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: 2.5 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein SMY2
A, B, C, D, E
100Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SMY2
Find proteins for P32909 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32909
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Branchpoint-bridging protein
L, M, N, O, P
11Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MSL5 (BBP, SF1)
Find proteins for Q12186 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12186
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D 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: 2.5 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.225 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.400α = 90.00
b = 101.400β = 90.00
c = 150.700γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
SHELXCDphasing
SHELXEmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-12-19 
  • Released Date: 2009-12-22 
  • Deposition Author(s): Ash, M.R., Faelber, K.

Revision History 

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description