5NQO

CU(I)-CSP3 (COPPER STORAGE PROTEIN 3) FROM METHYLOSINUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.125 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Visualizing Biological Copper Storage: The Importance of Thiolate-Coordinated Tetranuclear Clusters.

Basle, A.Platsaki, S.Dennison, C.

(2017) Angew. Chem. Int. Ed. Engl. 56: 8697-8700

  • DOI: 10.1002/anie.201703107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacteria possess cytosolic proteins (Csp3s) capable of binding large quantities of copper and preventing toxicity. Crystal structures of a Csp3 plus increasing amounts of CuI provide atomic-level information about how a storage protein loads with met ...

    Bacteria possess cytosolic proteins (Csp3s) capable of binding large quantities of copper and preventing toxicity. Crystal structures of a Csp3 plus increasing amounts of CuI provide atomic-level information about how a storage protein loads with metal ions. Many more sites are occupied than CuI equiv added, with binding by twelve central sites dominating. These can form [Cu4 (S-Cys)4 ] intermediates leading to [Cu4 (S-Cys)5 ]- , [Cu4 (S-Cys)6 ]2- , and [Cu4 (S-Cys)5 (O-Asn)]- clusters. Construction of the five CuI sites at the opening of the bundle lags behind the main core, and the two least accessible sites at the opposite end of the bundle are occupied last. Facile CuI cluster formation, reminiscent of that for inorganic complexes with organothiolate ligands, is largely avoided in biology but is used by proteins that store copper in the cytosol of prokaryotes and eukaryotes, where this reactivity is also key to toxicity.


    Organizational Affiliation

    Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CSP3
A
133Methylosinus trichosporium OB3bMutation(s): 0 
Find proteins for A0A1I9GEP2 (Methylosinus trichosporium OB3b)
Go to UniProtKB:  A0A1I9GEP2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CU1
Query on CU1

Download SDF File 
Download CCD File 
A
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.125 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 44.901α = 90.00
b = 105.691β = 90.00
c = 45.625γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K008439/1

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-06-28
    Type: Database references
  • Version 1.2: 2017-07-19
    Type: Database references
  • Version 1.3: 2017-08-30
    Type: Author supporting evidence