9NGV image
Deposition Date 2025-02-22
Release Date 2025-09-17
Last Version Date 2025-09-17
Entry Detail
PDB ID:
9NGV
Keywords:
PROTEIN TRANSPORT
Title:
In situ cryo-EM structure of periplasmic ring (PR) of the Legionella Dot/Icm T4SS machine.
Biological Source:
Source Organism:
Legionella pneumophila subsp. pneumophila (Taxon ID: 91891)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.04 Å
Aggregation State:
CELL
Reconstruction Method:
SINGLE PARTICLE
9NGV validation report
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:unknown peptide A
Chain IDs:A (auth: Aa), H (auth: Ah), O (auth: Ao), V (auth: Av), CA (auth: Bc), JA (auth: Bj), QA (auth: Bq), XA (auth: Bx), EB (auth: Ce), LB (auth: Cl), SB (auth: Cs), ZB (auth: Cz), GC (auth: Dg), NC (auth: Dn), UC (auth: Du), BD (auth: Eb), ID (auth: Ei), PD (auth: Ep)
Chain Length:16
Number of Molecules:18
Biological Source:Legionella pneumophila subsp. pneumophila
Polymer Type:polypeptide(L)
Molecule:unknown peptide B
Chain IDs:B (auth: Ab), I (auth: Ai), P (auth: Ap), W (auth: Aw), DA (auth: Bd), KA (auth: Bk), RA (auth: Br), YA (auth: By), FB (auth: Cf), MB (auth: Cm), TB (auth: Ct), AC (auth: Da), HC (auth: Dh), OC (auth: Do), VC (auth: Dv), CD (auth: Ec), JD (auth: Ej), QD (auth: Eq)
Chain Length:9
Number of Molecules:18
Biological Source:Legionella pneumophila subsp. pneumophila
Polymer Type:polypeptide(L)
Molecule:unknown peptide C
Chain IDs:C (auth: Ac), J (auth: Aj), Q (auth: Aq), X (auth: Ax), EA (auth: Be), LA (auth: Bl), SA (auth: Bs), ZA (auth: Bz), GB (auth: Cg), NB (auth: Cn), UB (auth: Cu), BC (auth: Db), IC (auth: Di), PC (auth: Dp), WC (auth: Dw), DD (auth: Ed), KD (auth: Ek), RD (auth: Er)
Chain Length:16
Number of Molecules:18
Biological Source:Legionella pneumophila subsp. pneumophila
Polymer Type:polypeptide(L)
Molecule:unknown peptide D
Chain IDs:D (auth: Ad), K (auth: Ak), R (auth: Ar), Y (auth: Ay), FA (auth: Bf), MA (auth: Bm), TA (auth: Bt), AB (auth: Ca), HB (auth: Ch), OB (auth: Co), VB (auth: Cv), CC (auth: Dc), JC (auth: Dj), QC (auth: Dq), XC (auth: Dx), ED (auth: Ee), LD (auth: El), SD (auth: Es)
Chain Length:5
Number of Molecules:18
Biological Source:Legionella pneumophila subsp. pneumophila
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:IcmG (DotF)
Gene (Uniprot):icmG
Chain IDs:E (auth: Ae), L (auth: Al), S (auth: As), Z (auth: Az), GA (auth: Bg), NA (auth: Bn), UA (auth: Bu), BB (auth: Cb), IB (auth: Ci), PB (auth: Cp), WB (auth: Cw), DC (auth: Dd), KC (auth: Dk), RC (auth: Dr), YC (auth: Dy), FD (auth: Ef), MD (auth: Em), TD (auth: Et)
Chain Length:269
Number of Molecules:18
Biological Source:Legionella pneumophila subsp. pneumophila
UniProt ID:Q5ZYC0
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:IcmE (DotG)
Gene (Uniprot):icmE
Chain IDs:F (auth: Af), M (auth: Am), T (auth: At), AA (auth: Ba), HA (auth: Bh), OA (auth: Bo), VA (auth: Bv), CB (auth: Cc), JB (auth: Cj), QB (auth: Cq), XB (auth: Cx), EC (auth: De), LC (auth: Dl), SC (auth: Ds), ZC (auth: Dz), GD (auth: Eg), ND (auth: En), UD (auth: Eu)
Chain Length:1048
Number of Molecules:18
Biological Source:Legionella pneumophila subsp. pneumophila
UniProt ID:Q5ZYC1 Pfam ID:PF13599, PF03743
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:IcmK (DotH)
Gene (Uniprot):icmK
Chain IDs:G (auth: Ag), N (auth: An), U (auth: Au), BA (auth: Bb), IA (auth: Bi), PA (auth: Bp), WA (auth: Bw), DB (auth: Cd), KB (auth: Ck), RB (auth: Cr), YB (auth: Cy), FC (auth: Df), MC (auth: Dm), TC (auth: Dt), AD (auth: Ea), HD (auth: Eh), OD (auth: Eo), VD (auth: Ev)
Chain Length:361
Number of Molecules:18
Biological Source:Legionella pneumophila subsp. pneumophila
UniProt ID:Q5ZYC2 Pfam ID:PF12293
Ligand Molecules
NA
Primary Citation
In-situ structures of the Legionella Dot/Icm T4SS identify the DotA-IcmX complex as the gatekeeper for effector translocation.
Biorxiv ? ? ? (2025)
PMID: 40666918 DOI: 10.1101/2025.06.23.660953

Abstact

The Dot/Icm machine in Legionella pneumophila 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 in-situ 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.

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Primary Citation of related structures
9NGV