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- PDB-3jc9: Architectural model of the type IVa pilus machine in a non-piliat... -

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Basic information

Entry
Database: PDB / ID: 3jc9
TitleArchitectural model of the type IVa pilus machine in a non-piliated state
Components
  • PilA
  • PilC
  • PilM
  • PilN
  • PilO
  • PilP
  • PilQ
  • TsaP
KeywordsMOTOR PROTEIN / motor / pilus / ring / membrane channel
Function / homology
Function and homology information


type IV pilus assembly / type IV pilus-dependent motility / protein secretion / cell outer membrane / cell division / membrane / plasma membrane
Similarity search - Function
Type IV pilus inner membrane component PilN / Fimbrial assembly protein (PilN) / Type IV pilus inner membrane component PilO / Pilus assembly protein, PilO / : / : / Type IV pilus inner membrane component PilM / Type IV pilus assembly protein PilM; / GspF/PilC family / Type IV pilus inner membrane component PilP ...Type IV pilus inner membrane component PilN / Fimbrial assembly protein (PilN) / Type IV pilus inner membrane component PilO / Pilus assembly protein, PilO / : / : / Type IV pilus inner membrane component PilM / Type IV pilus assembly protein PilM; / GspF/PilC family / Type IV pilus inner membrane component PilP / Type II secretion system protein GspF domain / Type II secretion system GspF domain superfamily / Type II secretion system (T2SS), protein F / Pilus assembly protein, PilP / Type IV pilus secretin PilQ / : / AMIN domain / AMIN domain / SHS2 domain inserted in FtsA / Cell division protein FtsA / : / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / GspD/PilQ family / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Translation elongation factor EF1B/ribosomal protein S6 / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Type IV pilus assembly protein PilC / Type IV pilus biogenesis protein PilM / LysM domain protein / PilP / PilO / PilN / PilQ
Similarity search - Component
Biological speciesMyxococcus xanthus DK 1622 (bacteria)
MethodELECTRON MICROSCOPY / electron tomography / cryo EM
AuthorsChang, Y.-W. / Rettberg, L.A. / Jensen, G.J.
CitationJournal: Science / Year: 2016
Title: Architecture of the type IVa pilus machine.
Authors: Yi-Wei Chang / Lee A Rettberg / Anke Treuner-Lange / Janet Iwasa / Lotte Søgaard-Andersen / Grant J Jensen /
Abstract: Type IVa pili are filamentous cell surface structures observed in many bacteria. They pull cells forward by extending, adhering to surfaces, and then retracting. We used cryo-electron tomography of ...Type IVa pili are filamentous cell surface structures observed in many bacteria. They pull cells forward by extending, adhering to surfaces, and then retracting. We used cryo-electron tomography of intact Myxococcus xanthus cells to visualize type IVa pili and the protein machine that assembles and retracts them (the type IVa pilus machine, or T4PM) in situ, in both the piliated and nonpiliated states, at a resolution of 3 to 4 nanometers. We found that T4PM comprises an outer membrane pore, four interconnected ring structures in the periplasm and cytoplasm, a cytoplasmic disc and dome, and a periplasmic stem. By systematically imaging mutants lacking defined T4PM proteins or with individual proteins fused to tags, we mapped the locations of all 10 T4PM core components and the minor pilins, thereby providing insights into pilus assembly, structure, and function.
History
DepositionNov 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id

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Assembly

Deposited unit
Aa: PilA
Ab: PilA
Ac: PilA
Ad: PilA
Ae: PilA
Ca: PilC
Cb: PilC
Na: PilN
Oa: PilO
Ma: PilM
Nb: PilN
Ob: PilO
Mb: PilM
Nc: PilN
Oc: PilO
Mc: PilM
Nd: PilN
Od: PilO
Md: PilM
Ne: PilN
Oe: PilO
Me: PilM
Nf: PilN
Of: PilO
Mf: PilM
Ng: PilN
Og: PilO
Mg: PilM
Nh: PilN
Oh: PilO
Mh: PilM
Ni: PilN
Oi: PilO
Mi: PilM
Nj: PilN
Oj: PilO
Mj: PilM
Nk: PilN
Ok: PilO
Mk: PilM
Nl: PilN
Ol: PilO
Ml: PilM
Qa: PilQ
Pa: PilP
Qb: PilQ
Pb: PilP
Qc: PilQ
Pc: PilP
Qd: PilQ
Pd: PilP
Qe: PilQ
Pe: PilP
Qf: PilQ
Pf: PilP
Qg: PilQ
Pg: PilP
Qh: PilQ
Ph: PilP
Qi: PilQ
Pi: PilP
Qj: PilQ
Pj: PilP
Qk: PilQ
Pk: PilP
Ql: PilQ
Pl: PilP
Ta: TsaP
Tb: TsaP
Tc: TsaP
Td: TsaP
Te: TsaP
Tf: TsaP
Tg: TsaP
Th: TsaP
Ti: TsaP
Tj: TsaP
Tk: TsaP
Tl: TsaP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,172,336103
Polymers3,165,95879
Non-polymers6,37824
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 8 types, 79 molecules AaAbAcAdAeCaCbNaNbNcNdNeNfNgNhNiNjNkNlOaObOcOdOeOfOgOhOiOjOk...

#1: Protein
PilA


Mass: 17210.494 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Myxococcus xanthus DK 1622 (bacteria)
#2: Protein PilC


Mass: 45191.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Myxococcus xanthus DK 1622 (bacteria) / References: UniProt: Q1D0A0
#3: Protein
PilN


Mass: 24889.914 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Myxococcus xanthus DK 1622 (bacteria) / References: UniProt: Q306N5
#4: Protein
PilO


Mass: 22911.150 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Myxococcus xanthus DK 1622 (bacteria) / References: UniProt: Q306N4
#5: Protein
PilM


Mass: 42267.102 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Myxococcus xanthus DK 1622 (bacteria) / References: UniProt: Q1D0B0
#6: Protein
PilQ


Mass: 96199.984 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Myxococcus xanthus DK 1622 (bacteria) / References: UniProt: Q9ZFG1
#7: Protein
PilP


Mass: 18154.627 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Myxococcus xanthus DK 1622 (bacteria) / References: UniProt: Q306N3
#8: Protein
TsaP


Mass: 44704.219 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Myxococcus xanthus DK 1622 (bacteria) / References: UniProt: Q1D813

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Non-polymers , 2 types, 24 molecules

#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#10: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: electron tomography

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Sample preparation

ComponentName: Type IVa pilus machine in vivo / Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE
Details: Plunged into liquid ethane (FEI VITROBOT MARK III).

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Dec 31, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 27500 X / Cs: 2.2 mm
Specimen holderTemperature: 77 K / Tilt angle max: -60 ° / Tilt angle min: 60 °
Image recordingElectron dose: 150 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter upper: 20 eV / Energyfilter lower: 0 eV

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Processing

EM software
IDNameCategory
1IMOD3D reconstruction
2PEET3D reconstruction
3TOMO3D3D reconstruction
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionMethod: Simultaneous iterative reconstruction technique / Nominal pixel size: 7.8 Å / Actual pixel size: 7.8 Å / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms77832 0 384 0 78216

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