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.

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)

wwPDB Validation 3D Report Full Report

Validation slider image for 3FMA

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.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32909
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12186
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

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Entry History

Deposition Data

Released Date: 2009-12-22

Deposition Author(s):

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.