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- PDB-3fma: Crystal structure of the GYF domain of Smy2 in complex with a pro... -

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Basic information

Entry
Database: PDB / ID: 3fma
TitleCrystal structure of the GYF domain of Smy2 in complex with a proline-rich peptide from BBP/ScSF1
Components
  • Branchpoint-bridging protein
  • Protein SMY2
KeywordsPROTEIN BINDING / GYF domain / poly-proline binding / proline-rich peptide / domain swap / PRS / RAGNYA
Function / homology
Function and homology information


pre-mRNA branch point binding / nuclear protein quality control by the ubiquitin-proteasome system / protein-containing complex disassembly / regulation of mRNA splicing, via spliceosome / commitment complex / spliceosomal complex assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / mRNA splicing, via spliceosome / mRNA binding / endoplasmic reticulum membrane ...pre-mRNA branch point binding / nuclear protein quality control by the ubiquitin-proteasome system / protein-containing complex disassembly / regulation of mRNA splicing, via spliceosome / commitment complex / spliceosomal complex assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / mRNA splicing, via spliceosome / mRNA binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
GYF domain / : / Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues ...GYF domain / : / Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / Clathrin adaptor, appendage, Ig-like subdomain superfamily / K Homology domain, type 1 superfamily / Dna Ligase; domain 1 / K Homology domain / K homology RNA-binding domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein SMY2 / Branchpoint-bridging protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsAsh, M.R. / Faelber, K.
CitationJournal: to be published
Title: SMY2-type GYF domain recognition in mRNA surveillance complexes
Authors: Ash, M.R. / Faelber, K. / Kosslick, D. / Albert, G. / Roske, Y. / Kofler, M. / Schuemann, M. / Krause, E. / Freund, C.
History
DepositionDec 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein SMY2
B: Protein SMY2
C: Protein SMY2
D: Protein SMY2
E: Protein SMY2
L: Branchpoint-bridging protein
M: Branchpoint-bridging protein
N: Branchpoint-bridging protein
O: Branchpoint-bridging protein
P: Branchpoint-bridging protein


Theoretical massNumber of molelcules
Total (without water)61,39510
Polymers61,39510
Non-polymers00
Water543
1
A: Protein SMY2
L: Branchpoint-bridging protein


Theoretical massNumber of molelcules
Total (without water)12,2792
Polymers12,2792
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein SMY2
M: Branchpoint-bridging protein


Theoretical massNumber of molelcules
Total (without water)12,2792
Polymers12,2792
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein SMY2
N: Branchpoint-bridging protein


Theoretical massNumber of molelcules
Total (without water)12,2792
Polymers12,2792
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein SMY2
O: Branchpoint-bridging protein


Theoretical massNumber of molelcules
Total (without water)12,2792
Polymers12,2792
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Protein SMY2
P: Branchpoint-bridging protein


Theoretical massNumber of molelcules
Total (without water)12,2792
Polymers12,2792
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.4, 101.4, 150.7
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21E
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1SERSERBB13 - 9613 - 96
2VALVALEE12 - 9612 - 96
3VALVALCC12 - 9612 - 96
4VALVALDD12 - 9612 - 96

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Components

#1: Protein
Protein SMY2 / Suppressor of MYO2-66 protein


Mass: 11296.908 Da / Num. of mol.: 5 / Fragment: GYF domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SMY2 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P32909
#2: Protein/peptide
Branchpoint-bridging protein / Splicing factor 1 / Zinc finger protein BBP / Mud synthetic-lethal 5 protein


Mass: 982.090 Da / Num. of mol.: 5 / Fragment: Proline-rich peptide / Source method: obtained synthetically / Details: Fmoc solid phase synthesis / References: UniProt: Q12186
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 1.2M (NH4)2SO4, 0.1M Bicine, pH 9.0, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978522, 0.97875
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9785221
20.978751
ReflectionResolution: 2.5→48.057 Å / Num. obs: 27942 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Biso Wilson estimate: 64.4 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 17.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 2.1 / Num. measured all: 41869 / Num. unique all: 4003 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.5→48.057 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.22 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.805 / SU B: 22.043 / SU ML: 0.205 / SU R Cruickshank DPI: 0.313 / SU Rfree: 0.235 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.313 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1411 5.1 %RANDOM
Rwork0.225 ---
obs0.226 27895 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 48.84 Å2 / Biso mean: 30.558 Å2 / Biso min: 18.71 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å20 Å2
2---2.1 Å20 Å2
3---4.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3596 0 0 3 3599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223704
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9555042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0585449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03624.481154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78215600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7941510
X-RAY DIFFRACTIONr_chiral_restr0.0770.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212769
X-RAY DIFFRACTIONr_mcbond_it0.2911.52262
X-RAY DIFFRACTIONr_mcangle_it0.55723696
X-RAY DIFFRACTIONr_scbond_it0.83831442
X-RAY DIFFRACTIONr_scangle_it1.3734.51344
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 670 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
BMEDIUM POSITIONAL0.340.5
EMEDIUM POSITIONAL0.310.5
CMEDIUM POSITIONAL0.320.5
DMEDIUM POSITIONAL0.380.5
BMEDIUM THERMAL0.32
EMEDIUM THERMAL0.22
CMEDIUM THERMAL0.272
DMEDIUM THERMAL0.22
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 102 -
Rwork0.332 1922 -
all-2024 -
obs-2024 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.79490.17140.1063.58780.61962.9598-0.23370.294-0.0497-0.40660.25350.51520.1673-0.1703-0.01980.4661-0.18060.02630.10320.03160.234-39.752-52.79222.181
21.49940.64690.37074.82432.07762.4677-0.24070.15910.2898-0.33360.21990.6401-0.3478-0.07970.02090.4714-0.06870.01770.06750.08110.2465-31.969-26.429.491
32.10011.8161-1.01763.5301-2.91893.2475-0.27040.1631-0.1898-0.05150.1032-0.3534-0.09880.29940.16720.5616-0.21310.09580.2582-0.06290.2361-10.974-32.35520.809
40.83250.53890.1175.7561-2.58823.1981-0.13160.1964-0.1858-0.48440.2047-0.52610.35480.2131-0.07310.5078-0.01640.13050.1106-0.07740.3181-18.922-60.86828.833
52.29911.8861-2.11764.567-2.18773.7976-0.0990.1369-0.50880.1318-0.0576-0.43270.6286-0.04310.15660.4279-0.1934-0.04450.2091-0.04440.2006-2.557-18.1254.108
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 93
2X-RAY DIFFRACTION1L4 - 10
3X-RAY DIFFRACTION2B13 - 96
4X-RAY DIFFRACTION2M3 - 9
5X-RAY DIFFRACTION3C11 - 96
6X-RAY DIFFRACTION3N4 - 9
7X-RAY DIFFRACTION4D12 - 96
8X-RAY DIFFRACTION4O4 - 10
9X-RAY DIFFRACTION5E12 - 96
10X-RAY DIFFRACTION5P4 - 10

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