3FMA | pdb_00003fma

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

• PDB DOI: https://doi.org/10.2210/pdb3FMA/pdb

• Classification: PROTEIN BINDING
• Organism(s): Saccharomyces cerevisiae, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.250 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 5 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 61.39 kDa 
• Atom Count: 3,609 
• Modeled Residue Count: 455 
• Deposited Residue Count: 555 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SMY2	A, B, C, D, E	100	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SMY2
UniProt
Find proteins for P32909 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32909  Go to UniProtKB:  P32909

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Branchpoint-bridging protein	F [auth L], G [auth M], H [auth N], I [auth O], J [auth P]	11	N/A	Mutation(s): 0
UniProt
Find proteins for Q12186 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12186  Go to UniProtKB:  Q12186

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.250 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.4	α = 90
b = 101.4	β = 90
c = 150.7	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• 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
  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