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 
  • R-Value Observed: 0.126 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1002/anie.201703107
  • Primary Citation of Related Structures:  
    5NQM, 5NQN, 5NQO

  • 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 Cu I provide atomic-level information about how a storage protein loads with metal ions. Many more sites are occupied than Cu I equiv added, with binding by twelve central sites dominating. These can form [Cu 4 (S-Cys) 4 ] intermediates leading to [Cu 4 (S-Cys) 5 ] - , [Cu 4 (S-Cys) 6 ] 2- , and [Cu 4 (S-Cys) 5 (O-Asn)] - clusters. Construction of the five Cu I 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 Cu I 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CSP3133Methylosinus trichosporium OB3bMutation(s): 0 
UniProt
Find proteins for A0A1I9GEP2 (Methylosinus trichosporium OB3b)
Explore A0A1I9GEP2 
Go to UniProtKB:  A0A1I9GEP2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I9GEP2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU1
Query on CU1

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
S [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.901α = 90
b = 105.691β = 90
c = 45.625γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2017-07-19
    Changes: Database references
  • Version 1.3: 2017-08-30
    Changes: Author supporting evidence
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description