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- PDB-6ve2: Tetradecameric PilQ bound by TsaP heptamer from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6ve2
TitleTetradecameric PilQ bound by TsaP heptamer from Pseudomonas aeruginosa
Components
  • Fimbrial assembly protein PilQ
  • LysM domain-containing protein
KeywordsPROTEIN TRANSPORT / Type IV pilus / T4P / PilQ / TsaP / secretin / pilotin / type IVa pilus / T4aP / pilus / outer membrane / periplasm / bacterial secretion system
Function / homology
Function and homology information


type IV pilus assembly / protein secretion / cell outer membrane
Similarity search - Function
Type IV pilus secretin PilQ / : / : / AMIN domain / AMIN domain / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. ...Type IV pilus secretin PilQ / : / : / AMIN domain / AMIN domain / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / 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 / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain
Similarity search - Domain/homology
Fimbrial assembly protein PilQ / LysM domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsMcCallum, M. / Tammam, S. / Rubinstein, J.L. / Burrows, L.L. / Howell, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Structure / Year: 2021
Title: CryoEM map of Pseudomonas aeruginosa PilQ enables structural characterization of TsaP.
Authors: Matthew McCallum / Stephanie Tammam / John L Rubinstein / Lori L Burrows / P Lynne Howell /
Abstract: The type IV pilus machinery is a multi-protein complex that polymerizes and depolymerizes a pilus fiber used for attachment, twitching motility, phage adsorption, natural competence, protein ...The type IV pilus machinery is a multi-protein complex that polymerizes and depolymerizes a pilus fiber used for attachment, twitching motility, phage adsorption, natural competence, protein secretion, and surface-sensing. An outer membrane secretin pore is required for passage of the pilus fiber out of the cell. Herein, the structure of the tetradecameric secretin, PilQ, from the Pseudomonas aeruginosa type IVa pilus system was determined to 4.3 Å and 4.4 Å resolution in the presence and absence of C symmetric spikes, respectively. The heptameric spikes were found to be two tandem C-terminal domains of TsaP. TsaP forms a belt around PilQ and while it is not essential for twitching motility, overexpression of TsaP triggers a signal cascade upstream of PilY1 leading to cyclic di-GMP up-regulation. These results resolve the identity of the spikes identified with Proteobacterial PilQ homologs and may reveal a new component of the surface-sensing cyclic di-GMP signal cascade.
History
DepositionDec 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Fimbrial assembly protein PilQ
B: Fimbrial assembly protein PilQ
C: Fimbrial assembly protein PilQ
D: Fimbrial assembly protein PilQ
E: Fimbrial assembly protein PilQ
F: Fimbrial assembly protein PilQ
G: Fimbrial assembly protein PilQ
H: Fimbrial assembly protein PilQ
I: Fimbrial assembly protein PilQ
J: Fimbrial assembly protein PilQ
K: Fimbrial assembly protein PilQ
L: Fimbrial assembly protein PilQ
M: Fimbrial assembly protein PilQ
N: Fimbrial assembly protein PilQ
O: LysM domain-containing protein
P: LysM domain-containing protein
Q: LysM domain-containing protein
R: LysM domain-containing protein
S: LysM domain-containing protein
T: LysM domain-containing protein
U: LysM domain-containing protein


Theoretical massNumber of molelcules
Total (without water)1,379,66621
Polymers1,379,66621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Fimbrial assembly protein PilQ


Mass: 79731.141 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: pilQ, PA5040 / Production host: Pseudomonas aeruginosa PAO1 (bacteria)
Strain (production host): ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: P34750
#2: Protein
LysM domain-containing protein


Mass: 37632.902 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA0020 / Production host: Pseudomonas aeruginosa PAO1 (bacteria)
Strain (production host): ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9I7A7

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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: PilQ with TsaP / Type: COMPLEX / Details: Affinity purified PilQ with pulled-down TsaP / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Source (recombinant)Organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 35.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
7Cootmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
19PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47468 / Symmetry type: POINT
Atomic model buildingB value: 98 / Protocol: FLEXIBLE FIT / Space: REAL

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