Crystal structure of GNA1946

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

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This is version 1.3 of the entry. See complete history


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.

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
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
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]
C5 H11 N O2 S
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]
O4 S
Experimental Data & Validation

Experimental Data

  • 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
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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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
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations