9FVK | pdb_00009fvk

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

• PDB DOI: https://doi.org/10.2210/pdb9FVK/pdb

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


• Deposited: 2024-06-27 Released: 2025-07-09 
• Deposition Author(s): Polsinelli, I., Puri, S., Broggini, L., Gadda, A., Petralia, U., Ricagno, S.
• Funding Organization(s): University and Research - University of Milan

---

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

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

• PubMed: 39842712 
• DOI: https://doi.org/10.1016/j.jmb.2025.168958
• Primary Citation of 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.
Department of Biosciences, University of Milan, Italy.
Institute of Molecular and Translational Cardiology, IRCCS, Policlinico San Donato, Milan, Italy.
Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milano, Italy.
Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy.
Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
Department of Pathophysiology and Transplantation, University of Milan, Italy.
Department of Molecular Medicine, University of Pavia, Pavia, Italy; Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617 Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM(2)), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
Department of Biosciences, University of Milan, Italy; Institute of Molecular and Translational Cardiology, IRCCS, Policlinico San Donato, Milan, Italy. Electronic address: [e-mail].

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)

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AL55	A, B, C	217	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	F [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	E [auth A], I [auth C], J [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	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 = 111.817	α = 90
b = 208.381	β = 90
c = 72.03	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
BUSTER	refinement
REFMAC	refinement
EDNA	data collection
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Polsinelli, I., Puri, S., Broggini, L., Gadda, A., Petralia, U., Ricagno, S.

---

Funding Organization	Location	Grant Number
University and Research - University of Milan	Italy	--

Revision History  

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