Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23942.24 
• Atom Count: 1970 
• Residue Count: 218 
• Unique protein chains: 1

2Q20

Structure of the germline Vk1 O18/O8 light chain variable domain homodimer

• DOI: 10.2210/pdb2Q20/pdb

• Classification: PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2007-05-25 Released: 2008-04-08 
• Deposition Author(s): Thompson, J.R., Ramirez-Alvarado, M., Baden, E.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.3 Å
• R-Value Free: 0.148 
• R-Value Work: 0.119 

Literature

Altered dimer interface decreases stability in an amyloidogenic protein.

Baden, E.M., Owen, B.A., Peterson, F.C., Volkman, B.F., Ramirez-Alvarado, M., Thompson, J.R.

(2008) J.Biol.Chem. 283: 15853-15860

• PubMed: 18400753 
• DOI: 10.1074/jbc.M705347200
• Primary Citation of Related Structures:  
  2Q1E


• PubMed Abstract: 
  

Amyloidoses are devastating and currently incurable diseases in which the process of amyloid formation causes fatal cellular and organ damage. The molecular mechanisms underlying amyloidoses are not well known. In this study, we address the structural basis of immunoglobulin light chain amyloidosis, which results from deposition of light chains produced by clonal plasma cells. We compare light chain amyloidosis protein AL-09 to its wild-type counterpart, the kappaI O18/O8 light chain germline. Crystallographic studies indicate that both proteins form dimers. However, AL-09 has an altered dimer interface that is rotated 90 degrees from the kappaI O18/O8 dimer interface. The three non-conservative mutations in AL-09 are located within the dimer interface, consistent with their role in the decreased stability of this amyloidogenic protein. Moreover, AL-09 forms amyloid fibrils more quickly than kappaI O18/O8 in vitro. These results support the notion that the increased stability of the monomer and delayed fibril formation, together with a properly formed dimer, may be protective against amyloidogenesis. This could open a new direction into rational drug design for amyloidogenic proteins.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, College of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Vk1 O18/O8 germline light chain variable domain	A, B	109	Homo sapiens	Mutation(s): 0  Gene Names: IGKV1-33
Find proteins for P01594 (Homo sapiens) Go to UniProtKB:  P01594

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.3 Å
• R-Value Free: 0.148 
• R-Value Work: 0.119 
• Space Group: P 6₁

Unit Cell:

Length (Å)	Angle (°)
a = 74.265	α = 90.00
b = 74.265	β = 90.00
c = 99.051	γ = 120.00

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
SBC-Collect	data collection
PHASER	phasing
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-05-25 
• Released Date: 2008-04-08 
• Deposition Author(s): Thompson, J.R., Ramirez-Alvarado, M., Baden, E.M.

Revision History 

• Version 1.0: 2008-04-08
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-10-18
  Type: Refinement description