[English] 日本語
Yorodumi
- EMDB-10093: Structure of the core of the flagellar export apparatus from Vibr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10093
TitleStructure of the core of the flagellar export apparatus from Vibrio mimicus, the FliPQR-FlhB complex.
Map dataStructure of the core of the flagellar export apparatus from Vibrio mimicus, the FliPQR-FlhB complex.
Sample
  • Complex: FliPQR-FlhB
    • Protein or peptide: Flagellar biosynthetic protein FliP
    • Protein or peptide: Flagellar biosynthetic protein FliR
    • Protein or peptide: Flagellar biosynthetic protein FliQ
    • Protein or peptide: Flagellar biosynthetic protein FlhB
Keywordsflagella / T3SS / export apparatus / export gate / PROTEIN TRANSPORT
Function / homology
Function and homology information


bacterial-type flagellum organization / bacterial-type flagellum basal body / bacterial-type flagellum assembly / protein secretion / protein targeting / plasma membrane
Similarity search - Function
Flagellar biosynthetic protein FlhB / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / Flagellar biosynthesis protein FliQ / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Bacterial export proteins, family 1 ...Flagellar biosynthetic protein FlhB / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / Flagellar biosynthesis protein FliQ / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / 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.
Similarity search - Domain/homology
Flagellar biosynthetic protein FliQ / Flagellar biosynthetic protein FlhB / Flagellar biosynthetic protein FliR / Flagellar biosynthetic protein FliP
Similarity search - Component
Biological speciesVibrio mimicus CAIM 602 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKuhlen L / Johnson S
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Wellcome Trust100298 United Kingdom
Wellcome Trust109136 United Kingdom
Wellcome Trust201536 United Kingdom
Medical Research Council (United Kingdom)M011984 United Kingdom
Wolfson FoundationWL160052 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: The substrate specificity switch FlhB assembles onto the export gate to regulate type three secretion.
Authors: Lucas Kuhlen / Steven Johnson / Andreas Zeitler / Sandra Bäurle / Justin C Deme / Joseph J E Caesar / Rebecca Debo / Joseph Fisher / Samuel Wagner / Susan M Lea /
Abstract: Protein secretion through type-three secretion systems (T3SS) is critical for motility and virulence of many bacteria. Proteins are transported through an export gate containing three proteins ...Protein secretion through type-three secretion systems (T3SS) is critical for motility and virulence of many bacteria. Proteins are transported through an export gate containing three proteins (FliPQR in flagella, SctRST in virulence systems). A fourth essential T3SS protein (FlhB/SctU) functions to "switch" secretion substrate specificity once the growing hook/needle reach their determined length. Here, we present the cryo-electron microscopy structure of an export gate containing the switch protein from a Vibrio flagellar system at 3.2 Å resolution. The structure reveals that FlhB/SctU extends the helical export gate with its four predicted transmembrane helices wrapped around FliPQR/SctRST. The unusual topology of the FlhB/SctU helices creates a loop wrapped around the bottom of the closed export gate. Structure-informed mutagenesis suggests that this loop is critical in gating secretion and we propose that a series of conformational changes in the T3SS trigger opening of the gate through interactions between FlhB/SctU and FliPQR/SctRST.
History
DepositionJun 25, 2019-
Header (metadata) releaseJul 10, 2019-
Map releaseMar 25, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0255
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0255
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6s3l
  • Surface level: 0.0255
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10093.png

Downloads & links

-
Map

FileDownload / File: emd_10093.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the core of the flagellar export apparatus from Vibrio mimicus, the FliPQR-FlhB complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 288 pix.
= 236.736 Å		0.82 Å/pix.
x 288 pix.
= 236.736 Å		0.82 Å/pix.
x 288 pix.
= 236.736 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0255 / Movie #1: 0.0255
Minimum - Maximum-0.06778669 - 0.13658862
Average (Standard dev.)-0.000022053937 (±0.004109645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 236.73601 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z236.736236.736236.736
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0680.137-0.000

-
Supplemental data

-
Mask #1

Fileemd_10093_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: refinement map

Fileemd_10093_additional.map
Annotationrefinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half1 map

Fileemd_10093_half_map_1.map
Annotationhalf1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half2 map

Fileemd_10093_half_map_2.map
Annotationhalf2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : FliPQR-FlhB

EntireName: FliPQR-FlhB
Components
  • Complex: FliPQR-FlhB
    • Protein or peptide: Flagellar biosynthetic protein FliP
    • Protein or peptide: Flagellar biosynthetic protein FliR
    • Protein or peptide: Flagellar biosynthetic protein FliQ
    • Protein or peptide: Flagellar biosynthetic protein FlhB

-
Supramolecule #1: FliPQR-FlhB

SupramoleculeName: FliPQR-FlhB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio mimicus CAIM 602 (bacteria)
Molecular weightTheoretical: 260 KDa

-
Macromolecule #1: Flagellar biosynthetic protein FliP

MacromoleculeName: Flagellar biosynthetic protein FliP / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Vibrio mimicus CAIM 602 (bacteria)
Molecular weightTheoretical: 32.431307 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MKRTQRLNLT SWLTTGLLTW LLSGMLGFAS LAFAEEPLNT GIPSTAAGAS SVTVTALEKE QGNAKTIALG SSSGGSGIPA FTMTTNPDG SEDYSINLQI LALMTMLGFL PAMVILMTSF TRIVVVMSIL RQAMGLQQTP SNQVIIGIAL FLTFFIMAPV F NQINEQAV ...String:
MKRTQRLNLT SWLTTGLLTW LLSGMLGFAS LAFAEEPLNT GIPSTAAGAS SVTVTALEKE QGNAKTIALG SSSGGSGIPA FTMTTNPDG SEDYSINLQI LALMTMLGFL PAMVILMTSF TRIVVVMSIL RQAMGLQQTP SNQVIIGIAL FLTFFIMAPV F NQINEQAV QPYLNEQISA RQAFDLAQEP MKAFMLKQTR IKDLETFVEM SGSQVTAPEQ VSMAVLIPAF ITSELKTAFQ IG FMLFLPF LIIDLVVASV LMAMGMMMLS PMIVSLPFKL MLFVLVDGWN LILSTLAGSF AL

UniProtKB: Flagellar biosynthetic protein FliP

-
Macromolecule #2: Flagellar biosynthetic protein FliR

MacromoleculeName: Flagellar biosynthetic protein FliR / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio mimicus CAIM 602 (bacteria)
Molecular weightTheoretical: 28.764324 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEYPASVVLD FIANYFWPYT RIAAMLMVMT VTGARFVPAR VRLYLGLALT FAVMPAIPAV PSDIALLSLQ GFMITFEQIV IGMAMGMVT QFLVQIFVML GQILGMQSSL GFASMVDPAN GQNTPLLGQM FMLLATLFFL SSDGHLKMIQ LVVFSFKSLP I GSGSLTTV ...String:
MEYPASVVLD FIANYFWPYT RIAAMLMVMT VTGARFVPAR VRLYLGLALT FAVMPAIPAV PSDIALLSLQ GFMITFEQIV IGMAMGMVT QFLVQIFVML GQILGMQSSL GFASMVDPAN GQNTPLLGQM FMLLATLFFL SSDGHLKMIQ LVVFSFKSLP I GSGSLTTV DYRELALWLG IMFKASLAVS LSGIIALLTV NLSFGVMTRA APQLNIFSLG FSFALLVGLL LCWYILSGLY TH YEIYWQE TEEQICRLIR LNC

UniProtKB: Flagellar biosynthetic protein FliR

-
Macromolecule #3: Flagellar biosynthetic protein FliQ

MacromoleculeName: Flagellar biosynthetic protein FliQ / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vibrio mimicus CAIM 602 (bacteria)
Molecular weightTheoretical: 10.333578 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTPEIFVELF KESLWLVLIM VCAIIIPSLL IGLVVAIFQA ATSINEQTLS FLPRLIITLL ALMFFGHWMT QMLMDFFYSM IERLPQVLY

UniProtKB: Flagellar biosynthetic protein FliQ

-
Macromolecule #4: Flagellar biosynthetic protein FlhB

MacromoleculeName: Flagellar biosynthetic protein FlhB / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio mimicus CAIM 602 (bacteria)
Molecular weightTheoretical: 46.26573 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAESDGQERT EEATPRRLQQ AKEKGQVARS KELASVSVLV VGAVSLMWFG EALAQGLFTA MQRLFSLDRE EIFDIGKLFD IIGGSLVNL LLPLLMILIT LFIAALIGAA GVGGINFSAE AAMPKLSKMN PLSGFKRMFG LQSWVELLKS ILKVMLVAGV A FYLIEASQ ...String:
MAESDGQERT EEATPRRLQQ AKEKGQVARS KELASVSVLV VGAVSLMWFG EALAQGLFTA MQRLFSLDRE EIFDIGKLFD IIGGSLVNL LLPLLMILIT LFIAALIGAA GVGGINFSAE AAMPKLSKMN PLSGFKRMFG LQSWVELLKS ILKVMLVAGV A FYLIEASQ KDLFQLSLDV YPQNIFHALD ILLNFVLLIS CSLLVVVAID IPFQIWQHAN QLKMTKQEVK DEYKDTEGKP EV KGRIRML QREAAQRRMM AALPQADVII TNPEHFSVAL RYKQNTDKAP VVIAKGVDHM ALKIREIARE YDIAIVPAPP LAR ALYHTT ELEQQIPDGL FVAVAQVLAF VFQLKQYRRK GGQRPKLNEE NMPIPPDMRY ENLYFQGQFG SWSHPQFEKG GGSG GGSGG GSWSHPQFEK

UniProtKB: Flagellar biosynthetic protein FlhB

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMC4H11NO3Tris
150.0 mMNaClsodium chloride
1.0 mMC10H16N2O8EDTA
0.01 %C47H88O22LMNG
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: 10 seconds wait time.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1386230
Startup modelType of model: EMDB MAP
EMDB ID:

4173

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 162408
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4 / Software - Name: RELION
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