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- PDB-3jc8: Architectural model of the type IVa pilus machine in a piliated state -

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Basic information

Entry
Database: PDB / ID: 3jc8
TitleArchitectural model of the type IVa pilus machine in a piliated state
Components
  • LysM domain protein
  • PilA
  • PilN
  • PilO
  • PilP
  • PilQ
  • Type 4 fimbrial assembly protein PilC
  • Type IV pilus biogenesis protein PilM
  • Type IV-A pilus assembly ATPase PilB
KeywordsMOTOR PROTEIN / motor / pilus / ring / membrane channel
Function / homology
Function and homology information


type IV pilus assembly / type IV pilus-dependent motility / pilus assembly / protein secretion / cell outer membrane / cell division / ATP hydrolysis activity / ATP binding / membrane / metal ion binding ...type IV pilus assembly / type IV pilus-dependent motility / pilus assembly / protein secretion / cell outer membrane / cell division / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm
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 / ATPase, type IV, pilus assembly, PilB ...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 / ATPase, type IV, pilus assembly, PilB / 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 / Type II secretion system protein GspE, N-terminal / MshEN domain / Cell division protein FtsA / Type II secretion system protein GspE, N-terminal superfamily / Secretin and TonB N terminus short domain / Bacterial type II secretion system protein E signature. / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / GspD/PilQ family / Type II/IV secretion system protein / Type II/IV secretion system protein / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Type IV pilus assembly ATPase PilB / 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_imaging_optics / em_software
Item: _em_imaging_optics.energyfilter_name / _em_software.image_processing_id

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Assembly

Deposited unit
Aa: PilA
Ab: PilA
Ac: PilA
Ad: PilA
Ae: PilA
Af: PilA
Ag: PilA
Ah: PilA
Ai: PilA
Aj: PilA
Ak: PilA
Al: PilA
Am: PilA
An: PilA
Ao: PilA
Ap: PilA
Aq: PilA
Ar: PilA
As: PilA
At: PilA
Au: PilA
Av: PilA
Aw: PilA
Ax: PilA
Ay: PilA
Az: PilA
A1: PilA
A2: PilA
A3: PilA
A4: PilA
A5: PilA
A6: PilA
A7: PilA
A8: PilA
A9: PilA
Ba: Type IV-A pilus assembly ATPase PilB
Bb: Type IV-A pilus assembly ATPase PilB
Bc: Type IV-A pilus assembly ATPase PilB
Bd: Type IV-A pilus assembly ATPase PilB
Be: Type IV-A pilus assembly ATPase PilB
Bf: Type IV-A pilus assembly ATPase PilB
Ca: Type 4 fimbrial assembly protein PilC
Cb: Type 4 fimbrial assembly protein PilC
Na: PilN
Oa: PilO
Ma: Type IV pilus biogenesis protein PilM
Nb: PilN
Ob: PilO
Mb: Type IV pilus biogenesis protein PilM
Nc: PilN
Oc: PilO
Mc: Type IV pilus biogenesis protein PilM
Nd: PilN
Od: PilO
Md: Type IV pilus biogenesis protein PilM
Ne: PilN
Oe: PilO
Me: Type IV pilus biogenesis protein PilM
Nf: PilN
Of: PilO
Mf: Type IV pilus biogenesis protein PilM
Ng: PilN
Og: PilO
Mg: Type IV pilus biogenesis protein PilM
Nh: PilN
Oh: PilO
Mh: Type IV pilus biogenesis protein PilM
Ni: PilN
Oi: PilO
Mi: Type IV pilus biogenesis protein PilM
Nj: PilN
Oj: PilO
Mj: Type IV pilus biogenesis protein PilM
Nk: PilN
Ok: PilO
Mk: Type IV pilus biogenesis protein PilM
Nl: PilN
Ol: PilO
Ml: Type IV pilus biogenesis protein 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: LysM domain protein
Tb: LysM domain protein
Tc: LysM domain protein
Td: LysM domain protein
Te: LysM domain protein
Tf: LysM domain protein
Tg: LysM domain protein
Th: LysM domain protein
Ti: LysM domain protein
Tj: LysM domain protein
Tk: LysM domain protein
Tl: LysM domain protein


Theoretical massNumber of molelcules
Total (without water)4,057,982115
Polymers4,057,982115
Non-polymers00
Water0
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 , 9 types, 115 molecules AaAbAcAdAeAfAgAhAiAjAkAlAmAnAoApAqArAsAtAuAvAwAxAyAzA1A2A3A4...

#1: Protein ...
PilA


Mass: 17210.494 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Source: (natural) Myxococcus xanthus DK 1622 (bacteria)
#2: Protein
Type IV-A pilus assembly ATPase PilB


Mass: 62618.117 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Myxococcus xanthus DK 1622 (bacteria) / References: UniProt: Q1D098
#3: Protein Type 4 fimbrial assembly 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
#4: Protein
PilN / Type IV pilus biogenesis 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
#5: Protein
PilO / Type IV pilus biogenesis 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
#6: Protein
Type IV pilus biogenesis 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
#7: 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
#8: 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
#9: Protein
LysM domain protein /


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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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: Aug 26, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 27500 X / Cs: 2.2 mm
Specimen holderSpecimen holder type: GATAN LIQUID NITROGEN / Temperature: 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 name: GIF / Energyfilter 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. atoms107640 0 0 0 107640

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