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- EMDB-54884: Native Neisseria meninigitidis PilQ, Gate Domain focused map -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-54884
TitleNative Neisseria meninigitidis PilQ, Gate Domain focused map
Map data
Sample
  • Complex: Protomer of the tetradecamer secretin PilQ of Neisseria meningitidis
KeywordsSecretin / Barrel / Outer Membrane / Secretion / MEMBRANE PROTEIN
Biological speciesNeisseria meningitidis 8013 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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 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, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54884.png

Downloads & links

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Map

FileDownload / File: emd_54884.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.459
Minimum - Maximum-0.6042199 - 1.2112452
Average (Standard dev.)0.0020104481 (±0.016180933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 372.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54884_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54884_half_map_2.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 : Protomer of the tetradecamer secretin PilQ of Neisseria meningitidis

EntireName: Protomer of the tetradecamer secretin PilQ of Neisseria meningitidis
Components
  • Complex: Protomer of the tetradecamer secretin PilQ of Neisseria meningitidis

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Supramolecule #1: Protomer of the tetradecamer secretin PilQ of Neisseria meningitidis

SupramoleculeName: Protomer of the tetradecamer secretin PilQ of Neisseria meningitidis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Neisseria meningitidis 8013 (bacteria)

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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

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1014078
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 31178
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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