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- PDB-4fxx: Structure of SF1 coiled-coil domain -

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Basic information

Entry
Database: PDB / ID: 4fxx
TitleStructure of SF1 coiled-coil domain
ComponentsSplicing factor 1
KeywordsRNA BINDING PROTEIN / splicing factor 1 / coiled-coil / pre-mRNA splicing / U2AF65-UHM binding
Function / homology
Function and homology information


U2AF complex / regulation of mRNA splicing, via spliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition / mRNA Splicing - Major Pathway / spliceosomal complex / negative regulation of smooth muscle cell proliferation / mRNA splicing, via spliceosome / transcription corepressor activity / ribosome ...U2AF complex / regulation of mRNA splicing, via spliceosome / spliceosomal complex assembly / mRNA 3'-splice site recognition / mRNA Splicing - Major Pathway / spliceosomal complex / negative regulation of smooth muscle cell proliferation / mRNA splicing, via spliceosome / transcription corepressor activity / ribosome / mRNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Helix Hairpins - #1790 / Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Helix Hairpins ...Helix Hairpins - #1790 / Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Helix Hairpins / Helix non-globular / Special / K Homology domain / K homology RNA-binding domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
IMIDAZOLE / MALONATE ION / Splicing factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4801 Å
AuthorsGupta, A. / Bauer, W.J. / Wang, W. / Kielkopf, C.L.
CitationJournal: Structure / Year: 2013
Title: Structure of Phosphorylated SF1 Bound to U2AF(65) in an Essential Splicing Factor Complex.
Authors: Wang, W. / Maucuer, A. / Gupta, A. / Manceau, V. / Thickman, K.R. / Bauer, W.J. / Kennedy, S.D. / Wedekind, J.E. / Green, M.R. / Kielkopf, C.L.
History
DepositionJul 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Splicing factor 1
B: Splicing factor 1
C: Splicing factor 1
D: Splicing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,80714
Polymers51,0504
Non-polymers75710
Water1,29772
1
A: Splicing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9343
Polymers12,7631
Non-polymers1712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Splicing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9013
Polymers12,7631
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Splicing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0034
Polymers12,7631
Non-polymers2403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Splicing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9704
Polymers12,7631
Non-polymers2073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Splicing factor 1
B: Splicing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8346
Polymers25,5252
Non-polymers3094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-10 kcal/mol
Surface area12310 Å2
MethodPISA
6
C: Splicing factor 1
hetero molecules

D: Splicing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9738
Polymers25,5252
Non-polymers4476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
Buried area2540 Å2
ΔGint-14 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.030, 37.970, 144.680
Angle α, β, γ (deg.)90.000, 107.380, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Splicing factor 1 / Mammalian branch point-binding protein / BBP / mBBP / Transcription factor ZFM1 / Zinc finger gene ...Mammalian branch point-binding protein / BBP / mBBP / Transcription factor ZFM1 / Zinc finger gene in MEN1 locus / Zinc finger protein 162


Mass: 12762.532 Da / Num. of mol.: 4 / Fragment: UNP Residues 26-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF1, ZFM1, ZNF162 / Plasmid: pGEX-6p / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q15637
#2: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.34 M sodium malonate pH 6.0, 0.1 M imidazole maleate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.48→48 Å / Num. all: 18175 / Num. obs: 16211 / % possible obs: 89.19 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.08 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.5645
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
2.48-2.615.290.37103551959175.39
2.61-2.775.160.2699581929177.33
2.77-2.964.870.294251935182.99
2.96-3.24.680.1691151949188.46
3.2-3.514.630.1488811919196.56
3.51-3.9250.1191931838199.83
3.92-4.535.460.0987311598199.97
4.53-5.555.540.0976761385199.96
5.55-7.845.460.0859181083199.95
7.84-485.130.083158616197.59

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.2.19data scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
Web-Icedata collection
MOSFLMdata reduction
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4801→34.966 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7967 / SU ML: 0.87 / σ(F): 0 / Phase error: 27.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2698 1271 7.92 %
Rwork0.2365 --
obs0.2393 16049 88.6 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.151 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 117.25 Å2 / Biso mean: 46.2666 Å2 / Biso min: 11.78 Å2
Baniso -1Baniso -2Baniso -3
1-8.843 Å2-0 Å20.4129 Å2
2---6.3552 Å20 Å2
3----2.4879 Å2
Refinement stepCycle: LAST / Resolution: 2.4801→34.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 54 72 2984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122975
X-RAY DIFFRACTIONf_angle_d0.874025
X-RAY DIFFRACTIONf_chiral_restr0.058450
X-RAY DIFFRACTIONf_plane_restr0.009539
X-RAY DIFFRACTIONf_dihedral_angle_d12.2321165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4801-2.57930.34161150.27321326144172
2.5793-2.69670.28091210.25671359148075
2.6967-2.83880.31711280.24131453158179
2.8388-3.01650.2711270.23691531165883
3.0165-3.24930.29331370.24821664180190
3.2493-3.5760.23591530.22481785193897
3.576-4.09280.24381640.215718562020100
4.0928-5.15380.25551660.207318762042100
5.1538-34.96940.29881600.27771928208899

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