1WTL

COMPARISON OF CRYSTAL STRUCTURES OF TWO HOMOLOGOUS PROTEINS: STRUCTURAL ORIGIN OF ALTERED DOMAIN INTERACTIONS IN IMMUNOGLOBULIN LIGHT CHAIN DIMERS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Comparison of crystal structures of two homologous proteins: structural origin of altered domain interactions in immunoglobulin light-chain dimers.

Huang, D.B.Chang, C.H.Ainsworth, C.Brunger, A.T.Eulitz, M.Solomon, A.Stevens, F.J.Schiffer, M.

(1994) Biochemistry 33: 14848-14857


  • PubMed Abstract: 
  • The sequence and structure of a second human kappa 1 immunoglobulin light-chain variable domain, Wat, has been determined. The R-factor is 15.7% for 1.9-A data. One hundred and ninety-five water molecules were identified; 30 water molecules were loca ...

    The sequence and structure of a second human kappa 1 immunoglobulin light-chain variable domain, Wat, has been determined. The R-factor is 15.7% for 1.9-A data. One hundred and ninety-five water molecules were identified; 30 water molecules were located in identical positions in each of the monomers. Some of the water molecules are integral parts of the domains. This light chain is encoded by the same variable domain gene that encoded the previously characterized kappa I variable domain, Rei. Due to limited somatic mutation, the two highly homologous proteins differ in only 20 of the 108 residues. Wat crystallized in space group P6(4) while Rei crystallized in space group P6(1); in both crystals, the asymmetric unit was the noncovalent dimer. Although the basic domain structure is the same for both proteins, the relative positions of the domains within the two dimers differ. This difference is most likely accounted for by the replacement of Tyr36 in Rei by Phe in the Wat protein. Residue Tyr36 is part of the hydrogen-bonding network in the interface between the domains in Rei. Losing the hydrogen-bonding capability of residue 36 by replacement of Tyr by Phe alters the network of hydrogen bonds between the domains, resulting in a different domain-domain contact. The details of lattice contacts in the two crystals were compared. One type of contact that extends the beta-sheet of the individual domains was conserved, but because it involved different symmetry elements within the crystal, different crystal packing resulted. In the Wat crystal, one of the contacts shows an example of how a symmetrical binding site can "bind" an asymmetrical object. Further, the examination of the Wat crystal also illustrates how the different crystalline environments of the domains of the dimer results in different distributions of temperature factors for the residues within the domains.


    Related Citations: 
    • Characterization and Preliminary Crystallographic Data on the Vl-Related Fragment of the Human Ki Bence-Jones Protein Wat
      Stevens, F.J.,Westholm, F.A.,Panagiotopoulos, N.,Schiffer, M.,Popp, R.A.,Solomon, A.
      (1981) J.Mol.Biol. 147: 185
    • The Molecular Structure of a Dimer Composed of the Variable Portions of the Bence-Jones Protein Rei Refined at 2.0 Angstroms Resolution
      Schiffer, M.,Epp, O.,Lattman, E.E.,Schiffer, M.,Huber, R.,Palm, W.
      (1975) Biochemistry 14: 4943


    Organizational Affiliation

    Center for Mechanistic Biology and Biotechnology, Argonne National Laboratory, Illinois 60439-4833.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BENCE-JONES PROTEIN MCG (LIGHT CHAIN)
A, B
108Homo sapiensMutation(s): 0 
Gene Names: IGKV1D-33
Find proteins for P01593 (Homo sapiens)
Go to UniProtKB:  P01593
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 82.250α = 90.00
b = 82.250β = 90.00
c = 61.200γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-11-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance