5WMJ | pdb_00005wmj

KVWGSI segment from Superoxide Dismutase 1,residues 30-35

• PDB DOI: https://doi.org/10.2210/pdb5WMJ/pdb

• Classification: PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2017-07-28 Released: 2018-03-28 
• Deposition Author(s): Sangwan, S., Sawaya, M., Eisenberg, D.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.170 (Depositor), 0.167 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: in silico

Literature

Atomic structures of corkscrew-forming segments of SOD1 reveal varied oligomer conformations.

Sangwan, S., Sawaya, M.R., Murray, K.A., Hughes, M.P., Eisenberg, D.S.

(2018) Protein Sci 27: 1231-1242

• PubMed: 29453800 
• DOI: https://doi.org/10.1002/pro.3391
• Primary Citation Related Structures: 
  5WMJ, 5WOR, 6B79


• PubMed Abstract: 
  

  The aggregation cascade of disease-related amyloidogenic proteins, terminating in insoluble amyloid fibrils, involves intermediate oligomeric states. The structural and biochemical details of these oligomers have been largely unknown. Here we report crystal structures of variants of the cytotoxic oligomer-forming segment residues 28-38 of the ALS-linked protein, SOD1. The crystal structures reveal three different architectures: corkscrew oligomeric structure, nontwisting curved sheet structure and a steric zipper proto-filament structure. Our work highlights the polymorphism of the segment 28-38 of SOD1 and identifies the molecular features of amyloidogenic entities.

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Organizational Affiliation: 
• Department of Biological Chemistry Los Angeles, Howard Hughes Medical Institute, UCLA-DOE and Molecular Biology Institute, California.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 1.49 kDa 
• Atom Count: 123 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A, B	6	Homo sapiens	Mutation(s): 0  EC: 1.15.1.1 (PDB Primary Data), 1.8 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens) Explore P00441  Go to UniProtKB:  P00441
PHAROS:  P00441 GTEx:  ENSG00000142168

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TFA	C [auth B]	trifluoroacetic acid C2 H F3 O2 DTQVDTLACAAQTR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.170 (Depositor), 0.167 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 9.518	α = 90
b = 20.282	β = 90
c = 44.249	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-03-28 
Deposition Author(s): Sangwan, S., Sawaya, M., Eisenberg, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	AG054022
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2018-03-28
  Type: Initial release
  
• Version 1.1: 2018-07-18
  Changes: Data collection, Database references
• Version 1.2: 2019-11-06
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2019-11-20
  Changes: Author supporting evidence
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references
• Version 1.5: 2024-04-03
  Changes: Refinement description