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- EMDB-49394: In-situ cryo-EM structure of periplasmic ring (PR) of the Dot/Icm... -

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Basic information

Entry
Database: EMDB / ID: EMD-49394
TitleIn-situ cryo-EM structure of periplasmic ring (PR) of the Dot/Icm machine
Map datastructure of periplasmic ring (PR) of the Dot/Icm machine
Sample
  • Complex: periplasmic ring (PR)
    • Protein or peptide: unknown peptide A
    • Protein or peptide: unknown peptide B
    • Protein or peptide: unknown peptide C
    • Protein or peptide: unknown peptide D
    • Protein or peptide: IcmG (DotF)
    • Protein or peptide: IcmE (DotG)
    • Protein or peptide: IcmK (DotH)
KeywordsType IVB Dot/Icm Secretion Machine / PROTEIN TRANSPORT
Function / homology
Function and homology information


: / : / Decapeptide repeat region / Putative outer membrane core complex of type IVb secretion / Putative outer membrane core complex of type IVb secretion / 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
IcmG (DotF) / IcmE (DotG) / IcmK (DotH)
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsYue J / Jun L
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_49394.png

Downloads & links

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Map

FileDownload / File: emd_49394.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of periplasmic ring (PR) 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-1.763983 - 2.5032604
Average (Standard dev.)0.006742055 (±0.049149875)
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_49394_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_49394_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 : periplasmic ring (PR)

EntireName: periplasmic ring (PR)
Components
  • Complex: periplasmic ring (PR)
    • Protein or peptide: unknown peptide A
    • Protein or peptide: unknown peptide B
    • Protein or peptide: unknown peptide C
    • Protein or peptide: unknown peptide D
    • Protein or peptide: IcmG (DotF)
    • Protein or peptide: IcmE (DotG)
    • Protein or peptide: IcmK (DotH)

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Supramolecule #1: periplasmic ring (PR)

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

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Macromolecule #1: unknown peptide A

MacromoleculeName: unknown peptide A / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila (bacteria)
Molecular weightTheoretical: 1.679849 KDa
SequenceString:
CTDAALAALE YHKSNA

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Macromolecule #2: unknown peptide B

MacromoleculeName: unknown peptide B / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila (bacteria)
Molecular weightTheoretical: 910.095 Da
SequenceString:
CVSMIGGSR

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Macromolecule #3: unknown peptide C

MacromoleculeName: unknown peptide C / type: protein_or_peptide / ID: 3 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila (bacteria)
Molecular weightTheoretical: 1.775978 KDa
SequenceString:
RVSIGGTVYT AKKYDD

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Macromolecule #4: unknown peptide D

MacromoleculeName: unknown peptide D / type: protein_or_peptide / ID: 4 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila (bacteria)
Molecular weightTheoretical: 505.521 Da
SequenceString:
PFGAD

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Macromolecule #5: IcmG (DotF)

MacromoleculeName: IcmG (DotF) / type: protein_or_peptide / ID: 5 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. 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: IcmG (DotF)

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Macromolecule #6: IcmE (DotG)

MacromoleculeName: IcmE (DotG) / type: protein_or_peptide / ID: 6 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. 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 (DotG)

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Macromolecule #7: IcmK (DotH)

MacromoleculeName: IcmK (DotH) / type: protein_or_peptide / ID: 7 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. 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: IcmK (DotH)

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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: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76406
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9ngv:
In situ cryo-EM structure of periplasmic ring (PR) of the Legionella Dot/Icm T4SS machine.

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