2 Å / C: 315 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z8484300
origin x/y/z0.0000.0000.000
length x/y/z88.20088.200315.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-42-42-150
NC/NR/NS8484300
D min/max/mean-0.0440.1130.012

-
Supplemental data

-
Sample components

-
Entire PulG pseudopilus

EntireName: PulG pseudopilus / Number of components: 3

-
Component #1: cellular-component, PulG pseudopilus

Cellular-componentName: PulG pseudopilus / Recombinant expression: No
SourceSpecies: Klebsiella oxytoca (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

-
Component #2: protein, General secretion pathway protein G

ProteinName: General secretion pathway protein G / Recombinant expression: No
MassTheoretical: 14.525482 kDa
Source (engineered)Expression System: Klebsiella oxytoca (bacteria)

-
Component #3: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 25 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 10.2 Å / Delta phi: 83.2 deg.
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 1819

-
Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: BACK PROJECTION / Software: IHRSR / Resolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

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