9FVK | pdb_00009fvk

Crystal structure of amyloidogenic light chain AL-55 in open conformation.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 
    0.225 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9FVK

This is version 1.1 of the entry. See complete history

Literature

The Critical Role of the Variable Domain in Driving Proteotoxicity and Aggregation in Full-length Light Chains.

Puri, S.Gadda, A.Polsinelli, I.Barzago, M.M.Toto, A.Sriramoju, M.K.Visentin, C.Broggini, L.Valerie Bonnet, D.M.Russo, R.Chaves-Sanjuan, A.Merlini, G.Nuvolone, M.Palladini, G.Gianni, S.Hsu, S.D.Diomede, L.Ricagno, S.

(2025) J Mol Biology 437: 168958-168958

  • DOI: https://doi.org/10.1016/j.jmb.2025.168958
  • Primary Citation Related Structures: 
    9FVK

  • PubMed Abstract: 

    Light chain (AL) amyloidosis is the most common systemic amyloid disease characterized by abnormal accumulation of amyloid fibrils derived from immunoglobulin light chains (LCs). Both full-length (FL) LCs and their isolated variable (VL) and constant (CL) domains contribute to amyloid deposits in multiple organs, with the VL domain predominantly forming the fibril core. However, the role and interplay of these domains in amyloid aggregation and toxicity are poorly understood. Characterizing the amyloidogenic λ6-LC AL55, this study explores the properties of both FL and isolated domains and compares them with the available patient-derived data. FL AL55 biophysical features result from the interplay between its VL and CL domains where the limited VL-CL interface might play a major role. Slow refolding kinetic of FL confirms the unfolded VL domain as a kinetic trap possibly shifting the process towards misfolding. The X-ray structure of FL AL55 shows that VL domains may detach from the native dimeric assembly and establish non-native interdimeric interfaces. Additionally, isolated VL domains display significantly lower soluble toxicity compared to FL and do not form fibrils similar to those found ex vivo. Thus the data obtained in this work allowed us to draw a molecular sketch of the aggregation pathway for amyloidogenic LCs.


  • Organizational Affiliation
    • Department of Biosciences, University of Milan, Italy; Biology Department, Indian Institute of Science Education and Research (IISER) Pune, India.

Macromolecule Content 

  • Total Structure Weight: 70.61 kDa 
  • Atom Count: 5,048 
  • Modeled Residue Count: 648 
  • Deposited Residue Count: 651 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AL55
A, B, C
217Homo sapiensMutation(s): 0 

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE

Query on PGE



Download:Ideal Coordinates CCD File
F [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
D [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
E [auth A],
I [auth C],
J [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
H [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free:  0.225 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.817α = 90
b = 208.381β = 90
c = 72.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
BUSTERrefinement
REFMACrefinement
EDNAdata collection
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
University and Research - University of MilanItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Database references