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- EMDB-24006: Legionella pneumophila Dot/Icm T4SS PR -

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Basic information

Entry
Database: EMDB / ID: EMD-24006
TitleLegionella pneumophila Dot/Icm T4SS PR
Map dataReconstruction of the Legionella pneumophila Dot/Icm T4SS PR
Sample
  • Complex: Legionella pneumophila Dot/Icm T4SS PR
    • Protein or peptide: DotF
    • Protein or peptide: Type IV secretion protein IcmK
    • Protein or peptide: Unknown protein fragment
    • Protein or peptide: IcmE protein
KeywordsDot/Icm / Secretion / T4SS / TRANSLOCASE
Function / homology
Function and homology information


: / : / Putative outer membrane core complex of type IVb secretion / Putative outer membrane core complex of type IVb secretion / Pentapeptide repeats (9 copies) / Pentapeptide repeat / Type IV secretion system, VirB10/TrbI / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Type IV secretion protein IcmK / IcmE protein / DotF
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSheedlo MJ / Durie CL
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI118932 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32 AI150027-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2T32DK007673 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD020011 United States
CitationJournal: Elife / Year: 2021
Title: Cryo-EM reveals new species-specific proteins and symmetry elements in the Dot/Icm T4SS.
Authors: Michael J Sheedlo / Clarissa L Durie / Jeong Min Chung / Louise Chang / Jacquelyn Roberts / Michele Swanson / Dana Borden Lacy / Melanie D Ohi /
Abstract: is an opportunistic pathogen that causes the potentially fatal pneumonia known as Legionnaires' disease. The pathology associated with infection depends on bacterial delivery of effector proteins ... is an opportunistic pathogen that causes the potentially fatal pneumonia known as Legionnaires' disease. The pathology associated with infection depends on bacterial delivery of effector proteins into the host via the membrane spanning Dot/Icm type IV secretion system (T4SS). We have determined sub-3.0 Å resolution maps of the Dot/Icm T4SS core complex by single particle cryo-EM. The high-resolution structural analysis has allowed us to identify proteins encoded outside the Dot/Icm genetic locus that contribute to the core T4SS structure. We can also now define two distinct areas of symmetry mismatch, one that connects the C18 periplasmic ring (PR) and the C13 outer membrane cap (OMC) and one that connects the C13 OMC with a 16-fold symmetric dome. Unexpectedly, the connection between the PR and OMC is DotH, with five copies sandwiched between the OMC and PR to accommodate the symmetry mismatch. Finally, we observe multiple conformations in the reconstructions that indicate flexibility within the structure.
History
DepositionMay 14, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mue
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7mue
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24006.png

Downloads & links

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Map

FileDownload / File: emd_24006.map.gz / Format: CCP4 / Size: 506 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the Legionella pneumophila Dot/Icm T4SS PR
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 510 pix.
= 561. Å		1.1 Å/pix.
x 510 pix.
= 561. Å		1.1 Å/pix.
x 510 pix.
= 561. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.05256339 - 0.12365949
Average (Standard dev.)0.00007272136 (±0.0019584338)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions510510510
Spacing510510510
CellA=B=C: 561.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z510510510
origin x/y/z0.0000.0000.000
length x/y/z561.000561.000561.000
α/β/γ90.00090.00090.000
start NX/NY/NZ484647
NX/NY/NZ97101117
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS510510510
D min/max/mean-0.0530.1240.000

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Supplemental data

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Sample components

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Entire : Legionella pneumophila Dot/Icm T4SS PR

EntireName: Legionella pneumophila Dot/Icm T4SS PR
Components
  • Complex: Legionella pneumophila Dot/Icm T4SS PR
    • Protein or peptide: DotF
    • Protein or peptide: Type IV secretion protein IcmK
    • Protein or peptide: Unknown protein fragment
    • Protein or peptide: IcmE protein

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Supramolecule #1: Legionella pneumophila Dot/Icm T4SS PR

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

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Macromolecule #1: DotF

MacromoleculeName: DotF / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 29.729969 KDa
SequenceString: MMAEHDQNND EYKFAELDSY DMDQAGESDL DSEASYQSGK EGLTKKKDIK RNALIAIGAV VFIMVMYKII GWMFFSDKSS QVTSKPAIP PVTQVATPQP VQTIPTTTPI QQVQPTTIIE DDPDLKKKVS AIEMTQQSLR SEVNALSEQI NAVNNNIKNL N AQIVNLNQ ...String:
MMAEHDQNND EYKFAELDSY DMDQAGESDL DSEASYQSGK EGLTKKKDIK RNALIAIGAV VFIMVMYKII GWMFFSDKSS QVTSKPAIP PVTQVATPQP VQTIPTTTPI QQVQPTTIIE DDPDLKKKVS AIEMTQQSLR SEVNALSEQI NAVNNNIKNL N AQIVNLNQ IIGNMSNQIA RQSEVINVLM ARTTPKKVVK VSRPIVQARI IYYIQAVIPG RAWLIGSNGS TLTVREGSKI PG YGMVKLI DSLQGRILTS SGQVIKFSQE DS

UniProtKB: DotF

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Macromolecule #2: Type IV secretion protein IcmK

MacromoleculeName: Type IV secretion protein IcmK / type: protein_or_peptide / ID: 2 / Number of copies: 18 / 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 #3: Unknown protein fragment

MacromoleculeName: Unknown protein fragment / type: protein_or_peptide / ID: 3 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 4.103049 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)

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Macromolecule #4: IcmE protein

MacromoleculeName: IcmE protein / type: protein_or_peptide / ID: 4 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 107.911891 KDa
SequenceString: MASKKENLKS LFSNTRTRVI IIFTAALLII AVVIGFFKIR GATTGSIAAA EVSTVPGGIQ SIPGVLDPTA QYAKLQEEQN ITQAQVAEK TGGSAIPTII RTQALGEGVG VIGSQSGVGF AALAQEELGG PQRSLWIQEL QDGSCSKSVI TKVVNQGAQL T DLKAACSC ...String:
MASKKENLKS LFSNTRTRVI IIFTAALLII AVVIGFFKIR GATTGSIAAA EVSTVPGGIQ SIPGVLDPTA QYAKLQEEQN ITQAQVAEK TGGSAIPTII RTQALGEGVG VIGSQSGVGF AALAQEELGG PQRSLWIQEL QDGSCSKSVI TKVVNQGAQL T DLKAACSC VQLKDSGYGL QELEQVCECK ELKSAGYNAR QLKEAGYSAG RLRNCGFDAC ELRNAGFTAQ EMKDGGFSDG EL KGAGFSD AEIAKASGLP DGITADDVRK AGCGAAALAK LRQAGVSASA IRKISGCTAE QLKAAGYTAK ELKDAGFSAA DLR RAGFSA AELKDAGFTA RDLLNAGFTP ADLAKAGFSD AQIKAAQAEL PPGITPQDVK NAGCDVEALK KEREAGVSAA LIRQ YAGCS AQALKAAGFT DADLANAGFT PAQISAATPL SDAEIKAAGC DPDKLKKLFS AGVSAKRIKE LNGCSAEALK AAGYD AQSL LAAGFTPQEL LAAGFTPKQL EDAGLNPVSI IADGRVADCS VESLKKARAA GVSALTIKQT LGCSAAALKA AGYTAK ELK DAGFTAAELK AAGFSAKELK DAGFTAKELR DAGFSAQELK DVGFSAKDLK DAGFSAAELK AAGFTAAQLK AAGFSAK DL KDAGFSAAEL KAAGFSAKEL KDAGFSASDL KNAGFSAKEL KDAGFSASDL KSAGFSASEL KNAGYSADEL KKAGYTSA E LRNAGFSPQE SAVAGLQGPD LQQLDSSITG IPSIPGATPR PTTSDAASSA EQLQAILQKQ NEQLAEQKYQ QEIQQRTSD MLTAATQLVQ DWKQVETQVY TEGTEETKTS GGESAVPGTG TGTGSNNQPV DQGAVSAQNQ AIIKTGDIMF AVLDTSVNSD EPGPILATI VTGKLKGSKL IGSFNLPSNA DKMVITFNTM SIPGAEKTIS ISAYAIDPNT ARTALASRTN HHYLMRYGSL F ASSFLQGF GNAFQSANTT ITIGGTGGGN NITVANGVGR STLENAVIGL ATVGKAWSQQ AQQLFNTPTT VEVYSGTGLG IL FTQDVTT I

UniProtKB: IcmE 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43907
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7mue:
Legionella pneumophila Dot/Icm T4SS PR

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