1NGP

N1G9 (IGG1-LAMBDA) FAB FRAGMENT COMPLEXED WITH (4-HYDROXY-3-NITROPHENYL) ACETATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Three-dimensional structures of the Fab fragment of murine N1G9 antibody from the primary immune response and of its complex with (4-hydroxy-3-nitrophenyl)acetate.

Mizutani, R.Miura, K.Nakayama, T.Shimada, I.Arata, Y.Satow, Y.

(1995) J Mol Biol 254: 208-222

  • DOI: 10.1006/jmbi.1995.0612
  • Primary Citation of Related Structures:  
    1NGQ, 1NGP

  • PubMed Abstract: 
  • The three-dimensional structures of the Fab fragment, in its unliganded and liganded crystals, of mouse anti-(4-hydroxy-3-nitrophenyl)acetate (NP) antibody N1G9 have been determined by the molecular replacement method. The unliganded and NP-liganded ...

    The three-dimensional structures of the Fab fragment, in its unliganded and liganded crystals, of mouse anti-(4-hydroxy-3-nitrophenyl)acetate (NP) antibody N1G9 have been determined by the molecular replacement method. The unliganded and NP-liganded structures were refined at 2.4 A resolution to crystallographic R-factors of 0.194 and 0.196, respectively. Antibody N1G9 bears lambda light chains, and is one of the primary immune response antibodies. Fab N1G9 exhibits an elbow angle of 197 degrees in both structures. This large angle is ascribed to the VL-CL interface formed by lambda-chain residues. A hydrophobic pocket surrounded by the complementarity-determining regions except L2 is identified as a hapten-binding site. Between the liganded and unliganded structures, root-mean-square (r.m.s.) positional deviations are 0.42 A for the main-chain atoms, and 0.74 A for all the protein atoms. The major structural differences between these structures are localized in the hapten-binding site, and yield an r.m.s. deviation of 1.03 A for the side-chain atoms. The soaked NP ligand is in van der Waals contact with the aromatic side-chains of Tyr32L and Trp91L of the light chain, and Trp33H and Tyr97H of the heavy chain, and is hydrogen-bonded to the side-chains of Trp96L, His35H, Arg50H, Tyr95H, and Ser100aH. The side-chain of Lys58H is salt-bridged to the NP hydroxyl group. The side-chains of Arg50H, Trp33H, and Tyr97H are shifted toward the NP carboxyl group. The side-chain of Trp33H, whose replacement to Leu increases affinity by tenfold, is sandwiched between the Arg50H and Tyr97H side-chains, and is in cramped contact both with the ligand and with these side-chains. Affinity increases in the maturation of the anti-NP antibodies are ascribable to conformational relief of these cramped contacts through the replacement of Trp33H or through suitable structural alterations in the H3 region.


    Related Citations: 
    • Antibody Engineering for the Analysis of Affinity Maturation of an Anti-Hapten Response
      Allen, D., Simon, T., Sablitzky, F., Rajewsky, K., Cumano, A.
      (1988) EMBO J 7: 1995
    • Structure of Primary Anti-(4-Hydroxy-3-Nitrophenyl)Acetyl (Np) Antibodies in Normal and Idiotypically Suppressed C57Bl/6 Mice
      Cumano, A., Rajewsky, K.
      (1985) Eur J Immunol 15: 512
    • Somatic Variants of Murine Immunoglobulin Lambda Light Chains
      Bothwell, A.L., Paskind, M., Reth, M., Imanishi-Kari, T., Rajewsky, K., Baltimore, D.
      (1982) Nature 298: 380

    Organizational Affiliation

    Faculty of Pharmaceutical Sciences, University of Tokyo, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N1G9 (IGG1-LAMBDA)L215Mus musculusMutation(s): 0 
Find proteins for G0YP42 (Mus musculus)
Explore G0YP42 
Go to UniProtKB:  G0YP42
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N1G9 (IGG1-LAMBDA)H222Mus musculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NPA
Query on NPA

Download CCD File 
H
2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID
C8 H7 N O5
QBHBHOSRLDPIHG-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.196 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.691α = 90
b = 110.691β = 90
c = 98.25γ = 90
Software Package:
Software NamePurpose
OSCMGRdata collection
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
OSCdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-07-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection, Other