3GXA

Crystal structure of GNA1946


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of lipoprotein GNA1946 from Neisseria meningitidis

Yang, X.Wu, Z.Wang, X.Yang, C.Xu, H.Shen, Y.

(2009) J Struct Biol 168: 437-443

  • DOI: https://doi.org/10.1016/j.jsb.2009.09.001
  • Primary Citation of Related Structures:  
    3GXA, 3IR1

  • PubMed Abstract: 

    GNA1946, a conserved outer membrane lipoprotein from Neisseria meningitidis, has been identified as a candidate antigen for an urgently needed broad-spectrum meningococcal vaccine. It has been predicted to be a periplasmic receptor in the D-methionine uptake ABC transporter system. The crystal structure of GNA1946 was solved by the single-wavelength anomalous dispersion (SAD) method to a resolution of 2.25 A, and it reveals a Venus flytrap-like structure. GNA1946 consists of two globular lobes connected by a hinge region. Surprisingly, the structure showed an L-methionine bound within the cleft between the lobes. A comparison of GNA1946 with two other outer membrane lipoproteins, the L-methionine-binding Tp32 from Treponema pallidum and the dipeptide GlyMet-binding protein Pg110 from Staphylococcus aureus, revealed that although these three proteins share low sequence similarities, there is a high degree of structural conservation and similar substrate-binding frameworks. Our results reveal that GNA1946 is an L-methionine binding lipoprotein in the outer membrane, and should function as an initial receptor for ABC transporters with high affinity and specificity. The GNA1946 structure reported here should provide a valuable starting point for the development of a broad-spectrum meningococcal vaccine.


  • Organizational Affiliation

    Tianjin Key Laboratory of Protein Science, The College of Life Science, Nankai University, Tianjin, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane lipoprotein GNA1946
A, B, C, D, E
A, B, C, D, E, F
275Neisseria meningitidisMutation(s): 0 
Gene Names: gna1946
UniProt
Find proteins for Q7BMQ8 (Neisseria meningitidis)
Explore Q7BMQ8 
Go to UniProtKB:  Q7BMQ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7BMQ8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MET
Query on MET

Download Ideal Coordinates CCD File 
BA [auth F]
I [auth A]
P [auth B]
R [auth C]
W [auth D]
BA [auth F],
I [auth A],
P [auth B],
R [auth C],
W [auth D],
Y [auth E]
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth F]
G [auth A]
H [auth A]
J [auth B]
K [auth B]
AA [auth F],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
Q [auth C],
S [auth D],
T [auth D],
U [auth D],
V [auth D],
X [auth E],
Z [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.395α = 90
b = 122.809β = 90
c = 160.906γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXSphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-12
    Changes: Database references