8FO3

Structure of full-length amyloidogenic immunoglobulin light chain H9 in complex with (E)-3-nitro-4-(2-(2-phenylpropylidene)hydrazineyl)benzenesulfonamide

• PDB DOI: https://doi.org/10.2210/pdb8FO3/pdb

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


• Deposited: 2022-12-29 Released: 2023-05-24 
• Deposition Author(s): Yan, N.L., Wilson, I.A., Kelly, J.W.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.280 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 

Literature

Crystal Structures of Diaryl Hydrazone and Sulfone Stabilizers in Complex with an Amyloidogenic Light Chain Reveal an Alternate Ligand-Binding Cavity

Yan, N.L., Wilson, I.A., Kelly, J.W.

(2023) Isr J Chem 

• DOI: https://doi.org/10.1002/ijch.202300002

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 273.27 kDa 
• Atom Count: 20,516 
• Modelled Residue Count: 2,553 
• Deposited Residue Count: 2,592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H9 immunoglobulin light chain	A, B, C, D, E [auth G], F [auth H], G [auth I], H [auth J], I [auth E], J [auth F], K, L	216	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y4K (Subject of Investigation/LOI)	M [auth A], P [auth C], Q [auth G], T [auth I], U [auth E], W [auth K]	3-nitro-4-{2-[(2S)-2-phenylpropyl]hydrazinyl}benzene-1-sulfonamide C15 H18 N4 O4 S NSSXWTMELVHXJK-LLVKDONJSA-N
PO4	N [auth A], O [auth B], R [auth G], S [auth H], V [auth E], X [auth K]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.280 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.141	α = 106.31
b = 95.655	β = 92.93
c = 125.918	γ = 90.16

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Yan, N.L., Wilson, I.A., Kelly, J.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL157566
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL154732

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description