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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.258
R-Value Work: 0.225
R-Value Observed: 0.227

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This is version 2.0 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9RP17
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CXE Query on CXE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ETA Query on ETA Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ETHANOLAMINE C₂ H₇ N O HZAXFHJVJLSVMW-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.258
R-Value Work: 0.225
R-Value Observed: 0.227
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

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Entry History

Deposition Data

Released Date: 2003-07-22

Deposition Author(s):

Vandeputte-Rutten, L.

Bos, M.P.

Tommassen, J.

Gros, P.

Revision History (Full details and data files)

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