[English] 日本語
Yorodumi
- PDB-6rwx: Periplasmic inner membrane ring of the Shigella type 3 secretion ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rwx
TitlePeriplasmic inner membrane ring of the Shigella type 3 secretion system
Components
  • Lipoprotein MxiJ
  • Protein MxiG
KeywordsPROTEIN TRANSPORT / type 3 secretion system / shigella / ring-forming membrane protein
Function / homology
Function and homology information


protein secretion / cell outer membrane / plasma membrane
Similarity search - Function
Type III secretion system lipoprotein HrcJ/YscJ / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Protein MxiG / Lipoprotein MxiJ
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsKamprad, A. / Lunelli, M.
Funding support2items
OrganizationGrant numberCountry
European Research Council311371
European Union653706
CitationJournal: PLoS Pathog / Year: 2020
Title: Cryo-EM structure of the Shigella type III needle complex.
Authors: Michele Lunelli / Antje Kamprad / Jörg Bürger / Thorsten Mielke / Christian M T Spahn / Michael Kolbe /
Abstract: The Type III Secretion Systems (T3SS) needle complex is a conserved syringe-shaped protein translocation nanomachine with a mass of about 3.5 MDa essential for the survival and virulence of many Gram- ...The Type III Secretion Systems (T3SS) needle complex is a conserved syringe-shaped protein translocation nanomachine with a mass of about 3.5 MDa essential for the survival and virulence of many Gram-negative bacterial pathogens. This system is composed of a membrane-embedded basal body and an extracellular needle that deliver effector proteins into host cells. High-resolution structures of the T3SS from different organisms and infection stages are needed to understand the underlying molecular mechanisms of effector translocation. Here, we present the cryo-electron microscopy structure of the isolated Shigella T3SS needle complex. The inner membrane (IM) region of the basal body adopts 24-fold rotational symmetry and forms a channel system that connects the bacterial periplasm with the export apparatus cage. The secretin oligomer adopts a heterogeneous architecture with 16- and 15-fold cyclic symmetry in the periplasmic N-terminal connector and C-terminal outer membrane ring, respectively. Two out of three IM subunits bind the secretin connector via a β-sheet augmentation. The cryo-EM map also reveals the helical architecture of the export apparatus core, the inner rod, the needle and their intervening interfaces.
History
DepositionJun 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-10045
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
S: Protein MxiG
T: Protein MxiG
R: Protein MxiG
Q: Protein MxiG
P: Protein MxiG
O: Protein MxiG
N: Protein MxiG
M: Protein MxiG
L: Protein MxiG
K: Protein MxiG
J: Protein MxiG
I: Protein MxiG
H: Protein MxiG
G: Protein MxiG
F: Protein MxiG
E: Protein MxiG
D: Protein MxiG
C: Protein MxiG
B: Protein MxiG
A: Protein MxiG
W: Protein MxiG
V: Protein MxiG
U: Protein MxiG
X: Protein MxiG
a: Lipoprotein MxiJ
b: Lipoprotein MxiJ
c: Lipoprotein MxiJ
d: Lipoprotein MxiJ
e: Lipoprotein MxiJ
f: Lipoprotein MxiJ
g: Lipoprotein MxiJ
h: Lipoprotein MxiJ
i: Lipoprotein MxiJ
j: Lipoprotein MxiJ
k: Lipoprotein MxiJ
l: Lipoprotein MxiJ
m: Lipoprotein MxiJ
n: Lipoprotein MxiJ
o: Lipoprotein MxiJ
p: Lipoprotein MxiJ
q: Lipoprotein MxiJ
r: Lipoprotein MxiJ
s: Lipoprotein MxiJ
t: Lipoprotein MxiJ
u: Lipoprotein MxiJ
v: Lipoprotein MxiJ
w: Lipoprotein MxiJ
x: Lipoprotein MxiJ


Theoretical massNumber of molelcules
Total (without water)1,694,30248
Polymers1,694,30248
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ...
Protein MxiG


Mass: 43053.844 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Shigella flexneri (bacteria) / Plasmid details: encoded on pWR100 plasmid / Variant: M90T / References: UniProt: P0A221
#2: Protein ...
Lipoprotein MxiJ


Mass: 27542.055 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Shigella flexneri (bacteria) / Variant: M90T / References: UniProt: Q06081

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: The periplasmic inner membrane ring of the Shigella type 3 secretion system
Type: COMPLEX
Details: Focused reconstruction from isolated needle complexes of the Shigella type 3 secretion system
Entity ID: all / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Shigella flexneri (bacteria) / Strain: M90T / Cellular location: Membrane
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Isolated needle complex in detergent solution
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K
Details: Sample applied on grid 5 ul, incubation time 5 min on ice, then moved into Vitrobot and 5 ul sample applied again. Blot time: 2 sec Blot force: -2 Drain time: 0 sec

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 101179 X / Nominal defocus max: 4 nm / Nominal defocus min: 1.5 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5238
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 7

-
Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1RELION1.4particle selection
4CTFFIND3.5CTF correction
7UCSF Chimera1.11.2model fitting
8Coot0.8.8model fitting
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
14PHENIX1.13-2998model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 171833
SymmetryPoint symmetry: C24 (24 fold cyclic)
3D reconstructionResolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72298 / Symmetry type: POINT
Atomic model buildingB value: 140 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient and geometry
Details: Model was built and refined in the map low-pass filtered at 3.2 A
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-IDPdb chain residue range
13GR0

3gr0

D1183-362
22Y9J

2y9j

t121-190
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00972048
ELECTRON MICROSCOPYf_angle_d0.88197272
ELECTRON MICROSCOPYf_dihedral_angle_d14.42944592
ELECTRON MICROSCOPYf_chiral_restr0.05811208
ELECTRON MICROSCOPYf_plane_restr0.00612456

+
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://pdbjlc1.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