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- PDB-9ngu: In situ cryo-EM structure of outer membrane cap (OMC) of the Legi... -

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Basic information

Entry
Database: PDB / ID: 9ngu
TitleIn situ cryo-EM structure of outer membrane cap (OMC) of the Legionella Dot/Icm T4SS machine
Components
  • DotC
  • DotD
  • IcmG (DotF)
  • IcmK (DotH)
  • LphA (DotK)
  • Neurogenic locus notch protein homolog
  • Outer membrane protein, OmpA family protein
  • Putative auto-transporter adhesin head GIN domain-containing protein
  • Secreted protein
KeywordsPROTEIN TRANSPORT / Type IVB Dot/Icm Secretion Machine
Function / homology
Function and homology information


Putative auto-transporter adhesin, head GIN domain / Putative auto-transporter adhesin, head GIN domain / 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 / : ...Putative auto-transporter adhesin, head GIN domain / Putative auto-transporter adhesin, head GIN domain / 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
Secreted protein / Putative auto-transporter adhesin head GIN domain-containing protein / DotC / DotD / Neurogenic locus notch protein homolog / Outer membrane protein, OmpA family protein / IcmG (DotF) / IcmK (DotH) / LphA (DotK)
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsYue, J. / Jun, L.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Aa: DotD
Ab: LphA (DotK)
Ac: Putative auto-transporter adhesin head GIN domain-containing protein
Ad: Neurogenic locus notch protein homolog
Ae: DotD
Af: IcmG (DotF)
Ag: IcmK (DotH)
Ah: Outer membrane protein, OmpA family protein
Ai: DotC
Aj: Secreted protein
Ak: DotD
Al: LphA (DotK)
Am: Putative auto-transporter adhesin head GIN domain-containing protein
An: Neurogenic locus notch protein homolog
Ao: DotD
Ap: IcmG (DotF)
Aq: IcmK (DotH)
Ar: Outer membrane protein, OmpA family protein
As: DotC
At: Secreted protein
Au: DotD
Av: LphA (DotK)
Aw: Putative auto-transporter adhesin head GIN domain-containing protein
Ax: Neurogenic locus notch protein homolog
Ay: DotD
Az: IcmG (DotF)
Ba: IcmK (DotH)
Bb: Outer membrane protein, OmpA family protein
Bc: DotC
Bd: Secreted protein
Be: DotD
Bf: LphA (DotK)
Bg: Putative auto-transporter adhesin head GIN domain-containing protein
Bh: Neurogenic locus notch protein homolog
Bi: DotD
Bj: IcmG (DotF)
Bk: IcmK (DotH)
Bl: Outer membrane protein, OmpA family protein
Bm: DotC
Bn: Secreted protein
Bo: DotD
Bp: LphA (DotK)
Bq: Putative auto-transporter adhesin head GIN domain-containing protein
Br: Neurogenic locus notch protein homolog
Bs: DotD
Bt: IcmG (DotF)
Bu: IcmK (DotH)
Bv: Outer membrane protein, OmpA family protein
Bw: DotC
Bx: Secreted protein
By: DotD
Bz: LphA (DotK)
Ca: Putative auto-transporter adhesin head GIN domain-containing protein
Cb: Neurogenic locus notch protein homolog
Cc: DotD
Cd: IcmG (DotF)
Ce: IcmK (DotH)
Cf: Outer membrane protein, OmpA family protein
Cg: DotC
Ch: Secreted protein
Ci: DotD
Cj: LphA (DotK)
Ck: Putative auto-transporter adhesin head GIN domain-containing protein
Cl: Neurogenic locus notch protein homolog
Cm: DotD
Cn: IcmG (DotF)
Co: IcmK (DotH)
Cp: Outer membrane protein, OmpA family protein
Cq: DotC
Cr: Secreted protein
Cs: DotD
Ct: LphA (DotK)
Cu: Putative auto-transporter adhesin head GIN domain-containing protein
Cv: Neurogenic locus notch protein homolog
Cw: DotD
Cx: IcmG (DotF)
Cy: IcmK (DotH)
Cz: Outer membrane protein, OmpA family protein
Da: DotC
Db: Secreted protein
Dc: DotD
Dd: LphA (DotK)
De: Putative auto-transporter adhesin head GIN domain-containing protein
Df: Neurogenic locus notch protein homolog
Dg: DotD
Dh: IcmG (DotF)
Di: IcmK (DotH)
Dj: Outer membrane protein, OmpA family protein
Dk: DotC
Dl: Secreted protein
Dm: DotD
Dn: LphA (DotK)
Do: Putative auto-transporter adhesin head GIN domain-containing protein
Dp: Neurogenic locus notch protein homolog
Dq: DotD
Dr: IcmG (DotF)
Ds: IcmK (DotH)
Dt: Outer membrane protein, OmpA family protein
Du: DotC
Dv: Secreted protein
Dw: DotD
Dx: LphA (DotK)
Dy: Putative auto-transporter adhesin head GIN domain-containing protein
Dz: Neurogenic locus notch protein homolog
Ea: DotD
Eb: IcmG (DotF)
Ec: IcmK (DotH)
Ed: Outer membrane protein, OmpA family protein
Ee: DotC
Ef: Secreted protein
Eg: DotD
Eh: LphA (DotK)
Ei: Putative auto-transporter adhesin head GIN domain-containing protein
Ej: Neurogenic locus notch protein homolog
Ek: DotD
El: IcmG (DotF)
Em: IcmK (DotH)
En: Outer membrane protein, OmpA family protein
Eo: DotC
Ep: Secreted protein
Eq: DotD
Er: LphA (DotK)
Es: Putative auto-transporter adhesin head GIN domain-containing protein
Et: Neurogenic locus notch protein homolog
Eu: DotD
Ev: IcmG (DotF)
Ew: IcmK (DotH)
Ex: Outer membrane protein, OmpA family protein
Ey: DotC
Ez: Secreted protein


Theoretical massNumber of molelcules
Total (without water)3,214,815130
Polymers3,214,815130
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 9 types, 130 molecules AaAeAkAoAuAyBeBiBoBsByCcCiCmCsCwDcDgDmDqDwEaEgEkEqEuAbAlAvBf...

#1: Protein ...
DotD


Mass: 17860.678 Da / Num. of mol.: 26 / Source method: isolated from a natural source
Source: (natural) Legionella pneumophila subsp. pneumophila (bacteria)
References: UniProt: Q5ZS45
#2: Protein
LphA (DotK)


Mass: 21096.492 Da / Num. of mol.: 13 / Source method: isolated from a natural source
Source: (natural) Legionella pneumophila subsp. pneumophila (bacteria)
References: UniProt: Q5ZYC5
#3: Protein
Putative auto-transporter adhesin head GIN domain-containing protein


Mass: 36095.367 Da / Num. of mol.: 13 / Source method: isolated from a natural source
Source: (natural) Legionella pneumophila subsp. pneumophila (bacteria)
References: UniProt: Q5ZRN3
#4: Protein
Neurogenic locus notch protein homolog


Mass: 13598.854 Da / Num. of mol.: 13 / Source method: isolated from a natural source
Source: (natural) Legionella pneumophila subsp. pneumophila (bacteria)
References: UniProt: Q5ZXA9
#5: Protein
IcmG (DotF)


Mass: 29729.969 Da / Num. of mol.: 13 / Source method: isolated from a natural source
Source: (natural) Legionella pneumophila subsp. pneumophila (bacteria)
References: UniProt: Q5ZYC0
#6: Protein
IcmK (DotH)


Mass: 38958.926 Da / Num. of mol.: 13 / Source method: isolated from a natural source
Source: (natural) Legionella pneumophila subsp. pneumophila (bacteria)
References: UniProt: Q5ZYC2
#7: Protein
Outer membrane protein, OmpA family protein


Mass: 27582.047 Da / Num. of mol.: 13 / Source method: isolated from a natural source
Source: (natural) Legionella pneumophila subsp. pneumophila (bacteria)
References: UniProt: Q5ZXS4
#8: Protein
DotC


Mass: 34162.441 Da / Num. of mol.: 13 / Source method: isolated from a natural source
Source: (natural) Legionella pneumophila subsp. pneumophila (bacteria)
References: UniProt: Q5ZS44
#9: Protein
Secreted protein


Mass: 10348.009 Da / Num. of mol.: 13 / Source method: isolated from a natural source
Source: (natural) Legionella pneumophila subsp. pneumophila (bacteria)
References: UniProt: A0AAN5PM39

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: outer membrane cap (OMC) / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila (bacteria)
Buffer solutionpH: 6.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 12
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 73 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76409 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 70.6 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044150358
ELECTRON MICROSCOPYf_angle_d0.5999203632
ELECTRON MICROSCOPYf_chiral_restr0.045622997
ELECTRON MICROSCOPYf_plane_restr0.004226156
ELECTRON MICROSCOPYf_dihedral_angle_d6.36220982

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