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- PDB-6x64: Legionella pneumophila Dot T4SS PR -

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Entry
Database: PDB / ID: 6x64
TitleLegionella pneumophila Dot T4SS PR
ComponentsType IV secretion system unknown protein fragmentSecretion
KeywordsPROTEIN TRANSPORT / Secretion / Dot
Biological speciesLegionella pneumophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDurie, C.L. / Sheedlo, M.J. / Chung, J.M. / Byrne, B.G. / Su, M. / Knight, T. / Swanson, M.S. / Lacy, D.B. / Ohi, M.D.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150027-01 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)2T32DK007673 United States
National Institutes of Health/Office of the DirectorS10OD020011 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129539 United States
Other privateSF349247 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI095755-10 United States
Other government1I01BX004447 United States
CitationJournal: Elife / Year: 2020
Title: Structural analysis of the Dot/Icm type IV secretion system core complex.
Authors: Clarissa L Durie / Michael J Sheedlo / Jeong Min Chung / Brenda G Byrne / Min Su / Thomas Knight / Michele Swanson / D Borden Lacy / Melanie D Ohi /
Abstract: is an opportunistic pathogen that causes the potentially fatal pneumonia Legionnaires' Disease. This infection and subsequent pathology require the Dot/Icm Type IV Secretion System (T4SS) to deliver ... is an opportunistic pathogen that causes the potentially fatal pneumonia Legionnaires' Disease. This infection and subsequent pathology require the Dot/Icm Type IV Secretion System (T4SS) to deliver effector proteins into host cells. Compared to prototypical T4SSs, the Dot/Icm assembly is much larger, containing ~27 different components including a core complex reported to be composed of five proteins: DotC, DotD, DotF, DotG, and DotH. Using single particle cryo-electron microscopy (cryo-EM), we report reconstructions of the core complex of the Dot/Icm T4SS that includes a symmetry mismatch between distinct structural features of the outer membrane cap (OMC) and periplasmic ring (PR). We present models of known core complex proteins, DotC, DotD, and DotH, and two structurally similar proteins within the core complex, DotK and Lpg0657. This analysis reveals the stoichiometry and contact interfaces between the key proteins of the Dot/Icm T4SS core complex and provides a framework for understanding a complex molecular machine.
History
DepositionMay 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
AV: Type IV secretion system unknown protein fragment
AW: Type IV secretion system unknown protein fragment
BV: Type IV secretion system unknown protein fragment
BW: Type IV secretion system unknown protein fragment
CV: Type IV secretion system unknown protein fragment
CW: Type IV secretion system unknown protein fragment
DV: Type IV secretion system unknown protein fragment
DW: Type IV secretion system unknown protein fragment
EV: Type IV secretion system unknown protein fragment
EW: Type IV secretion system unknown protein fragment
FV: Type IV secretion system unknown protein fragment
FW: Type IV secretion system unknown protein fragment
GV: Type IV secretion system unknown protein fragment
GW: Type IV secretion system unknown protein fragment
HV: Type IV secretion system unknown protein fragment
HW: Type IV secretion system unknown protein fragment
IV: Type IV secretion system unknown protein fragment
IW: Type IV secretion system unknown protein fragment
JV: Type IV secretion system unknown protein fragment
JW: Type IV secretion system unknown protein fragment
KV: Type IV secretion system unknown protein fragment
KW: Type IV secretion system unknown protein fragment
LV: Type IV secretion system unknown protein fragment
LW: Type IV secretion system unknown protein fragment
MV: Type IV secretion system unknown protein fragment
MW: Type IV secretion system unknown protein fragment
NV: Type IV secretion system unknown protein fragment
NW: Type IV secretion system unknown protein fragment
OV: Type IV secretion system unknown protein fragment
OW: Type IV secretion system unknown protein fragment
PV: Type IV secretion system unknown protein fragment
PW: Type IV secretion system unknown protein fragment
QV: Type IV secretion system unknown protein fragment
QW: Type IV secretion system unknown protein fragment
RV: Type IV secretion system unknown protein fragment
RW: Type IV secretion system unknown protein fragment


Theoretical massNumber of molelcules
Total (without water)1,011,69036
Polymers1,011,69036
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area45440 Å2
ΔGint-490 kcal/mol
Surface area163260 Å2

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Components

#1: Protein ...
Type IV secretion system unknown protein fragment / Secretion / T4SS


Mass: 28102.492 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) Legionella pneumophila (bacteria)
Sequence detailsThe authors state that the sequences are unknown. The sample was imaged from a purification that ...The authors state that the sequences are unknown. The sample was imaged from a purification that was derived directly from L. pneumophila and the polymer chains could not be identified.

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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 T4SS PR / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Legionella pneumophila (bacteria)
Buffer solutionpH: 7
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 FIELDBright-field microscopy
Image recordingElectron dose: 58.1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 771806
SymmetryPoint symmetry: C18 (18 fold cyclic)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6850 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 60.71 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00715804
ELECTRON MICROSCOPYf_angle_d0.996222068
ELECTRON MICROSCOPYf_chiral_restr0.04243168
ELECTRON MICROSCOPYf_plane_restr0.00713132
ELECTRON MICROSCOPYf_dihedral_angle_d9.32163132

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