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- EMDB-55084: Native N.meningitidis PorB bound to the N-terminal domain of rmpM -

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Basic information

Entry
Database: EMDB / ID: EMD-55084
TitleNative N.meningitidis PorB bound to the N-terminal domain of rmpM
Map dataSharpened map of Neisseria meningitidis Native PorB-RmpM
Sample
  • Complex: Ternary complex of the native porB trimer with the N-terminal domain of rmpM
    • Protein or peptide: Major outer membrane protein P.IB
    • Protein or peptide: Outer-membrane protein class 4
KeywordsBeta-barrel / trimer / porin / outer membrane / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsFernandez-Martinez D / Dumenil G
Funding support France, 1 items
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 YO / Miyata M / Bonomi M / Chamot-Rooke J / Dumenil G
History
DepositionSep 17, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55084.png

Downloads & links

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Map

FileDownload / File: emd_55084.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of Neisseria meningitidis Native PorB-RmpM
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.276
Minimum - Maximum-1.3216212 - 1.8292705
Average (Standard dev.)-0.000117768905 (±0.02457777)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 380.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55084_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Raw map of Neisseria meningitidis Native PorB-RmpM

Fileemd_55084_additional_1.map
AnnotationRaw map of Neisseria meningitidis Native PorB-RmpM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Deepemhancer tight-sharpened map of Neisseria meningitidis Native PorB-RmpM....

Fileemd_55084_additional_2.map
AnnotationDeepemhancer tight-sharpened map of Neisseria meningitidis Native PorB-RmpM.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of the Neisseria meningitidis Native PorB-RmpM map

Fileemd_55084_half_map_1.map
AnnotationHalf map B of the Neisseria meningitidis Native PorB-RmpM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of the Neisseria meningitidis Native PorB-RmpM map

Fileemd_55084_half_map_2.map
AnnotationHalf map A of the Neisseria meningitidis Native PorB-RmpM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of the native porB trimer with the N-terminal dom...

EntireName: Ternary complex of the native porB trimer with the N-terminal domain of rmpM
Components
  • Complex: Ternary complex of the native porB trimer with the N-terminal domain of rmpM
    • Protein or peptide: Major outer membrane protein P.IB
    • Protein or peptide: Outer-membrane protein class 4

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Supramolecule #1: Ternary complex of the native porB trimer with the N-terminal dom...

SupramoleculeName: Ternary complex of the native porB trimer with the N-terminal domain of rmpM
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Neisseria meningitidis 8013 (bacteria)

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Macromolecule #1: Major outer membrane protein P.IB

MacromoleculeName: Major outer membrane protein P.IB / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis 8013 (bacteria)
Molecular weightTheoretical: 38.561969 KDa
SequenceString: MKKSLIALTL AALPVAAMAD VTLYGTIKAG VEVSRVKDAG TYKAQGGKSK TATQIADFGS KIGFKGQEDL GNGMKAIWQL EQKASIAGT NSGWGNRQSF IGLKGGFGTV RAGNLNTVLK DSGDNVNAWE SGSNTEDVLG LGTIGRVESR EISVRYDSPV F AGFSGSVQ ...String:
MKKSLIALTL AALPVAAMAD VTLYGTIKAG VEVSRVKDAG TYKAQGGKSK TATQIADFGS KIGFKGQEDL GNGMKAIWQL EQKASIAGT NSGWGNRQSF IGLKGGFGTV RAGNLNTVLK DSGDNVNAWE SGSNTEDVLG LGTIGRVESR EISVRYDSPV F AGFSGSVQ YVPRDNANDV DKYKHTKSSR ESYHAGLKYE NAGFFGQYAG SFAKYADLKD NAERVAVGTT GAHPVKDYQV HR VVAGYDA NDLYVSVAGQ YEAAKNNDGT ANQGKKHEQT QVAATAAYRF GNVTPRVSYA HGFKAKVNGK KAARYQYDQV IVG ADYDFS KRTSALVSAG WLKEGKGVNK TEKTASMVGL SHKF

UniProtKB: Major outer membrane protein P.IB

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Macromolecule #2: Outer-membrane protein class 4

MacromoleculeName: Outer-membrane protein class 4 / type: protein_or_peptide / ID: 2 / Details: N-terminal domain / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis 8013 (bacteria)
Molecular weightTheoretical: 26.004312 KDa
SequenceString: MTKQLKLSAL FVALLASGTA VAGEASVQGY TVSGQSNEIV RNNYGECWKN AYFDKASQGR VECGDAVAAP EPEPEPEPAP VVVVEQAPQ YVDETISLSA KTLFGFDKDS LRAEAQDNLK VLAQRLGQTN IQSVRVEGHT DFMGSDKYNQ ALSERRAYVV A NNLVSNGV ...String:
MTKQLKLSAL FVALLASGTA VAGEASVQGY TVSGQSNEIV RNNYGECWKN AYFDKASQGR VECGDAVAAP EPEPEPEPAP VVVVEQAPQ YVDETISLSA KTLFGFDKDS LRAEAQDNLK VLAQRLGQTN IQSVRVEGHT DFMGSDKYNQ ALSERRAYVV A NNLVSNGV PVSRISAVGL GESQAQMTQV CEAEVAKLGA KVSKAKKREA LIACIEPDRR VDVKIRSIVT RQVVPAHNHH QH

UniProtKB: Outer-membrane protein class 4

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.2 mg/mL
BufferpH: 7.4
GridMesh: 300
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 91290
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: Coot (ver. 0.9.8.96)
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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