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

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Basic information

Entry
Database: PDB / ID: 5kua
TitleCryo-EM reconstruction of Neisseria meningitidis Type IV pilus
Componentspilin
KeywordsPROTEIN FIBRIL / melted helix / Type IV pili
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6 Å
AuthorsKolappan, S. / Coureuil, M. / Yu, X. / Nassif, X. / Craig, L. / Egelman, E.H.
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 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 30, 2016Group: Refinement description
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pilin
B: pilin
C: pilin
D: pilin
E: pilin
F: pilin
G: pilin
H: pilin
I: pilin
J: pilin
K: pilin
L: pilin
M: pilin
N: pilin
O: pilin
P: pilin
Q: pilin
R: pilin
S: pilin
T: pilin
U: pilin
V: pilin
W: pilin
X: pilin
Y: pilin
Z: pilin


Theoretical massNumber of molelcules
Total (without water)443,74726
Polymers443,74726
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area102490 Å2
ΔGint-684 kcal/mol
Surface area120260 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 26 / Rise per n subunits: 10.3 Å / Rotation per n subunits: 100.8 °)
DetailsThe biological unit is a helical fibril comprising an indeterminate number of identical subunits. The provided helical parameters should be applied to a single subunit to generate an extended fibril.

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Components

#1: Protein ...
pilin


Mass: 17067.182 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Neisseria meningitidis (bacteria) / References: UniProt: A0A1I9GEU1*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Type IV pilus / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Source (natural)Organism: Neisseria meningitidis (bacteria)
Buffer solutionpH: 10.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 297 K / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV)

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2299: / Classification: refinement
EM softwareName: SPIDER / Version: 13 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 100.8 ° / Axial rise/subunit: 10.3 Å / Axial symmetry: C1
3D reconstructionResolution: 6 Å / Resolution method: FSC 0.33 CUT-OFF / Num. of particles: 15586 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00912170
ELECTRON MICROSCOPYf_angle_d1.04216570
ELECTRON MICROSCOPYf_dihedral_angle_d9.899950
ELECTRON MICROSCOPYf_chiral_restr0.0581990
ELECTRON MICROSCOPYf_plane_restr0.0072110

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