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- PDB-9spg: Native N.meningitidis PorB bound to the N-terminal domain of rmpM -

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Basic information

Entry
Database: PDB / ID: 9spg
TitleNative N.meningitidis PorB bound to the N-terminal domain of rmpM
Components
  • Major outer membrane protein P.IB
  • Outer-membrane protein class 4
KeywordsMEMBRANE PROTEIN / Beta-barrel / trimer / porin / outer membrane
Function / homology
Function and homology information


porin activity / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Porin, Neisseria sp. type / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / : ...Porin, Neisseria sp. type / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / : / : / OmpA-like domain profile. / OmpA family / OmpA-like domain / OmpA-like domain superfamily / Porin domain superfamily
Similarity search - Domain/homology
Outer-membrane protein class 4 / Major outer membrane protein P.IB
Similarity search - Component
Biological speciesNeisseria meningitidis 8013 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 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 Neisseria meningitidis full length PilQ in the context of the bacterial envelope
Authors: Fernandez-Martinez, D. / Deist, P. / Morozova, T. / Nouchikian, L. / Goussard, S. / Nishiguchi, D. / Rey, M. / Boneca, I. / Tahara, Y.O. / Miyata, M. / Bonomi, M. / Chamot-Rooke, J. / Dumenil, G.
History
DepositionSep 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 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: Major outer membrane protein P.IB
B: Major outer membrane protein P.IB
C: Major outer membrane protein P.IB
D: Outer-membrane protein class 4


Theoretical massNumber of molelcules
Total (without water)141,6904
Polymers141,6904
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Major outer membrane protein P.IB / Porin


Mass: 38561.969 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Neisseria meningitidis 8013 (bacteria) / References: UniProt: A0A9K2PSB6
#2: Protein Outer-membrane protein class 4


Mass: 26004.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: N-terminal domain / Source: (natural) Neisseria meningitidis 8013 (bacteria) / References: UniProt: A0A9K2KNB1
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: Ternary complex of the native porB trimer with the N-terminal domain of rmpM
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Neisseria meningitidis 8013 (bacteria)
Buffer solutionpH: 7.4
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 300 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3particle selection
2EPUimage acquisition
4cryoSPARC3CTF correction
7Coot0.9.8.96model fitting
9cryoSPARC3initial Euler assignment
10cryoSPARC3final Euler assignment
11cryoSPARCclassification
12cryoSPARC33D reconstruction
13PHENIX2.0_5793:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91290 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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