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- EMDB-9747: Type VI secretion system membrane core complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-9747
TitleType VI secretion system membrane core complex
Map dataT6SS membrane core complex
Sample
  • Complex: Type VI Secretion System membrane core complex TssJLM
    • Protein or peptide: Type VI Secretion System TssJ
    • Protein or peptide: Type VI Secretion System TssM
KeywordsType VI secretion system membrane core complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


IcmF-related / Intracellular multiplication and human macrophage-killing / : / : / Type VI secretion protein IcmF helical domain / 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
Type VI secretion system lipoprotein TssJ / Type VI secretion protein VasK
Similarity search - Component
Biological speciesEscherichia coli 55989 (bacteria) / Escherichia coli (strain 55989 / EAEC) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsMeng Y / Zhaofeng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31722015 and 31570730 China
CitationJournal: Cell Res / Year: 2019
Title: Architecture of type VI secretion system membrane core complex.
Authors: Meng Yin / Zhaofeng Yan / Xueming Li /
History
DepositionDec 10, 2018-
Header (metadata) releaseJan 23, 2019-
Map releaseJan 23, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ixh
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ixh
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9747.png

Downloads & links

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Map

FileDownload / File: emd_9747.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT6SS membrane core complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 340 pix.
= 448.8 Å		1.32 Å/pix.
x 340 pix.
= 448.8 Å		1.32 Å/pix.
x 340 pix.
= 448.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.13804519 - 0.22493486
Average (Standard dev.)0.0007299888 (±0.005843512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 448.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z448.800448.800448.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.1380.2250.001

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Supplemental data

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Sample components

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Entire : Type VI Secretion System membrane core complex TssJLM

EntireName: Type VI Secretion System membrane core complex TssJLM
Components
  • Complex: Type VI Secretion System membrane core complex TssJLM
    • Protein or peptide: Type VI Secretion System TssJ
    • Protein or peptide: Type VI Secretion System TssM

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Supramolecule #1: Type VI Secretion System membrane core complex TssJLM

SupramoleculeName: Type VI Secretion System membrane core complex TssJLM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli 55989 (bacteria) / Strain: 55989

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Macromolecule #1: Type VI Secretion System TssJ

MacromoleculeName: Type VI Secretion System TssJ / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain 55989 / EAEC) (bacteria) / Strain: 55989 / EAEC
Molecular weightTheoretical: 19.27109 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAIIAGKAGY GLIIALFSLS LSGCGLTQRV ADGTVSATKS LFYRQIKTLH LDIRAREAIN TSAAGIPLSV VVRIYQLKDN RSFDSADYQ ALFTGDNEIL AGDIIAQKDV WLQPGGSVAV DMPLDDAAKF TGVAAMFLEP DQKKNTWRVV LGRDELEPDT P RLIEVSGN TLTLLPVKDK

UniProtKB: Type VI secretion system lipoprotein TssJ

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Macromolecule #2: Type VI Secretion System TssM

MacromoleculeName: Type VI Secretion System TssM / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain 55989 / EAEC) (bacteria) / Strain: 55989 / EAEC
Molecular weightTheoretical: 127.11307 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNKLACLSGR FGRPGIVFIG VAALWWLITR YGAYLGAETR RDQILLLILL SLGVLFVCYL PVMKKYVQEL TYRRRARKEQ RLPDDEERL AQTPPRYVTV QDIRHTLRRQ YGRFWGRKIR ILLITGTASE VELLTPGLTE QFWQEEQGTL LLWGGDPSQP E NADWLAAL ...String:
MNKLACLSGR FGRPGIVFIG VAALWWLITR YGAYLGAETR RDQILLLILL SLGVLFVCYL PVMKKYVQEL TYRRRARKEQ RLPDDEERL AQTPPRYVTV QDIRHTLRRQ YGRFWGRKIR ILLITGTASE VELLTPGLTE QFWQEEQGTL LLWGGDPSQP 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 AVVMPLYAQN 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 KAQTLSDVTE QLTLMADVRQ SPLVALMN T LAVQGCTGQP REAVTDSLVK SARNLLSQEK QPVAVPESRL HGPLATTFGP VLALMDNQNN SADMLNLQTY LTRVTQVRL RLQQIAGSSD PQAMMQLLAQ 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: Type VI secretion protein VasK

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44069
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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