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- EMDB-49399: In-situ cryo-EM structure of porinI of the Dot/Icm machine -

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Basic information

Entry
Database: EMDB / ID: EMD-49399
TitleIn-situ cryo-EM structure of porinI of the Dot/Icm machine
Map datastructure of porinI of the Dot/Icm machine
Sample
  • Complex: porinI
    • Protein or peptide: Major outer membrane protein
    • Protein or peptide: Outer membrane protein, OmpA family protein
    • Protein or peptide: LphA (DotK)
KeywordsType IVB Dot/Icm Secretion Machine / PROTEIN TRANSPORT
Function / homology
Function and homology information


Major outer membrane precursor, Legionella pneumophila-type / Legionella pneumophila major outer membrane protein precursor / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Major outer membrane protein / Outer membrane protein, OmpA family protein / LphA (DotK)
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 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 23, 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_49399.png

Downloads & links

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Map

FileDownload / File: emd_49399.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of porinI of the Dot/Icm machine
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 213.6 Å		1.07 Å/pix.
x 200 pix.
= 213.6 Å		1.07 Å/pix.
x 200 pix.
= 213.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.43931067 - 0.7013018
Average (Standard dev.)0.011225531 (±0.028468557)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 213.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_49399_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: Half Map B

Fileemd_49399_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : porinI

EntireName: porinI
Components
  • Complex: porinI
    • Protein or peptide: Major outer membrane protein
    • Protein or peptide: Outer membrane protein, OmpA family protein
    • Protein or peptide: LphA (DotK)

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Supramolecule #1: porinI

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

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Macromolecule #1: Major outer membrane protein

MacromoleculeName: Major outer membrane protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila (bacteria)
Molecular weightTheoretical: 32.155463 KDa
SequenceString: MFSLKKTAVA VLALGSGAVF AGTMGPVCTP GNVTVPCERT AWDIGITALY LQPIYDADWG YNGFTQVGGW RHWHDVDHEW DWGFKLEGS YHFNTGNDIN VNWYHFDNDS DHWFDFANWH NYNNKWDAVN AELGQFVDFS ANKKMRFHGG VQYARIEADV N RYFNNFAF ...String:
MFSLKKTAVA VLALGSGAVF AGTMGPVCTP GNVTVPCERT AWDIGITALY LQPIYDADWG YNGFTQVGGW RHWHDVDHEW DWGFKLEGS YHFNTGNDIN VNWYHFDNDS DHWFDFANWH NYNNKWDAVN AELGQFVDFS ANKKMRFHGG VQYARIEADV N RYFNNFAF NGFNSKFNGF GPRTGLDMNY VFGNGFGIYA KGAAAILVGT SDFYDGIGFV TGSKNAIVPE LEAKLGADYT YA MAQGDLT LDVGYMWFNY FNAMHNTATN GLETDFAASG PYIGLKYVGN V

UniProtKB: Major outer membrane protein

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Macromolecule #2: Outer membrane protein, OmpA family protein

MacromoleculeName: Outer membrane protein, OmpA family protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. 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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Macromolecule #3: LphA (DotK)

MacromoleculeName: LphA (DotK) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. 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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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: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 993337
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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