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- EMDB-8287: Cryo-EM reconstruction of Neisseria meningitidis Type IV pilus -

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Basic information

Entry
Database: EMDB / ID: EMD-8287
TitleCryo-EM reconstruction of Neisseria meningitidis Type IV pilus
Map data3D cryo-EM reconstruction of Nm Type IV pilus
Sample
  • Organelle or cellular component: pilus
    • Other: pilin
Function / homology
Function and homology information


pilus / cell adhesion / membrane
Similarity search - Function
Fimbrial protein pilin / Pilin (bacterial filament) / : / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Biological speciesNeisseria meningitidis (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsKolappan S / Coureuil M / Yu X / Nassif X / Craig L / Egelman EH
CitationJournal: Nat Commun / Year: 2016
Title: Structure of the Neisseria meningitidis Type IV pilus.
Authors: Subramania Kolappan / Mathieu Coureuil / Xiong Yu / Xavier Nassif / Edward H Egelman / Lisa Craig /
Abstract: Neisseria meningitidis use Type IV pili (T4P) to adhere to endothelial cells and breach the blood brain barrier, causing cause fatal meningitis. T4P are multifunctional polymers of the major pilin ...Neisseria meningitidis use Type IV pili (T4P) to adhere to endothelial cells and breach the blood brain barrier, causing cause fatal meningitis. T4P are multifunctional polymers of the major pilin protein, which share a conserved hydrophobic N terminus that is a curved extended α-helix, α1, in X-ray crystal structures. Here we report a 1.44 Å crystal structure of the N. meningitidis major pilin PilE and a ∼6 Å cryo-electron microscopy reconstruction of the intact pilus, from which we built an atomic model for the filament. This structure reveals the molecular arrangement of the N-terminal α-helices in the filament core, including a melted central portion of α1 and a bridge of electron density consistent with a predicted salt bridge necessary for pilus assembly. This structure has important implications for understanding pilus biology.
History
DepositionJul 12, 2016-
Header (metadata) releaseOct 5, 2016-
Map releaseOct 12, 2016-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5kua
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8287.png

Downloads & links

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Map

FileDownload / File: emd_8287.map.gz / Format: CCP4 / Size: 7.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D cryo-EM reconstruction of Nm Type IV pilus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 200 pix.
= 210. Å		1.05 Å/pix.
x 100 pix.
= 105. Å		1.05 Å/pix.
x 100 pix.
= 105. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45 / Movie #1: 0.45
Minimum - Maximum-0.39593023 - 0.9242279
Average (Standard dev.)0.073884055 (±0.20737447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-100
Dimensions100100200
Spacing100100200
CellA: 104.99999 Å / B: 104.99999 Å / C: 209.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z100100200
origin x/y/z0.0000.0000.000
length x/y/z105.000105.000210.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS-50-50-100
NC/NR/NS100100200
D min/max/mean-0.3960.9240.074

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Supplemental data

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Sample components

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Entire : pilus

EntireName: pilus
Components
  • Organelle or cellular component: pilus
    • Other: pilin

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Supramolecule #1: pilus

SupramoleculeName: pilus / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Neisseria meningitidis (bacteria)

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Macromolecule #1: pilin

MacromoleculeName: pilin / type: other / ID: 1 / Classification: other
Source (natural)Organism: Neisseria meningitidis (bacteria)
SequenceString:
FTLIELMIVI AIVGILAAVA LPAYQDYTAR AQVSEAILLA EGQKSAVTEY YLNHGEWPGD NSSAGVATSA DIKGKYVQSV TVANGVITAQ MASSNVNNEI KSKKLSLWAK RQNGSVKWFC GQPVTRTTAT ATDVAAANGK TDDKINTKHL PSTCRDDSSA S

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 10.5
GridModel: lacey / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 541 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 10.3 Å
Applied symmetry - Helical parameters - Δ&Phi: 100.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: OTHER / Number images used: 15586
CTF correctionSoftware - Name: CTFFIND3
Segment selectionNumber selected: 15586
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-5kua:
Cryo-EM reconstruction of Neisseria meningitidis Type IV pilus

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