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- PDB-9sh2: Neisseria meningitidis Native PilQ tetradecamer -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9sh2
TitleNeisseria meningitidis Native PilQ tetradecamer
ComponentsType IV pilus biogenesis and competence protein PilQ
KeywordsMEMBRANE PROTEIN / Secretin / Barrel / Outer Membrane / Secretion
Function / homology
Function and homology information


establishment of competence for transformation / 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 II secretion system protein GspD, conserved site ...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
Similarity search - Domain/homology
Type IV pilus biogenesis and competence protein PilQ
Similarity search - Component
Biological speciesNeisseria meningitidis 8013 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.14 Å
AuthorsFernandez-Martinez, D. / Dumenil, G.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR 18 CE11 0022 France
CitationJournal: To Be Published
Title: Structural organization of the PilQ secretins network of interactions in the Neisseria meningitidis bacterial envelope
Authors: Fernandez-Martinez, D. / Nouchikian, L. / Goussard, S. / Deist, P. / Morozova, T. / Nishiguchi, D. / Miyata, M. / England, P. / Bonomi, M. / Chamot-Rooke, J. / Dumenil, G.
History
DepositionAug 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type IV pilus biogenesis and competence protein PilQ
B: Type IV pilus biogenesis and competence protein PilQ
C: Type IV pilus biogenesis and competence protein PilQ
D: Type IV pilus biogenesis and competence protein PilQ
E: Type IV pilus biogenesis and competence protein PilQ
F: Type IV pilus biogenesis and competence protein PilQ
G: Type IV pilus biogenesis and competence protein PilQ
H: Type IV pilus biogenesis and competence protein PilQ
I: Type IV pilus biogenesis and competence protein PilQ
J: Type IV pilus biogenesis and competence protein PilQ
K: Type IV pilus biogenesis and competence protein PilQ
L: Type IV pilus biogenesis and competence protein PilQ
M: Type IV pilus biogenesis and competence protein PilQ
N: Type IV pilus biogenesis and competence protein PilQ


Theoretical massNumber of molelcules
Total (without water)1,149,25014
Polymers1,149,25014
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, C14
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Type IV pilus biogenesis and competence protein PilQ


Mass: 82089.297 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis 8013 (bacteria) / Gene: pilQ, NMV_1972 / Production host: Neisseria meningitidis 8013 (bacteria) / References: UniProt: A0A9K2PSI0
Has protein modificationY

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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: Protomer of the tetradecamer secretin PilQ of Neisseria meningitidis
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Neisseria meningitidis 8013 (bacteria)
Source (recombinant)Organism: Neisseria meningitidis 8013 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
9PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1014078
SymmetryPoint symmetry: C14 (14 fold cyclic)
3D reconstructionResolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154572 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00243568
ELECTRON MICROSCOPYf_angle_d0.55358842
ELECTRON MICROSCOPYf_dihedral_angle_d3.6875936
ELECTRON MICROSCOPYf_chiral_restr0.0447098
ELECTRON MICROSCOPYf_plane_restr0.0037588

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