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- EMDB-49395: In-situ cryo-EM structure of Dome of the Dot/Icm machine -

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Basic information

Entry
Database: EMDB / ID: EMD-49395
TitleIn-situ cryo-EM structure of Dome of the Dot/Icm machine
Map datastructure of Dome of the Dot/Icm machine
Sample
  • Complex: Dome
    • Protein or peptide: IcmE (DotG)
KeywordsType IVB Dot/Icm Secretion Machine / PROTEIN TRANSPORT
Function / homology
Function and homology information


: / : / Decapeptide repeat region / Type IV secretion system, VirB10/TrbI / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI / Outer membrane protein/outer membrane enzyme PagP, beta-barrel
Similarity search - Domain/homology
Outer membrane protein beta-barrel domain-containing protein / IcmE (DotG)
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsYue J / Liu J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR01AI152421 United States
CitationJournal: bioRxiv / Year: 2025
Title: structures of the Dot/Icm T4SS identify the DotA-IcmX complex as the gatekeeper for effector translocation.
Authors: Jian Yue / Samira Heydari / Donghyun Park / David Chetrit / Shoichi Tachiyama / Wangbiao Guo / Jack M Botting / Shenping Wu / Craig R Roy / Jun Liu
Abstract: The Dot/Icm machine in is one of the most versatile type IV secretion systems (T4SSs), with a remarkable capacity to translocate over 330 different effector proteins across the bacterial envelope ...The Dot/Icm machine in is one of the most versatile type IV secretion systems (T4SSs), with a remarkable capacity to translocate over 330 different effector proteins across the bacterial envelope into host cells. At least 27 Dot and Icm proteins are required for assembly and function of the system, yet the architecture and activation mechanism remain poorly understood at the molecular level. Here, we deploy cryo-electron microscopy to reveal structures of the Dot/Icm machine at near-atomic resolution. Importantly, two proteins essential for effector translocation, DotA and IcmX, form a pentameric protochannel at an inactive state. Upon activation, the DotA-IcmX protochannel undergoes extensive rearrangements to form an extended transenvelope passage capable of transporting effector proteins from the bacterial cytoplasm into host cells as revealed by cryo-electron tomography. Collectively, our findings suggest that the DotA-IcmX complex functions as the gatekeeper for effector translocation of the Dot/Icm T4SS.
History
DepositionFeb 22, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49395.png

Downloads & links

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Map

FileDownload / File: emd_49395.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of Dome of the Dot/Icm machine
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 448 pix.
= 598.08 Å		1.34 Å/pix.
x 448 pix.
= 598.08 Å		1.34 Å/pix.
x 448 pix.
= 598.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.335 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.7239634 - 2.2843134
Average (Standard dev.)0.0067896596 (±0.04420675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 598.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_49395_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49395_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dome

EntireName: Dome
Components
  • Complex: Dome
    • Protein or peptide: IcmE (DotG)

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Supramolecule #1: Dome

SupramoleculeName: Dome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Legionella pneumophila subsp. pneumophila (bacteria)

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Macromolecule #1: IcmE (DotG)

MacromoleculeName: IcmE (DotG) / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila (bacteria)
Molecular weightTheoretical: 108.012031 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 NITVANGVRR STLENAVIGL ATVGKAWSQQ AQQLFNTPTT VEVYSGTGLG IL FTQDVTT I

UniProtKB: IcmE (DotG)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 6.7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 73.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76400
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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