1P4T

Crystal structure of Neisserial surface protein A (NspA)

• PDB DOI: https://doi.org/10.2210/pdb1P4T/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Neisseria meningitidis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2003-04-24 Released: 2003-07-22 
• Deposition Author(s): Vandeputte-Rutten, L., Bos, M.P., Tommassen, J., Gros, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal structure of Neisserial Surface Protein A (NspA), a conserved outer membrane protein with vaccine potential

Vandeputte-Rutten, L., Bos, M.P., Tommassen, J., Gros, P.

(2003) J Biol Chem 278: 24825-24830

• PubMed: 12716881 
• DOI: https://doi.org/10.1074/jbc.M302803200
• Primary Citation of Related Structures:  
  1P4T


• PubMed Abstract: 
  

  The neisserial surface protein A (NspA) from Neisseria meningitidis is a promising vaccine candidate because it is highly conserved among meningococcal strains and induces bactericidal antibodies. NspA is a homolog of the Opa proteins, which mediate adhesion to host cells. Here, we present the crystal structure of NspA, determined to 2.55-A resolution. NspA forms an eight-stranded antiparallel beta-barrel. The four loops at the extracellular side of the NspA molecule form a long cleft, which contains mainly hydrophobic residues and harbors a detergent molecule, suggesting that the protein might function in the binding of hydrophobic ligands, such as lipids. In addition, the structure provides a starting point for structure-based vaccine design.

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Organizational Affiliation: 

Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht, The Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.63 kDa 
• Atom Count: 1,262 
• Modelled Residue Count: 155 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
outer membrane protein NspA	A	155	Neisseria meningitidis	Mutation(s): 0  Gene Names: nspa Membrane Entity: Yes
UniProt
Find proteins for Q9RP17 (Neisseria meningitidis) Explore Q9RP17  Go to UniProtKB:  Q9RP17

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CXE	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	PENTAETHYLENE GLYCOL MONODECYL ETHER C20 H42 O6 QAXPOSPGRHYIHE-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ETA	H [auth A]	ETHANOLAMINE C2 H7 N O HZAXFHJVJLSVMW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.372	α = 90
b = 97.372	β = 90
c = 171.939	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-22 
Deposition Author(s): Vandeputte-Rutten, L., Bos, M.P., Tommassen, J., Gros, P.

Revision History  

• Version 1.0: 2003-07-22
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations