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- PDB-7mue: Legionella pneumophila Dot/Icm T4SS PR -

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Basic information

Entry
Database: PDB / ID: 7mue
TitleLegionella pneumophila Dot/Icm T4SS PR
Components
  • DotF
  • IcmE protein
  • Type IV secretion protein IcmK
  • Unknown protein fragment
KeywordsTRANSLOCASE / Dot/Icm / Secretion / T4SS
Function / homology
Function and homology information


: / Putative outer membrane core complex of type IVb secretion / Putative outer membrane core complex of type IVb secretion / Pentapeptide repeats (9 copies) / Pentapeptide repeat / 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
Type IV secretion protein IcmK / IcmE protein / DotF
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSheedlo, M.J. / Durie, C.L. / Swanson, M. / Lacy, D.B. / Ohi, M.D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI118932 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32 AI150027-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2T32DK007673 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD020011 United States
CitationJournal: Elife / Year: 2021
Title: Cryo-EM reveals new species-specific proteins and symmetry elements in the Dot/Icm T4SS.
Authors: Michael J Sheedlo / Clarissa L Durie / Jeong Min Chung / Louise Chang / Jacquelyn Roberts / Michele Swanson / Dana Borden Lacy / Melanie D Ohi /
Abstract: is an opportunistic pathogen that causes the potentially fatal pneumonia known as Legionnaires' disease. The pathology associated with infection depends on bacterial delivery of effector proteins ... is an opportunistic pathogen that causes the potentially fatal pneumonia known as Legionnaires' disease. The pathology associated with infection depends on bacterial delivery of effector proteins into the host via the membrane spanning Dot/Icm type IV secretion system (T4SS). We have determined sub-3.0 Å resolution maps of the Dot/Icm T4SS core complex by single particle cryo-EM. The high-resolution structural analysis has allowed us to identify proteins encoded outside the Dot/Icm genetic locus that contribute to the core T4SS structure. We can also now define two distinct areas of symmetry mismatch, one that connects the C18 periplasmic ring (PR) and the C13 outer membrane cap (OMC) and one that connects the C13 OMC with a 16-fold symmetric dome. Unexpectedly, the connection between the PR and OMC is DotH, with five copies sandwiched between the OMC and PR to accommodate the symmetry mismatch. Finally, we observe multiple conformations in the reconstructions that indicate flexibility within the structure.
History
DepositionMay 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
AF: DotF
XH: Type IV secretion protein IcmK
BF: DotF
YH: Type IV secretion protein IcmK
ZH: Type IV secretion protein IcmK
AX: Unknown protein fragment
BX: Unknown protein fragment
CX: Unknown protein fragment
DX: Unknown protein fragment
EX: Unknown protein fragment
FX: Unknown protein fragment
GX: Unknown protein fragment
HX: Unknown protein fragment
IX: Unknown protein fragment
JX: Unknown protein fragment
KX: Unknown protein fragment
LX: Unknown protein fragment
MX: Unknown protein fragment
VX: Unknown protein fragment
WX: Unknown protein fragment
XX: Unknown protein fragment
YX: Unknown protein fragment
ZX: Unknown protein fragment
CF: DotF
DF: DotF
EF: DotF
FF: DotF
IG: IcmE protein
GF: DotF
HF: DotF
IF: DotF
JF: DotF
KF: DotF
LF: DotF
MF: DotF
VF: DotF
WF: DotF
XF: DotF
YF: DotF
ZF: DotF
AG: IcmE protein
BG: IcmE protein
CG: IcmE protein
DG: IcmE protein
EG: IcmE protein
FG: IcmE protein
GG: IcmE protein
HG: IcmE protein
JG: IcmE protein
KG: IcmE protein
LG: IcmE protein
MG: IcmE protein
VG: IcmE protein
WG: IcmE protein
XG: IcmE protein
YG: IcmE protein
ZG: IcmE protein
AH: Type IV secretion protein IcmK
BH: Type IV secretion protein IcmK
CH: Type IV secretion protein IcmK
DH: Type IV secretion protein IcmK
EH: Type IV secretion protein IcmK
FH: Type IV secretion protein IcmK
GH: Type IV secretion protein IcmK
HH: Type IV secretion protein IcmK
IH: Type IV secretion protein IcmK
JH: Type IV secretion protein IcmK
KH: Type IV secretion protein IcmK
LH: Type IV secretion protein IcmK
MH: Type IV secretion protein IcmK
VH: Type IV secretion protein IcmK
WH: Type IV secretion protein IcmK


Theoretical massNumber of molelcules
Total (without water)3,252,66972
Polymers3,252,66972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area197620 Å2
ΔGint-1281 kcal/mol
Surface area213350 Å2

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Components

#1: Protein
DotF / IcmG protein / Type IV secretion protein IcmG


Mass: 29729.969 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: O54615
#2: Protein
Type IV secretion protein IcmK


Mass: 38958.926 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: A0A2S6FBG9
#3: Protein/peptide
Unknown protein fragment


Mass: 4103.049 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria)
#4: Protein
IcmE protein / Type IV secretion protein IcmE


Mass: 107911.891 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria) / References: UniProt: O53087
Sequence detailsThe protein fragment sequence could not be directly identified as the sample was purified from a ...The protein fragment sequence could not be directly identified as the sample was purified from a native source.

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Legionella pneumophila Dot/Icm T4SS PR / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Legionella pneumophila (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.1_4122refinement
PHENIX1.19.1_4122refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43907 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 57.01 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003440950
ELECTRON MICROSCOPYf_angle_d0.705955818
ELECTRON MICROSCOPYf_chiral_restr0.0496606
ELECTRON MICROSCOPYf_plane_restr0.00727218
ELECTRON MICROSCOPYf_dihedral_angle_d4.67455814

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