2PIL | pdb_00002pil

Crystallographic Structure of Phosphorylated Pilin from Neisseria: Phosphoserine Sites Modify Type IV Pilus Surface Chemistry


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Work: 
    0.187 (Depositor) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2PIL

This is version 2.1 of the entry. See complete history

Literature

Crystallographic structure reveals phosphorylated pilin from Neisseria: phosphoserine sites modify type IV pilus surface chemistry and fibre morphology.

Forest, K.T.Dunham, S.A.Koomey, M.Tainer, J.A.

(1999) Mol Microbiol 31: 743-752

  • DOI: https://doi.org/10.1046/j.1365-2958.1999.01184.x
  • Primary Citation Related Structures: 
    2PIL

  • PubMed Abstract: 

    Understanding the structural biology of type IV pili, fibres responsible for the virulent attachment and motility of numerous bacterial pathogens, requires a detailed understanding of the three-dimensional structure and chemistry of the constituent pilin subunit. X-ray crystallographic refinement of Neisseria gonorrhoeae pilin against diffraction data to 2.6 A resolution, coupled with mass spectrometry of peptide fragments, reveals phosphoserine at residue 68. Phosphoserine is exposed on the surface of the modelled type IV pilus at the interface of neighbouring pilin molecules. The site-specific mutation of serine 68 to alanine showed that the loss of the phosphorylation alters the morphology of fibres examined by electron microscopy without a notable effect on adhesion, transformation, piliation or twitching motility. The structural and chemical characterization of protein phosphoserine in type IV pilin subunits is an important indication that this modification, key to numerous regulatory aspects of eukaryotic cell biology, exists in the virulence factor proteins of bacterial pathogens. These O-linked phosphate modifications, unusual in prokaryotes, thus merit study for possible roles in pilus biogenesis and modulation of pilin chemistry for optimal in vivo function.


  • Organizational Affiliation
    • Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 18.01 kDa 
  • Atom Count: 1,375 
  • Modeled Residue Count: 158 
  • Deposited Residue Count: 158 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TYPE 4 PILIN158Neisseria gonorrhoeaeMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for P02974 (Neisseria gonorrhoeae)
Explore P02974 
Go to UniProtKB:  P02974
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02974
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2O-Glycosylation
Glycosylation Resources
GlyTouCan: G15031WB
GlyCosmos: G15031WB
GlyGen: G15031WB

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PT

Query on PT



Download:Ideal Coordinates CCD File
C [auth A]PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
HTO

Query on HTO



Download:Ideal Coordinates CCD File
D [auth A]HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MEA
Query on MEA
A
L-PEPTIDE LINKINGC10 H13 N O2PHE
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Work:  0.187 (Depositor) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.58α = 90
b = 121.08β = 90
c = 26.86γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
ROTAVATA/AGROVATAdata reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
ROTAVATAdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2024-11-06
    Changes: Data collection, Database references, Structure summary