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- EMDB-22071: Legionella pneumophila dDot T4SS OMC -

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Basic information

Entry
Database: EMDB / ID: EMD-22071
TitleLegionella pneumophila dDot T4SS OMC
Map dataDot T4SS PR
Sample
  • Complex: dDotG Dot/Icm T4SS
    • Protein or peptide: DotC
    • Protein or peptide: DotD
    • Protein or peptide: Type IV secretion protein IcmK
    • Protein or peptide: Inner membrane lipoprotein YiaD
    • Protein or peptide: Type IV secretion system unknown protein fragment
    • Protein or peptide: Outer membrane protein, OmpA family protein
KeywordsSecretion / T4SS / Dot / PROTEIN TRANSPORT
Function / homology
Function and homology information


Putative type IV secretory system protein / Type IV secretory system, conjugal DNA-protein transfer / DotD protein / DotD superfamily / DotD protein / Putative outer membrane core complex of type IVb secretion / Putative outer membrane core complex of type IVb secretion / : / OmpA-like domain profile. / OmpA-like domain superfamily ...Putative type IV secretory system protein / Type IV secretory system, conjugal DNA-protein transfer / DotD protein / DotD superfamily / DotD protein / Putative outer membrane core complex of type IVb secretion / Putative outer membrane core complex of type IVb secretion / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Type IV secretion protein IcmK / DotD / DotC / LphA (DotK) / Outer membrane protein, OmpA family protein
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsDurie CL / Sheedlo MJ
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150027-01 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)2T32DK007673 United States
National Institutes of Health/Office of the DirectorS10OD020011 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129539 United States
Other privateSF349247 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI095755-10 United States
Other government1I01BX004447 United States
CitationJournal: 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
DepositionMay 27, 2020-
Header (metadata) releaseOct 28, 2020-
Map releaseOct 28, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6x66
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6x66
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22071.png

Downloads & links

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Map

FileDownload / File: emd_22071.map.gz / Format: CCP4 / Size: 506 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDot T4SS PR
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 510 pix.
= 688.5 Å		1.35 Å/pix.
x 510 pix.
= 688.5 Å		1.35 Å/pix.
x 510 pix.
= 688.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.129 / Movie #1: 0.35
Minimum - Maximum-0.2918179 - 0.95502996
Average (Standard dev.)0.005570734 (±0.045089487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions510510510
Spacing510510510
CellA=B=C: 688.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z510510510
origin x/y/z0.0000.0000.000
length x/y/z688.500688.500688.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS510510510
D min/max/mean-0.2920.9550.006

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Supplemental data

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Sample components

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Entire : dDotG Dot/Icm T4SS

EntireName: dDotG Dot/Icm T4SS
Components
  • Complex: dDotG Dot/Icm T4SS
    • Protein or peptide: DotC
    • Protein or peptide: DotD
    • Protein or peptide: Type IV secretion protein IcmK
    • Protein or peptide: Inner membrane lipoprotein YiaD
    • Protein or peptide: Type IV secretion system unknown protein fragment
    • Protein or peptide: Outer membrane protein, OmpA family protein

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Supramolecule #1: dDotG Dot/Icm T4SS

SupramoleculeName: dDotG Dot/Icm T4SS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Legionella pneumophila (bacteria)

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Macromolecule #1: DotC

MacromoleculeName: DotC / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 34.162441 KDa
SequenceString: 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

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Macromolecule #2: DotD

MacromoleculeName: DotD / type: protein_or_peptide / ID: 2 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 17.860678 KDa
SequenceString:
MNNNKIVIMF IFSALLAGCA GTMKFKKPPI NNPSDDATIK LAEAAVSVSD SMLEMAKVEK VITPPSKDNT LTIPNAYNLQ ARASVDWSG PIEELTARIA KAAHFRFRVL GKSPSVPVLI SISTKDESLA EILRDIDYQA GKKASIHVYP NSQVVELRYA K IYS

UniProtKB: DotD

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Macromolecule #3: Type IV secretion protein IcmK

MacromoleculeName: Type IV secretion protein IcmK / type: protein_or_peptide / ID: 3 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 38.958926 KDa
SequenceString: 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

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Macromolecule #4: Inner membrane lipoprotein YiaD

MacromoleculeName: Inner membrane lipoprotein YiaD / type: protein_or_peptide / ID: 4 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 21.096492 KDa
SequenceString:
MRSLRTNYIY VLFKTTGLLF LLLLSACNRS GYIPENEVPK LPCRVDGACD ATIIKMMTDL NKKGIKVASV GQNYLISIPA SALFADQSP RLNWASYSLL NEIAAFLKQF RKIAITVTSY SSKYVSVKRE RALTLARSRV VSEYLWSQGV DSRIIFTQGL G SDKPITSY TLGGDRSPNA RVEITFRRAV A

UniProtKB: LphA (DotK)

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Macromolecule #5: Type IV secretion system unknown protein fragment

MacromoleculeName: Type IV secretion system unknown protein fragment / type: protein_or_peptide / ID: 5 / Number of copies: 39 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 28.102492 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(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)

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Macromolecule #6: Outer membrane protein, OmpA family protein

MacromoleculeName: Outer membrane protein, OmpA family protein / type: protein_or_peptide / ID: 6 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 27.582047 KDa
SequenceString: 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

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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: 7
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: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6342
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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