5N1W

Structure of xEco2 acetyltransferase domain bound to K105-CoA conjugate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural Basis of Eco1-Mediated Cohesin Acetylation.

Chao, W.C.Wade, B.O.Bouchoux, C.Jones, A.W.Purkiss, A.G.Federico, S.O'Reilly, N.Snijders, A.P.Uhlmann, F.Singleton, M.R.

(2017) Sci Rep 7: 44313-44313

  • DOI: https://doi.org/10.1038/srep44313
  • Primary Citation of Related Structures:  
    5N1U, 5N1W, 5N22

  • PubMed Abstract: 

    Sister-chromatid cohesion is established by Eco1-mediated acetylation on two conserved tandem lysines in the cohesin Smc3 subunit. However, the molecular basis of Eco1 substrate recognition and acetylation in cohesion is not fully understood. Here, we discover and rationalize the substrate specificity of Eco1 using mass spectrometry coupled with in-vitro acetylation assays and crystallography. Our structures of the X. laevis Eco2 (xEco2) bound to its primary and secondary Smc3 substrates demonstrate the plasticity of the substrate-binding site, which confers substrate specificity by concerted conformational changes of the central β hairpin and the C-terminal extension.


  • Organizational Affiliation

    Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
XEco2
A, B
183Xenopus laevisMutation(s): 0 
Gene Names: xeco2
UniProt
Find proteins for A8QZK6 (Xenopus laevis)
Explore A8QZK6 
Go to UniProtKB:  A8QZK6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8QZK6
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA,ILE-GLY-ALA-LYX-LYS-ALA
C, D
7Xenopus laevisMutation(s): 0 
UniProt
Find proteins for O93309 (Xenopus laevis)
Explore O93309 
Go to UniProtKB:  O93309
Entity Groups  
UniProt GroupO93309
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8HB
Query on 8HB

Download Ideal Coordinates CCD File 
F [auth C],
H [auth D]
(2~{S})-2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]propanoic acid
C24 H40 N7 O18 P3 S
ULCSPOREAVNZTJ-IBNUZSNCSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth C],
G [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.301α = 90
b = 60.61β = 99.63
c = 66.905γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomFC001155
Wellcome TrustUnited KingdomFC001155
Medical Research Council (United Kingdom)United KingdomFC001155

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-03-29
    Changes: Database references
  • Version 2.0: 2017-09-13
    Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description