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- PDB-5jw8: Crystal structure of the Type IV pilin subunit PilE from Neisseri... -

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Basic information

Entry
Database: PDB / ID: 5jw8
TitleCrystal structure of the Type IV pilin subunit PilE from Neisseria meningitidis
ComponentsMajor pilin PilE
KeywordsCELL ADHESION / TYPE IV PILIN
Function / homology
Function and homology information


pilus / cell adhesion
Similarity search - Function
Glycoprotein, Type 4 Pilin / Glycoprotein, Type 4 Pilin / Fimbrial protein pilin / Pilin (bacterial filament) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major pilin PilE / :
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup C (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.439 Å
AuthorsKolappan, S. / Craig, L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-125959 Canada
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
DepositionMay 11, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionJul 6, 2016ID: 4XNP
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major pilin PilE


Theoretical massNumber of molelcules
Total (without water)14,4761
Polymers14,4761
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.450, 46.260, 48.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Major pilin PilE


Mass: 14476.022 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup C (bacteria)
Strain: 8013 / Gene: pilE, NMV_0019 / Production host: Escherichia coli (E. coli) / References: UniProt: C9X152, UniProt: A0A1C7D1B2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.68 Å3/Da / Density % sol: 26.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES PH 6.0, 34 % (W/V) PEG4000, 100 mM AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9753 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9753 Å / Relative weight: 1
ReflectionResolution: 1.439→33.432 Å / Num. obs: 18088 / % possible obs: 98.7 % / Redundancy: 6.6 % / Net I/σ(I): 21.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2299: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: modified 2HI2

2hi2


Resolution: 1.439→33.432 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.57
RfactorNum. reflection% reflection
Rfree0.2096 901 5 %
Rwork0.1867 --
obs0.1879 18030 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.439→33.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms986 0 0 156 1142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041059
X-RAY DIFFRACTIONf_angle_d0.6791450
X-RAY DIFFRACTIONf_dihedral_angle_d12.143386
X-RAY DIFFRACTIONf_chiral_restr0.068168
X-RAY DIFFRACTIONf_plane_restr0.003192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4385-1.52860.39861380.29692645X-RAY DIFFRACTION94
1.5286-1.64670.20791500.20762842X-RAY DIFFRACTION100
1.6467-1.81240.22211510.1882879X-RAY DIFFRACTION100
1.8124-2.07460.22931500.19322838X-RAY DIFFRACTION99
2.0746-2.61360.19661530.17522908X-RAY DIFFRACTION100
2.6136-33.44080.17941590.16923017X-RAY DIFFRACTION99

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