5ACM

Mcg immunoglobulin variable domain with methylene blue

• PDB DOI: https://doi.org/10.2210/pdb5ACM/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-17 Released: 2015-12-02 
• Deposition Author(s): Brumshtein, B., Esswein, S.R., Salwinski, L., Phillips, M.L., Ly, A.T., Cascio, D., Sawaya, M.R., Eisenberg, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.122 
• R-Value Work: 0.110 
• R-Value Observed: 0.111 

Starting Model: experimental

Literature

Inhibition by small-molecule ligands of formation of amyloid fibrils of an immunoglobulin light chain variable domain.

Brumshtein, B., Esswein, S.R., Salwinski, L., Phillips, M.L., Ly, A.T., Cascio, D., Sawaya, M.R., Eisenberg, D.S.

(2015) Elife 4: e10935-e10935

• PubMed: 26576950 
• DOI: https://doi.org/10.7554/eLife.10935
• Primary Citation of Related Structures:  
  5ACL, 5ACM


• PubMed Abstract: 
  

  Overproduction of immunoglobulin light chains leads to systemic amyloidosis, a lethal disease characterized by the formation of amyloid fibrils in patients' tissues. Excess light chains are in equilibrium between dimers and less stable monomers which can undergo irreversible aggregation to the amyloid state. The dimers therefore must disassociate into monomers prior to forming amyloid fibrils. Here we identify ligands that inhibit amyloid formation by stabilizing the Mcg light chain variable domain dimer and shifting the equilibrium away from the amyloid-prone monomer.

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Organizational Affiliation: 

Department of Biological Chemistry, Howard Hughes Medical Institute, UCLA, Los Angeles, United States.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.08 kDa 
• Atom Count: 1,873 
• Modelled Residue Count: 218 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MCG	A, B	111	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01709 (Homo sapiens) Explore P01709  Go to UniProtKB:  P01709
GTEx:  ENSG00000278196

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MBT	C [auth A]	3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM C16 H18 N3 S RBTBFTRPCNLSDE-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.122 
• R-Value Work: 0.110 
• R-Value Observed: 0.111 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.22	α = 90
b = 31.08	β = 90.09
c = 73.63	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-02 
Deposition Author(s): Brumshtein, B., Esswein, S.R., Salwinski, L., Phillips, M.L., Ly, A.T., Cascio, D., Sawaya, M.R., Eisenberg, D.S.

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2017-03-22
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Data collection
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary