1JVK

THREE-DIMENSIONAL STRUCTURE OF AN IMMUNOGLOBULIN LIGHT CHAIN DIMER ACTING AS A LETHAL AMYLOID PRECURSOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-dimensional structure of an immunoglobulin light-chain dimer with amyloidogenic properties.

Bourne, P.C.Ramsland, P.A.Shan, L.Fan, Z.C.DeWitt, C.R.Shultz, B.B.Terzyan, S.S.Moomaw, C.R.Slaughter, C.A.Guddat, L.W.Edmundson, A.B.

(2002) Acta Crystallogr.,Sect.D 58: 815-823


  • PubMed Abstract: 
  • The X-ray structure of an immunoglobulin light-chain dimer isolated from the urine as a "Bence-Jones protein" from a patient with multiple myeloma and amyloidosis (Sea) was determined at 1.94 A resolution and refined to R and R(free) factors of 0.22 ...

    The X-ray structure of an immunoglobulin light-chain dimer isolated from the urine as a "Bence-Jones protein" from a patient with multiple myeloma and amyloidosis (Sea) was determined at 1.94 A resolution and refined to R and R(free) factors of 0.22 and 0.25, respectively. This "amyloidogenic" protein crystallized in the orthorhombic P2(1)2(1)2(1) space group with unit-cell parameters a = 48.28, b = 83.32, c = 112.59 A as determined at 100 K. In the vital organs (heart and kidneys), the equivalent of the urinary protein produced fibrillar amyloid deposits which were fatal to the patient. Compared with the amyloidogenic Mcg light-chain dimer, the Sea protein was highly soluble in aqueous solutions and only crystallized at concentrations approaching 100 mg ml(-1). Both the Sea and Mcg proteins packed into crystals in highly ordered arrangements typical of strongly diffracting crystals of immunoglobulin fragments. Overall similarities and significant differences in the three-dimensional structures and crystalline properties are discussed for the Sea and Mcg Bence-Jones proteins, which together provide a generalized model of abnormalities present in lambda chains, facilitating a better understanding of amyloidosis of light-chain origin (AL).


    Organizational Affiliation

    OMRF, 825 N E 13th Street, Oklahoma City, OK 73104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN LAMBDA LIGHT CHAIN
A, B
216Homo sapiensMutation(s): 0 
Find proteins for Q6PJG0 (Homo sapiens)
Go to UniProtKB:  Q6PJG0
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, B
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.280α = 90.00
b = 83.320β = 90.00
c = 112.591γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance