+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9747 | |||||||||
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Title | Type VI secretion system membrane core complex | |||||||||
Map data | T6SS membrane core complex | |||||||||
Sample |
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Keywords | Type VI secretion system membrane core complex / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Escherichia coli 55989 (bacteria) / Escherichia coli (strain 55989 / EAEC) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Meng Y / Zhaofeng Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2019 Title: Architecture of type VI secretion system membrane core complex. Authors: Meng Yin / Zhaofeng Yan / Xueming Li / | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9747.map.gz | 15.5 MB | EMDB map data format | |
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Header (meta data) | emd-9747-v30.xml emd-9747.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_9747.png | 169.9 KB | ||
Filedesc metadata | emd-9747.cif.gz | 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9747 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9747 | HTTPS FTP |
-Validation report
Summary document | emd_9747_validation.pdf.gz | 406.6 KB | Display | EMDB validaton report |
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Full document | emd_9747_full_validation.pdf.gz | 406.2 KB | Display | |
Data in XML | emd_9747_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | emd_9747_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9747 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9747 | HTTPS FTP |
-Related structure data
Related structure data | 6ixhMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9747.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | T6SS membrane core complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Type VI Secretion System membrane core complex TssJLM
Entire | Name: Type VI Secretion System membrane core complex TssJLM |
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Components |
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-Supramolecule #1: Type VI Secretion System membrane core complex TssJLM
Supramolecule | Name: Type VI Secretion System membrane core complex TssJLM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli 55989 (bacteria) / Strain: 55989 |
-Macromolecule #1: Type VI Secretion System TssJ
Macromolecule | Name: Type VI Secretion System TssJ / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain 55989 / EAEC) (bacteria) / Strain: 55989 / EAEC |
Molecular weight | Theoretical: 19.27109 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #2: Type VI Secretion System TssM
Macromolecule | Name: Type VI Secretion System TssM / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain 55989 / EAEC) (bacteria) / Strain: 55989 / EAEC |
Molecular weight | Theoretical: 127.11307 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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: Uncharacterized protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44069 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |