[English] 日本語
Yorodumi
- EMDB-0264: Type VI membrane complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0264
TitleType VI membrane complex
Map dataMolRes Sharpened map
Sample
  • Complex: Membrane complex of the type VI secretion system (TssM and TssJ)
    • Protein or peptide: ImcF-like family protein
    • Protein or peptide: Type VI secretion system protein VasD
KeywordsMembrane complex / tether / MEMBRANE PROTEIN
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
IcmF-related / Intracellular multiplication and human macrophage-killing / Type VI secretion system IcmF, C-terminal / Type VI secretion system, lipoprotein SciN / Type VI secretion protein SciN-like superfamily / Type VI secretion protein IcmF C2-like domain / Type VI secretion lipoprotein, VasD, EvfM, TssJ, VC_A0113 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Putative type VI secretion protein / Type VI secretion system protein VasD / ImcF-like family protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsRapisarda C / Fronzes R
CitationJournal: EMBO J / Year: 2019
Title: and high-resolution cryo-EM structure of a bacterial type VI secretion system membrane complex.
Authors: Chiara Rapisarda / Yassine Cherrak / Romain Kooger / Victoria Schmidt / Riccardo Pellarin / Laureen Logger / Eric Cascales / Martin Pilhofer / Eric Durand / Rémi Fronzes /
Abstract: Bacteria have evolved macromolecular machineries that secrete effectors and toxins to survive and thrive in diverse environments. The type VI secretion system (T6SS) is a contractile machine that is ...Bacteria have evolved macromolecular machineries that secrete effectors and toxins to survive and thrive in diverse environments. The type VI secretion system (T6SS) is a contractile machine that is related to phages. It is composed of a phage tail-like structure inserted in the bacterial cell envelope by a membrane complex (MC) comprising the TssJ, TssL and TssM proteins. We previously reported the low-resolution negative-stain electron microscopy structure of the enteroaggregative MC and proposed a rotational 5-fold symmetry with a TssJ:TssL:TssM stoichiometry of 2:2:2. Here, cryo-electron tomography analyses of the T6SS MC confirm the 5-fold symmetry and identify the regions of the structure that insert into the bacterial membranes. A high-resolution model obtained by single-particle cryo-electron microscopy highlights new features: five additional copies of TssJ, yielding a TssJ:TssL:TssM stoichiometry of 3:2:2, an 11-residue loop in TssM, protruding inside the lumen of the MC and constituting a functionally important periplasmic gate, and hinge regions. Based on these data, we propose an updated model on MC structure and dynamics during T6SS assembly and function.
History
DepositionSep 28, 2018-
Header (metadata) releaseOct 31, 2018-
Map releaseMar 27, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6hs7
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0264.png

Downloads & links

-
Map

FileDownload / File: emd_0264.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMolRes Sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 500 pix.
= 620. Å		1.24 Å/pix.
x 500 pix.
= 620. Å		1.24 Å/pix.
x 500 pix.
= 620. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.0032616141 - 0.31601304
Average (Standard dev.)-0.00016434066 (±0.0034643826)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 620.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z620.000620.000620.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0030.316-0.000

-
Supplemental data

-
Additional map: Refinement map

Fileemd_0264_additional.map
AnnotationRefinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2

Fileemd_0264_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1

Fileemd_0264_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Membrane complex of the type VI secretion system (TssM and TssJ)

EntireName: Membrane complex of the type VI secretion system (TssM and TssJ)
Components
  • Complex: Membrane complex of the type VI secretion system (TssM and TssJ)
    • Protein or peptide: ImcF-like family protein
    • Protein or peptide: Type VI secretion system protein VasD

-
Supramolecule #1: Membrane complex of the type VI secretion system (TssM and TssJ)

SupramoleculeName: Membrane complex of the type VI secretion system (TssM and TssJ)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: ImcF-like family protein

MacromoleculeName: ImcF-like family protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 127.255367 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNKLACLSGR FGRPGIVFIG VAALWWLITR YGAFLGAETR RDQILLLILL SLGLLFVCYL PVMKKYVQEL TYRRRARKEQ RLPDDEERL AQTPPRYVTV QDIRHTLRRQ YGRFWGRKIR ILLITGTASE VELLTPGLTE QFWQEEQGTL LLWGGEPSQP E NADWLAAL ...String:
MNKLACLSGR FGRPGIVFIG VAALWWLITR YGAFLGAETR RDQILLLILL SLGLLFVCYL PVMKKYVQEL TYRRRARKEQ RLPDDEERL AQTPPRYVTV QDIRHTLRRQ YGRFWGRKIR ILLITGTASE VELLTPGLTE QFWQEEQGTL LLWGGEPSQP E NADWLAAL RRLRYRPADG IVWVTSGLSE TLSAPLTEDA LDRVSRAVSS CCERLGWRLP LYVWSLQESP DERGRITQPV GC LLPAECS SDKLKAQLQA MLPGLVAQGI QQICCAPRYY FLLSLAERFR RNIDAVVEPL SVLLRPYRQL LLAGIVFSPA TVG GERSVR HRWRMDNRWE ALPETVQQLP VRLQPSRTGH NWRRSLAVMA AILMMAQGTG MVVSFLANRS LVAEVQEQIR PAQN QQLSP AERLQALLNL QKSLARLQYR EEHGAPWYLR AGMNQNADLL VVVMPLYAQN AHLLLRDAAA AHLEQQLRTF IRLPP DSPQ RGKMAKAAYD QLRLYLMLAQ PQHMEPAWFS RTLMREWPQR DGVSAVFWQA NGPTLLAYYA SGIITHPQWK LTADEE LVS QSRTLLLRHL GTQNSDAMLY QKMLARVAHQ FADMRLTDMT GDTDVSRLFF TDEVVPGMFT RQAWEEAVLP SIDTVIN ER REEMDWVLTD GRQKAPSPVS PEALRQRLTT RYFADFGNAW LNFLNSLHLR KAQMLSDVTE QLTLMADVRQ SPLVALMN T LAVQGRTGQP REAVTDSLVK SARNLLSQEK QPVAVPESRL HGPLATTFGP VLALMDNQNN SADMLNLQTY LTRVTQVRL RLQQIAGSSD PQAMMQMLAQ TVLQGKSVDL TDTRDYGSLT AAGLGQEWYG FGQTVFVRPM EQAWQQVLTP AAESLNARWR TAVVDGWNN AFSGRYPFKN VSSDASLPLL AKYLNTDTGR IARFLQNNLS GVLHREGSRW VPDTINTRGL TFNPAFLKAI N TLSEIADV AFTTGNAGLH FELRPGTAAG VMQTTLITDN QKLIYVNQMP VWKRFTWPAD TEAPGASLSW VSTQAGTRQY AD LPGSWGL IRLLEMARRK AAPGVASGWS LSWQAQDGRM LNYTLRTEAG EGPLVLLKLR NFVLPETVFE LSGTSAFTGN DED AGDTVE ETD

UniProtKB: ImcF-like family protein

-
Macromolecule #2: Type VI secretion system protein VasD

MacromoleculeName: Type VI secretion system protein VasD / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 20.313236 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAIIAGKAGY GLIIALFSLS LSGCGLTQRV ADGTVSATKS LFYRQIKTLH LDIRAREAIN TSAAGIPLSV VVRIYQLKDN RSFDSADYQ ALFTGDNEIL AGDIIAQKDV WLQPGGSVAV DMPLDDAAKF TGVAAMFLEP DQKKNTWRVV LGRDELEPDT P RLIEVSGN TLTLLPVKDK WSHPQFEK

UniProtKB: Type VI secretion system protein VasD

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 8
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: GRAPHENE OXIDE
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 120.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 0.003 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.002 µm / Nominal defocus min: 0.0005 µm / Nominal magnification: 120000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 36828
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

+
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