3FMA

Crystal structure of the GYF domain of Smy2 in complex with a proline-rich peptide from BBP/ScSF1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

SMY2-type GYF domain recognition in mRNA surveillance complexes

Ash, M.R.Faelber, K.Kosslick, D.Albert, G.Roske, Y.Kofler, M.Schuemann, M.Krause, E.Freund, C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SMY2
A, B, C, D, E
100Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SMY2
UniProt
Find proteins for P32909 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32909 
Go to UniProtKB:  P32909
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32909
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Branchpoint-bridging proteinF [auth L],
G [auth M],
H [auth N],
I [auth O],
J [auth P]
11N/AMutation(s): 0 
UniProt
Find proteins for Q12186 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12186 
Go to UniProtKB:  Q12186
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12186
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.4α = 90
b = 101.4β = 90
c = 150.7γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SHELXCDphasing
SHELXEmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary