[English] 日本語
Yorodumi
- EMDB-5352: Structure of a type III secretion needle -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5352
TitleStructure of a type III secretion needleType three secretion system
Map dataThis is an reconstruction of the type III secretion needleType three secretion system
Sample
  • Sample: Shigella needle
  • Protein or peptide: MxiH
Keywordstype III secretion system / needle / helical filament
Function / homology
Function and homology information


type III protein secretion system complex / protein secretion by the type III secretion system / : / cell surface / extracellular region / identical protein binding
Similarity search - Function
Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein
Similarity search - Domain/homology
Type 3 secretion system needle filament protein / MxiH
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsFujii T / Cheung M / Blanco A / Kato T / Blocker AJ / Namba K
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Structure of a type III secretion needle at 7-Å resolution provides insights into its assembly and signaling mechanisms.
Authors: Takashi Fujii / Martin Cheung / Amandine Blanco / Takayuki Kato / Ariel J Blocker / Keiichi Namba /
Abstract: Type III secretion systems of Gram-negative bacteria form injection devices that deliver effector proteins into eukaryotic cells during infection. They span both bacterial membranes and the ...Type III secretion systems of Gram-negative bacteria form injection devices that deliver effector proteins into eukaryotic cells during infection. They span both bacterial membranes and the extracellular space to connect with the host cell plasma membrane. Their extracellular portion is a needle-like, hollow tube that serves as a secretion conduit for effector proteins. The needle of Shigella flexneri is approximately 50-nm long and 7-nm thick and is made by the helical assembly of one protein, MxiH. We provide a 7-Å resolution 3D image reconstruction of the Shigella needle by electron cryomicroscopy, which resolves α-helices and a β-hairpin that has never been observed in the crystal and solution structures of needle proteins, including MxiH. An atomic model of the needle based on the 3D-density map, in comparison with that of the bacterial-flagellar filament, provides insights into how such a thin tubular structure is stably assembled by intricate intermolecular interactions. The map also illuminates how the needle-length control protein functions as a ruler within the central channel during export of MxiH for assembly at the distal end of the needle, and how the secretion-activation signal may be transduced through a conformational change of the needle upon host-cell contact.
History
DepositionNov 2, 2011-
Header (metadata) releaseNov 28, 2011-
Map releaseFeb 20, 2012-
UpdateMar 6, 2012-
Current statusMar 6, 2012Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.76
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 6.76
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j0r
  • Surface level: 6.76
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j0r
  • Surface level: 6.76
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2mme
  • Surface level: 6.76
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2mme
  • Surface level: 6.76
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5352_1.jpg

Downloads & links

-
Map

FileDownload / File: emd_5352.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an reconstruction of the type III secretion needle
Voxel sizeX=Y=Z: 1.68 Å
Density
Contour LevelBy AUTHOR: 6.76 / Movie #1: 6.76
Minimum - Maximum-11.36894798 - 22.53497505
Average (Standard dev.)0.10644222 (±2.6820209)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 168.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.681.681.68
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z168.000168.000168.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-11.36922.5350.106

-
Supplemental data

-
Sample components

-
Entire : Shigella needle

EntireName: Shigella needle
Components
  • Sample: Shigella needle
  • Protein or peptide: MxiH

-
Supramolecule #1000: Shigella needle

SupramoleculeName: Shigella needle / type: sample / ID: 1000 / Oligomeric state: helical assembly of MxiH / Number unique components: 1

-
Macromolecule #1: MxiH

MacromoleculeName: MxiH / type: protein_or_peptide / ID: 1 / Name.synonym: MxiH / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: Shigella flexneri (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4 / Details: 20 mM Tris, pH 7.4, 150 mM NaCl, 2mM MgSO4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 3.5 seconds before plunging

-
Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 89285 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.6 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Specialist opticsEnergy filter - Name: JEOL Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 10.0 eV
Sample stageSpecimen holder: top entry / Specimen holder model: OTHER
TemperatureMin: 50 K / Max: 60 K / Average: 50 K
DateJul 2, 2008
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 330 / Average electron dose: 20 e/Å2 / Bits/pixel: 16

-
Image processing

CTF correctionDetails: CTFFIND3 Each particle
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.30 Å
Applied symmetry - Helical parameters - Δ&Phi: 64.06 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER

+
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