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- EMDB-54887: Neisseria meningitidis Native PilQ tetradecamer -

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Basic information

Entry
Database: EMDB / ID: EMD-54887
TitleNeisseria meningitidis Native PilQ tetradecamer
Map dataClean, sharpened map of N. meningitidis PilQ
Sample
  • Complex: Protomer of the tetradecamer secretin PilQ of Neisseria meningitidis
    • Protein or peptide: Type IV pilus biogenesis and competence protein PilQ
KeywordsSecretin / Barrel / Outer Membrane / Secretion / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.14 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_54887.png

Downloads & links

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Map

FileDownload / File: emd_54887.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClean, sharpened map of N. meningitidis PilQ
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: 0.201
Minimum - Maximum-0.015488904 - 1.6112889
Average (Standard dev.)0.0015823509 (±0.02750528)
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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Mask #1

Fileemd_54887_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Raw, unfiltered map from refinement job N. meningitidis PilQ

Fileemd_54887_additional_1.map
AnnotationRaw, unfiltered map from refinement job N. meningitidis PilQ
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Composite map used for refinement of the N. meningitidis PilQ model

Fileemd_54887_additional_2.map
AnnotationComposite map used for refinement of the N. meningitidis PilQ model
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A from refinement job N. meningitidis PilQ

Fileemd_54887_half_map_1.map
AnnotationHalf map A from refinement job N. meningitidis PilQ
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B from refinement job N. meningitidis PilQ

Fileemd_54887_half_map_2.map
AnnotationHalf map B from refinement job N. meningitidis PilQ
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
    • Protein or peptide: Type IV pilus biogenesis and competence protein PilQ

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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: all
Source (natural)Organism: Neisseria meningitidis 8013 (bacteria)

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

MacromoleculeName: Type IV pilus biogenesis and competence protein PilQ / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Neisseria meningitidis 8013 (bacteria)
Molecular weightTheoretical: 82.089297 KDa
Recombinant expressionOrganism: Neisseria meningitidis 8013 (bacteria)
SequenceString: MNTKLTKIIS GLFVATAAFQ TASAGNITDI KVSSLPNKQK IVKVSFDKEI VNPTGFVTSS PARIALDFEQ TGISMDQQVL EYADPLLSK ISAAQNSSRA RLVLNLNKPG QYNTEVRGNK VWIFINESDD TVSAPARPAV KAAPAAPAKQ QAAAPSTKSA V SVSKPFTP ...String:
MNTKLTKIIS GLFVATAAFQ TASAGNITDI KVSSLPNKQK IVKVSFDKEI VNPTGFVTSS PARIALDFEQ TGISMDQQVL EYADPLLSK ISAAQNSSRA RLVLNLNKPG QYNTEVRGNK VWIFINESDD TVSAPARPAV KAAPAAPAKQ QAAAPSTKSA V SVSKPFTP AKQQAAAPFT ESVVSVSAPF SPAKQQAAAS AKQQTAAPAK QQAAAPAKQT NIDFRKDGKN AGIIELAALG FA GQPDISQ QHDHIIVTLK NHTLPTTLQR SLDVADFKTP VQKVTLKRLN NDTQLIITTA GNWELVNKSA APGYFTFQVL PKK QNLESG GVNNAPKTFT GRKISLDFQD VEIRTILQIL AKESGMNIVA SDSVNGKMTL SLKDVPWDQA LDLVMQARNL DMRQ QGNIV NIAPRDELLA KDKAFLQAEK DIADLGALYS QNFQLKYKNV EEFRSILRLD NADTTGNRNT LVSGRGSVLI DPATN TLIV TDTRSVIEKF RKLIDELDVP AQQVMIEARI VEAADGFSRD LGVKFGATGK KKLKNDTSAF GWGVNSGFGG DDKWGA ETK INLPITAAAN SISLVRAISS GALNLELSAS ESLSKTKTLA NPRVLTQNRK EAKIESGYEI PFTVTSIANG GSSTNTE LK KAVLGLTVTP NITPDGQIIM TVKINKDSPA QCASGNQTIL CISTKNLNTQ AMVENGGTLI VGGIYEEDNG NTLTKVPL L GDIPVIGNLF KTRGKKTDRR ELLIFITPRI MGHHHHHHHH

UniProtKB: Type IV pilus biogenesis and competence protein PilQ

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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 correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold2
Final reconstructionApplied symmetry - Point group: C14 (14 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 154572
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
Output model

PDB-9sh2:
Neisseria meningitidis Native PilQ tetradecamer

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