3CDY | pdb_00003cdy

AL-09 H87Y, immunoglobulin light chain variable domain

• PDB DOI: https://doi.org/10.2210/pdb3CDY/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-27 Released: 2008-09-02 
• Deposition Author(s): Baden, E.M., Randles, E.G., Aboagye, A.K., Thompson, J.R., Ramirez-Alvarado, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 
  0.263 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the role of mutations in amyloidogenesis.

Baden, E.M., Randles, E.G., Aboagye, A.K., Thompson, J.R., Ramirez-Alvarado, M.

(2008) J Biological Chem 283: 30950-30956

• PubMed: 18768467 
• DOI: https://doi.org/10.1074/jbc.M804822200
• Primary Citation Related Structures: 
  3CDC, 3CDF, 3CDY


• PubMed Abstract: 
  

  Mechanisms of amyloidogenesis are not well understood, including potential structural contributions of mutations in the process. Our previous research indicated that the dimer interface of amyloidogenic immunoglobulin light chain protein AL-09 is twisted 90 degrees relative to the protein from its germline sequence, kappaI O18/O8. Here we report a systematic restoration of AL-09 to its germline sequence by mutating the non-conservative somatic mutations located in the light chain dimer interface. Among these mutants, we find a correlation between increased thermodynamic stability and an increase in the lag time for fibril formation. The restorative mutant AL-09 H87Y completes the trifecta and restores the dimer interface observed in kappaI O18/O8, emphasizing the potential importance of the structural integrity of these proteins to protect against amyloidogenicity. We also find that adding amyloidogenic mutations into the germline protein illustrates mutational cooperativity in promoting amyloidogenesis.

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Organizational Affiliation: 
• Department of Biochemistry, College of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.99 kDa 
• Atom Count: 1,785 
• Modeled Residue Count: 216 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN LIGHT CHAIN	A, B	109	Homo sapiens	Mutation(s): 0  Gene Names: kI O18/O8 germline
UniProt & NIH Common Fund Data Resources
Find proteins for P01594 (Homo sapiens) Explore P01594  Go to UniProtKB:  P01594
GTEx:  ENSG00000242076

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free:  0.263 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.971	α = 90
b = 73.971	β = 90
c = 95.07	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Baden, E.M., Randles, E.G., Aboagye, A.K., Thompson, J.R., Ramirez-Alvarado, M.

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary