+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22071 | ||||||||||||||||||||||||
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Title | Legionella pneumophila dDot T4SS OMC | ||||||||||||||||||||||||
Map data | Dot T4SS PR | ||||||||||||||||||||||||
Sample |
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Keywords | Secretion / T4SS / Dot / PROTEIN TRANSPORT | ||||||||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||||||||
Biological species | Legionella pneumophila (bacteria) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||||||||||||||
Authors | Durie CL / Sheedlo MJ | ||||||||||||||||||||||||
Funding support | United States, 7 items
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Citation | Journal: Elife / Year: 2020 Title: Structural analysis of the Dot/Icm type IV secretion system core complex. Authors: Clarissa L Durie / Michael J Sheedlo / Jeong Min Chung / Brenda G Byrne / Min Su / Thomas Knight / Michele Swanson / D Borden Lacy / Melanie D Ohi / Abstract: is an opportunistic pathogen that causes the potentially fatal pneumonia Legionnaires' Disease. This infection and subsequent pathology require the Dot/Icm Type IV Secretion System (T4SS) to deliver ... is an opportunistic pathogen that causes the potentially fatal pneumonia Legionnaires' Disease. This infection and subsequent pathology require the Dot/Icm Type IV Secretion System (T4SS) to deliver effector proteins into host cells. Compared to prototypical T4SSs, the Dot/Icm assembly is much larger, containing ~27 different components including a core complex reported to be composed of five proteins: DotC, DotD, DotF, DotG, and DotH. Using single particle cryo-electron microscopy (cryo-EM), we report reconstructions of the core complex of the Dot/Icm T4SS that includes a symmetry mismatch between distinct structural features of the outer membrane cap (OMC) and periplasmic ring (PR). We present models of known core complex proteins, DotC, DotD, and DotH, and two structurally similar proteins within the core complex, DotK and Lpg0657. This analysis reveals the stoichiometry and contact interfaces between the key proteins of the Dot/Icm T4SS core complex and provides a framework for understanding a complex molecular machine. | ||||||||||||||||||||||||
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_22071.map.gz | 253.4 MB | EMDB map data format | |
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Header (meta data) | emd-22071-v30.xml emd-22071.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
Images | emd_22071.png | 68.4 KB | ||
Filedesc metadata | emd-22071.cif.gz | 6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22071 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22071 | HTTPS FTP |
-Validation report
Summary document | emd_22071_validation.pdf.gz | 533.1 KB | Display | EMDB validaton report |
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Full document | emd_22071_full_validation.pdf.gz | 532.7 KB | Display | |
Data in XML | emd_22071_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | emd_22071_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22071 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22071 | HTTPS FTP |
-Related structure data
Related structure data | 6x66MC 6x62C 6x64C 6x65C 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_22071.map.gz / Format: CCP4 / Size: 506 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Dot T4SS PR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 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 : dDotG Dot/Icm T4SS
Entire | Name: dDotG Dot/Icm T4SS |
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Components |
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-Supramolecule #1: dDotG Dot/Icm T4SS
Supramolecule | Name: dDotG Dot/Icm T4SS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Legionella pneumophila (bacteria) |
-Macromolecule #1: DotC
Macromolecule | Name: DotC / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO |
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Source (natural) | Organism: Legionella pneumophila (bacteria) |
Molecular weight | Theoretical: 34.162441 KDa |
Sequence | String: MRKFILSLSI LLSALLVACS SRNHYGDTGS LAGLQAMADS KYTRAQKKQK MGKIREMALK ETALSVGAQA GLAWRAKIID EQLNKQARN LDAIYDFNSL VLEHNILPPV LLEGRNTLNL ADAQSIRISD RTYKVAKQAH FITTPPTWRQ YLWMDYVKPE A PNVTLLPK ...String: MRKFILSLSI LLSALLVACS SRNHYGDTGS LAGLQAMADS KYTRAQKKQK MGKIREMALK ETALSVGAQA GLAWRAKIID EQLNKQARN LDAIYDFNSL VLEHNILPPV LLEGRNTLNL ADAQSIRISD RTYKVAKQAH FITTPPTWRQ YLWMDYVKPE A PNVTLLPK TKAEKEIWCI YTERGWKNGI DQANTILEEN IARIKEDFGG MILYRKLLAM NMVSPPYVSH TDLGVTGDGS EI HIDDRVL RITALPELNV NSAEWRAAVA KDENALERFK NMEKLANQAK IVITNKSWQP IIAPVS UniProtKB: DotC |
-Macromolecule #2: DotD
Macromolecule | Name: DotD / type: protein_or_peptide / ID: 2 / Number of copies: 26 / Enantiomer: LEVO |
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Source (natural) | Organism: Legionella pneumophila (bacteria) |
Molecular weight | Theoretical: 17.860678 KDa |
Sequence | String: MNNNKIVIMF IFSALLAGCA GTMKFKKPPI NNPSDDATIK LAEAAVSVSD SMLEMAKVEK VITPPSKDNT LTIPNAYNLQ ARASVDWSG PIEELTARIA KAAHFRFRVL GKSPSVPVLI SISTKDESLA EILRDIDYQA GKKASIHVYP NSQVVELRYA K IYS UniProtKB: DotD |
-Macromolecule #3: Type IV secretion protein IcmK
Macromolecule | Name: Type IV secretion protein IcmK / type: protein_or_peptide / ID: 3 / Number of copies: 13 / Enantiomer: LEVO |
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Source (natural) | Organism: Legionella pneumophila (bacteria) |
Molecular weight | Theoretical: 38.958926 KDa |
Sequence | String: MMKKYDQLCK YCLVIGLTFS MSCSIYAADQ SDDAQQALQQ LRMLQQKLSQ NPSPDAQSGA GDGGDNAASD STQQPNQSGQ ANAPAANQT ATAGGDGQII SQDDAEVIDK KAFKDMTRNL YPLNPEQVVK LKQIYETSEY AKAATPGTPP KPTATSQFVN L SPGSTPPV ...String: MMKKYDQLCK YCLVIGLTFS MSCSIYAADQ SDDAQQALQQ LRMLQQKLSQ NPSPDAQSGA GDGGDNAASD STQQPNQSGQ ANAPAANQT ATAGGDGQII SQDDAEVIDK KAFKDMTRNL YPLNPEQVVK LKQIYETSEY AKAATPGTPP KPTATSQFVN L SPGSTPPV IRLSQGFVSS LVFLDSTGAP WPIAAYDLGD PSSFNIQWDK TSNTLMIQAT KLYNYGNLAV RLRGLNTPVM LT LIPGQKA VDYRVDLRVQ GYGPNAKSMP TEEGIPPSAN DLLLHVLEGV PPPGSRRLVV SGGDARAWLS NEKMYVRTNL TIL SPGWLA SMTSADGTHA YEMQKSPVLL VSWHGKVMQL KVEGL UniProtKB: Type IV secretion protein IcmK |
-Macromolecule #4: Inner membrane lipoprotein YiaD
Macromolecule | Name: Inner membrane lipoprotein YiaD / type: protein_or_peptide / ID: 4 / Number of copies: 13 / Enantiomer: LEVO |
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Source (natural) | Organism: Legionella pneumophila (bacteria) |
Molecular weight | Theoretical: 21.096492 KDa |
Sequence | String: MRSLRTNYIY VLFKTTGLLF LLLLSACNRS GYIPENEVPK LPCRVDGACD ATIIKMMTDL NKKGIKVASV GQNYLISIPA SALFADQSP RLNWASYSLL NEIAAFLKQF RKIAITVTSY SSKYVSVKRE RALTLARSRV VSEYLWSQGV DSRIIFTQGL G SDKPITSY TLGGDRSPNA RVEITFRRAV A UniProtKB: Inner membrane lipoprotein YiaD |
-Macromolecule #5: Type IV secretion system unknown protein fragment
Macromolecule | Name: Type IV secretion system unknown protein fragment / type: protein_or_peptide / ID: 5 / Number of copies: 39 / Enantiomer: LEVO |
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Source (natural) | Organism: Legionella pneumophila (bacteria) |
Molecular weight | Theoretical: 28.102492 KDa |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-Macromolecule #6: Outer membrane protein, OmpA family protein
Macromolecule | Name: Outer membrane protein, OmpA family protein / type: protein_or_peptide / ID: 6 / Number of copies: 13 / Enantiomer: LEVO |
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Source (natural) | Organism: Legionella pneumophila (bacteria) |
Molecular weight | Theoretical: 27.582047 KDa |
Sequence | String: MRNLMRCLIM IKSLIKGVDM SRKLAKTRIL GYGLMICFLA GCFHPPYNNF QPDRRAVKRV GVDTGIGAVA GAIASGTASG TLIGAAAGG TVGLVASIYR DSKRKIIRDL QKQDIQYVEY GDTRTLIIPT DKYFMFSSPR LNEICYPGLN NVIRLLNFYP Q STIYVAGF ...String: MRNLMRCLIM IKSLIKGVDM SRKLAKTRIL GYGLMICFLA GCFHPPYNNF QPDRRAVKRV GVDTGIGAVA GAIASGTASG TLIGAAAGG TVGLVASIYR DSKRKIIRDL QKQDIQYVEY GDTRTLIIPT DKYFMFSSPR LNEICYPGLN NVIRLLNFYP Q STIYVAGF TDNVGSRSHK RKLSQAQAET MMTFLWANGI AAKRLKAEGY GDKNAISDNA IIHGSAQNRR IEIQWFTSPA QP PQPQMAY VK UniProtKB: Outer membrane protein, OmpA family protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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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: 65.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6342 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |