1LVE

STRUCTURE OF THE VARIABLE DOMAIN OF HUMAN IMMUNOGLOBULIN K-4 LIGHT CHAIN LEN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Variable domain structure of kappaIV human light chain Len: high homology to the murine light chain McPC603.

Huang, D.B.Chang, C.H.Ainsworth, C.Johnson, G.Solomon, A.Stevens, F.J.Schiffer, M.

(1997) Mol.Immunol. 34: 1291-1301


  • PubMed Abstract: 
  • Antibody light chains of the kappa subgroup are the predominant light chain component in human immune responses and are used almost exclusively in the antibody repertoire of mice. Human kappa light chains comprise four subgroups. To date, all crystal ...

    Antibody light chains of the kappa subgroup are the predominant light chain component in human immune responses and are used almost exclusively in the antibody repertoire of mice. Human kappa light chains comprise four subgroups. To date, all crystallographic studies of human kappa light chains were carried out on proteins of the kappaI subgroup. The light chain produced by multiple myeloma patient Len. was of the kappaIV subgroup, it differed by only one residue from the germ-line gene encoded protein. The variable domain fragment of the light chain was crystallized from ammonium sulfate in space group C222(1). The crystal structure was determined by molecular replacement and refined at 1.95 A resolution to an R-factor of 0.15. Protein Len has six additional residues in its CDR1 segment compared to the kappaI proteins previously characterized. The kappaIV variable domain, Len, differs in only 23 of 113 residues from murine kappa light chain McPC603. The RMS deviation upon superimposing their alpha-carbons was 0.69 A. The CDR1 segment of the human and murine variable domains have the same length and conformation although their amino acid sequences differ in 5 out of 17 residues. Structural features were identified that could account for the significantly higher stability of the human kappaIV protein relative to its murine counterpart. This human kappaIV light chain structure is the closest human homolog to a murine light chain and can be expected to facilitate detailed structural comparisons necessary for effective humanization of murine antibodies.


    Related Citations: 
    • Recombinant Immunoglobulin Variable Domains Generated from Synthetic Genes Provide a System for in Vitro Characterization of Light-Chain Amyloid Proteins
      Stevens, P.W.,Raffen, R.,Hanson, D.K.,Deng, Y.L.,Berrios-Hammond, M.,Westholm, F.A.,Murphy, C.,Eulitz, M.,Wetzel, R.,Solomon, A.,Schiffer, M.,Stevens, F.J.
      (1995) Protein Sci. 4: 421
    • Structure of the Variable Domain of Human Immunoglobulin Kappa-Iv Light Chain Len
      Huang, D.-B.,Ainsworth, C.,Chang, C.-H.,Stevens, F.J.,Schiffer, M.
      (1996) Acta Crystallogr.,Sect.A 52: C-220


    Organizational Affiliation

    Center for Mechanistic Biology and Biotechnology, Argonne National Laboratory, IL 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEN, A VARIABLE DOMAIN FROM KAPPA-4 TYPE
A
122Homo sapiensGene Names: IGKV4-1
Find proteins for P06312 (Homo sapiens)
Go to UniProtKB:  P06312
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.150 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 43.110α = 90.00
b = 83.530β = 90.00
c = 54.470γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-21
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance