5C9K

Crystal structure of a highly fibrillogenic Arg24Gly mutant of the Recombinant variable domain 6AJL2

• PDB DOI: https://doi.org/10.2210/pdb5C9K/pdb

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


• Deposited: 2015-06-27 Released: 2015-08-05 
• Deposition Author(s): Hernandez-Santoyo, A., Rodriguez-Romero, A., Luna-Martinez, O.D., Becerril-Lujan, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.219 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Mutating amyloidogenic lambda6 light chain AR back to germline 6aJL2

Luna-Martinez, O.D., Villalba-Velazquez, M.I., Sanchez-Alcala, R., Hernandez-Santoyo, A., Fernandez-Velasco, D.A., Rodriguez-Romero, A., Becerril-Lujan, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors.

Biological Assembly 7  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 7 assigned by authors.

Biological Assembly 8  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 8 assigned by authors.

Biological Assembly 9  

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

Biological assembly 9 assigned by authors and generated by PISA (software)

Biological Assembly 10  

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

Biological assembly 10 assigned by authors and generated by PISA (software)

Biological Assembly 11  

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

Biological assembly 11 assigned by authors and generated by PISA (software)

Biological Assembly 12  

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

Biological assembly 12 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 95.13 kDa 
• Atom Count: 7,697 
• Modelled Residue Count: 887 
• Deposited Residue Count: 888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid lambda 6 light chain variable region PIP	A, B, C, D, E, F, G, H	111	Homo sapiens	Mutation(s): 0  Gene Names: VL GENE SEGMENT 6A AND JL2/3 GENE SEGMENT
UniProt
Find proteins for Q96JD1 (Homo sapiens) Explore Q96JD1  Go to UniProtKB:  Q96JD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	I [auth B], J [auth B], K [auth E], L [auth H]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.219 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.556	α = 90
b = 95.633	β = 96
c = 102.583	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-05 
Deposition Author(s): Hernandez-Santoyo, A., Rodriguez-Romero, A., Luna-Martinez, O.D., Becerril-Lujan, B.

Revision History  

• Version 1.0: 2015-08-05
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary