[English] 日本語
Yorodumi
- PDB-7ahi: Substrate-engaged type 3 secretion system needle complex from Sal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ahi
TitleSubstrate-engaged type 3 secretion system needle complex from Salmonella enterica typhimurium - SpaR state 2
Components
  • (Surface presentation of antigens protein ...) x 3
  • Lipoprotein PrgK
  • Protein PrgH
  • Protein PrgI
  • Protein PrgJ
  • SptP3x-GFP-FLAG
  • Type 3 secretion system secretin
KeywordsPROTEIN TRANSPORT / T3SS / Export Apparatus / Injectisome / Needle Complex / Substrate
Function / homology
Function and homology information


The IPAF inflammasome / type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / protein secretion / protein targeting / cell outer membrane / protein transport / cell surface / extracellular region ...The IPAF inflammasome / type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / protein secretion / protein targeting / cell outer membrane / protein transport / cell surface / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
: / Type III secretion protein SpaR/YscT / Type III secretion protein HrpO / Yop virulence translocation protein R / Type III secretion system, PrgH/EprH / Type III secretion system lipoprotein HrcJ/YscJ / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / : / SPI-1 type 3 secretion system secretin, N0 domain ...: / Type III secretion protein SpaR/YscT / Type III secretion protein HrpO / Yop virulence translocation protein R / Type III secretion system, PrgH/EprH / Type III secretion system lipoprotein HrcJ/YscJ / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / : / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / 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 / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Bacterial export proteins, family 1 / Bacterial export proteins, family 3 / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / FliP family / Flagella transport protein fliP family signature 2. / 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 / 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
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Surface presentation of antigens protein SpaQ / SPI-1 type 3 secretion system secretin / Surface presentation of antigens protein SpaP / Surface presentation of antigens protein SpaR / Protein PrgH / SPI-1 type 3 secretion system needle filament protein / Protein PrgJ / Lipoprotein PrgK
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsFahrenkamp, D. / Goessweiner-Mohr, N. / Miletic, S. / Wald, J. / Marlovits, T.
Funding support Austria, Germany, 2items
OrganizationGrant numberCountry
Austrian Science FundI 2408-B22 Austria
German Research Foundation (DFG)FA1518/2-1 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Substrate-engaged type III secretion system structures reveal gating mechanism for unfolded protein translocation.
Authors: Sean Miletic / Dirk Fahrenkamp / Nikolaus Goessweiner-Mohr / Jiri Wald / Maurice Pantel / Oliver Vesper / Vadim Kotov / Thomas C Marlovits /
Abstract: Many bacterial pathogens rely on virulent type III secretion systems (T3SSs) or injectisomes to translocate effector proteins in order to establish infection. The central component of the injectisome ...Many bacterial pathogens rely on virulent type III secretion systems (T3SSs) or injectisomes to translocate effector proteins in order to establish infection. The central component of the injectisome is the needle complex which assembles a continuous conduit crossing the bacterial envelope and the host cell membrane to mediate effector protein translocation. However, the molecular principles underlying type III secretion remain elusive. Here, we report a structure of an active Salmonella enterica serovar Typhimurium needle complex engaged with the effector protein SptP in two functional states, revealing the complete 800Å-long secretion conduit and unraveling the critical role of the export apparatus (EA) subcomplex in type III secretion. Unfolded substrates enter the EA through a hydrophilic constriction formed by SpaQ proteins, which enables side chain-independent substrate transport. Above, a methionine gasket formed by SpaP proteins functions as a gate that dilates to accommodate substrates while preventing leaky pore formation. Following gate penetration, a moveable SpaR loop first folds up to then support substrate transport. Together, these findings establish the molecular basis for substrate translocation through T3SSs and improve our understanding of bacterial pathogenicity and motility.
History
DepositionSep 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_sheet_hbond ...pdbx_database_status / pdbx_struct_sheet_hbond / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _pdbx_database_status.process_site
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-11781
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11781
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1A: Surface presentation of antigens protein SpaP
1B: Surface presentation of antigens protein SpaP
1C: Surface presentation of antigens protein SpaP
1D: Surface presentation of antigens protein SpaP
1E: Surface presentation of antigens protein SpaP
1F: Surface presentation of antigens protein SpaR
1G: Surface presentation of antigens protein SpaQ
1H: Surface presentation of antigens protein SpaQ
1I: Surface presentation of antigens protein SpaQ
1J: Surface presentation of antigens protein SpaQ
1K: Protein PrgJ
1L: Protein PrgJ
1M: Protein PrgJ
1N: Protein PrgJ
1O: Protein PrgJ
1P: Protein PrgJ
1Z: SptP3x-GFP-FLAG
2A: Protein PrgI
2B: Protein PrgI
2C: Protein PrgI
2D: Protein PrgI
2E: Protein PrgI
2F: Protein PrgI
2G: Protein PrgI
2H: Protein PrgI
2I: Protein PrgI
2J: Protein PrgI
2K: Protein PrgI
2L: Protein PrgI
2M: Protein PrgI
2N: Protein PrgI
2O: Protein PrgI
2P: Protein PrgI
2Q: Protein PrgI
2R: Protein PrgI
2S: Protein PrgI
2T: Protein PrgI
2U: Protein PrgI
2V: Protein PrgI
2W: Protein PrgI
2X: Protein PrgI
2Y: Protein PrgI
2Z: Protein PrgI
3A: Protein PrgI
3B: Protein PrgI
3C: Protein PrgI
3D: Protein PrgI
3E: Protein PrgI
3F: Protein PrgI
3G: Protein PrgI
3H: Protein PrgI
3I: Protein PrgI
3J: Protein PrgI
3K: Protein PrgI
3L: Protein PrgI
3M: Protein PrgI
3N: Protein PrgI
3O: Protein PrgI
3P: Protein PrgI
3Q: Protein PrgI
3R: Protein PrgI
3S: Protein PrgI
3T: Protein PrgI
3U: Protein PrgI
3V: Protein PrgI
3W: Protein PrgI
3X: Protein PrgI
3Y: Protein PrgI
3Z: Protein PrgI
4A: Protein PrgI
4B: Protein PrgI
4C: Protein PrgI
4D: Protein PrgI
4E: Protein PrgI
4F: Protein PrgI
4G: Protein PrgI
4H: Protein PrgI
4I: Protein PrgI
4J: Protein PrgI
4K: Protein PrgI
4L: Protein PrgI
4M: Protein PrgI
4N: Protein PrgI
4O: Protein PrgI
4P: Protein PrgI
4Q: Protein PrgI
4R: Protein PrgI
4S: Protein PrgI
4T: Protein PrgI
5A: Type 3 secretion system secretin
5B: Type 3 secretion system secretin
5C: Type 3 secretion system secretin
5D: Type 3 secretion system secretin
5E: Type 3 secretion system secretin
5F: Type 3 secretion system secretin
5G: Type 3 secretion system secretin
5H: Type 3 secretion system secretin
5I: Type 3 secretion system secretin
5J: Type 3 secretion system secretin
5K: Type 3 secretion system secretin
5L: Type 3 secretion system secretin
5M: Type 3 secretion system secretin
5N: Type 3 secretion system secretin
5O: Type 3 secretion system secretin
5P: Type 3 secretion system secretin
6A: Lipoprotein PrgK
6B: Lipoprotein PrgK
6C: Lipoprotein PrgK
6D: Lipoprotein PrgK
6E: Lipoprotein PrgK
6F: Lipoprotein PrgK
6G: Lipoprotein PrgK
6H: Lipoprotein PrgK
6I: Lipoprotein PrgK
6J: Lipoprotein PrgK
6K: Lipoprotein PrgK
6L: Lipoprotein PrgK
6M: Lipoprotein PrgK
6N: Lipoprotein PrgK
6O: Lipoprotein PrgK
6P: Lipoprotein PrgK
6Q: Lipoprotein PrgK
6R: Lipoprotein PrgK
6S: Lipoprotein PrgK
6T: Lipoprotein PrgK
6U: Lipoprotein PrgK
6V: Lipoprotein PrgK
6W: Lipoprotein PrgK
6X: Lipoprotein PrgK
7A: Protein PrgH
7B: Protein PrgH
7C: Protein PrgH
7D: Protein PrgH
7E: Protein PrgH
7F: Protein PrgH
7G: Protein PrgH
7H: Protein PrgH
7I: Protein PrgH
7J: Protein PrgH
7K: Protein PrgH
7L: Protein PrgH
7M: Protein PrgH
7N: Protein PrgH
7O: Protein PrgH
7P: Protein PrgH
7Q: Protein PrgH
7R: Protein PrgH
7S: Protein PrgH
7T: Protein PrgH
7U: Protein PrgH
7V: Protein PrgH
7W: Protein PrgH
7X: Protein PrgH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,649,166167
Polymers3,643,576153
Non-polymers5,59014
Water00
1


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

-
Components

-
Surface presentation of antigens protein ... , 3 types, 10 molecules 1A1B1C1D1E1F1G1H1I1J

#1: Protein
Surface presentation of antigens protein SpaP


Mass: 25249.596 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P40700
#2: Protein Surface presentation of antigens protein SpaR


Mass: 28499.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P40701
#3: Protein
Surface presentation of antigens protein SpaQ


Mass: 9363.229 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P0A1L7

-
Protein , 6 types, 143 molecules 1K1L1M1N1O1P1Z2A2B2C2D2E2F2G2H2I2J2K2L2M2N2O2P2Q2R2S2T2U2V2W...

#4: Protein
Protein PrgJ


Mass: 10934.425 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P41785
#5: Protein SptP3x-GFP-FLAG


Mass: 12017.806 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Production host: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
#6: Protein ...
Protein PrgI


Mass: 8864.868 Da / Num. of mol.: 72 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P41784
#7: Protein
Type 3 secretion system secretin / T3SS secretin / Protein InvG


Mass: 61835.559 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P35672
#8: Protein ...
Lipoprotein PrgK


Mass: 28245.287 Da / Num. of mol.: 24 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P41786
#9: Protein ...
Protein PrgH


Mass: 44509.367 Da / Num. of mol.: 24 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
References: UniProt: P41783

-
Non-polymers , 2 types, 14 molecules

#10: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C39H77O8P
#11: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Substrate-engaged T3SS needle complex / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL
Molecular weightValue: 2.84 MDa / Experimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18_3861refinement
PHENIX1.18_3861refinement
UCSF ChimeraX0.93/v8model building
EM software
IDNameVersionCategory
7Coot0.9bmodel fitting
8ISOLDE1.0b5model fitting
14ISOLDE1.0b5model refinement
15PHENIX1.18-6831model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77411 / Symmetry type: POINT

+
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