1DLF

HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 5.25


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The pH-dependent structural variation of complementarity-determining region H3 in the crystal structures of the Fv fragment from an anti-dansyl monoclonal antibody.

Nakasako, M.Takahashi, H.Shimba, N.Shimada, I.Arata, Y.

(1999) J.Mol.Biol. 291: 117-134

  • DOI: 10.1006/jmbi.1999.2931
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Fv fragment from an anti-dansyl antibody was optimally crystallized into two crystal forms having slightly different lattice dimensions at pH 5.25 and 6.75. The two crystal structures were determined and refined at high resolution at 112 K (at 1. ...

    The Fv fragment from an anti-dansyl antibody was optimally crystallized into two crystal forms having slightly different lattice dimensions at pH 5.25 and 6.75. The two crystal structures were determined and refined at high resolution at 112 K (at 1.45 A for the crystal at pH 5.25 and at 1.55 A for that at pH 6.75). In the two crystal structures, marked differences were identified in the first half of CDRH3 s having an amino acid sequence of Ile95H-Tyr96H-Tyr97H-His98H-Tyr99H-Pro1 00H-Trp100aH-Phe100bH-Ala101H- Tyr102H. NMR pH titration experiments revealed the p Kavalues of four histidine residues (His27dL, His93L, His55H and His98H) exposed to solvent. Only His98H (p Ka=6.3) completely changed its protonation state between the two crystallization conditions. In addition, the environmental structures including hydration water molecules around the four histidine residues were carefully compared. While the hydration structures around His27dL, His93L and His55H were almost invariant between the two crystal structures, those around His98Hs showed great difference in spite of the small conformational difference of His98H between the two crystal structures. These spectroscopic and crystallographic findings suggested that the change in the protonation state in His98H was responsible for the structural differences between pH 5.25 and 6.75. In addition, the most plausible binding site of the dansyl group was mapped into the present structural models with our previous NMR experimental results. The complementarity-determining regions H1, H3 and the N-terminal region in the VH domain formed the site. The side-chain of Tyr96H occupied the site and interacted with Phe27H of H1, giving a clue for the binding mode of the dansyl group in the site.


    Related Citations: 
    • Role of the Domain-Domain Interaction in the Construction of the Antigen Combining Site. A Comparative Study by 1H-15N Shift Correlation NMR Spectroscopy of the Fv and Fab Fragments of Anti-Dansyl Mouse Monoclonal Antibody
      Takahashi, H.,Tamura, H.,Shimba, N.,Shimada, I.,Arata, Y.
      (1994) J.Mol.Biol. 243: 494
    • Dynamical Structure of the Antibody Combining Site as Studied by 1H-15N Shift Correlation NMR Spectroscopy
      Takahashi, H.,Suzuki, E.,Shimada, I.,Arata, Y.
      (1992) Biochemistry 31: 2464
    • Preparation of the Fv Fragment from a Short-Chain Mouse Igg2A Anti-Dansyl Monoclonal Antibody and Use of Selectively Deuterated Fv Analogues for Two-Dimensional 1H NMR Analyses of the Antigen-Antibody Interactions
      Takahashi, H.,Igarashi, T.,Shimada, I.,Arata, Y.
      (1991) Biochemistry 30: 2840
    • Multinuclear NMR Study of the Structure of the Fv Fragment of Anti-Dansyl Mouse Igg2A Antibody
      Takahashi, H.,Odaka, A.,Kawaminami, S.,Matsunaga, C.,Kato, K.,Shimada, I.,Arata, Y.
      (1991) Biochemistry 30: 6611
    • Isotope-Edited Nuclear Magnetic Resonance Study of Fv Fragment of Anti-Dansyl Mouse Monoclonal Antibody: Recognition of the Dansyl Hapten
      Odaka, A.,Kim, J.I.,Takahashi, H.,Shimada, I.,Arata, Y.
      (1992) Biochemistry 31: 10686
    • Conformation and Stereoselective Reduction of Hapten Side Chain in the Antibody Combining Site
      Kim, T.,Nakano, I.,Higuchi, T.,Hirobe, M.,Shimada, I.,Arata, Y.
      (1991) J.Am.Chem.Soc. 113: 9392
    • Structure of a Mouse Immunoglobulin G that Lacks the Entire Ch1 Domain: Protein Sequencing and Small-Angle X-Ray Scattering Studies
      Igarashi, T.,Sato, M.,Katsube, Y.,Takio, K.,Tanaka, T.,Nakanishi, M.,Arata, Y.
      (1990) Biochemistry 29: 5725


    Organizational Affiliation

    Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Corporation (JST) Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi, Bunkyoku, Tokyo, 113-0032, Japan. nakasako@ian.u-tokyo.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)
L
113Mus musculusMutation(s): 0 
Find proteins for P01631 (Mus musculus)
Go to UniProtKB:  P01631
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)
H
124N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.101α = 90.00
b = 70.722β = 90.00
c = 53.464γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-26
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance