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- PDB-2pe8: Crystal structure of the UHM domain of human SPF45 (free form) -

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Basic information

Entry
Database: PDB / ID: 2pe8
TitleCrystal structure of the UHM domain of human SPF45 (free form)
ComponentsSplicing factor 45
KeywordsPROTEIN BINDING / RRM
Function / homology
Function and homology information


alternative mRNA splicing, via spliceosome / mRNA cis splicing, via spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / RNA binding / nucleoplasm
Similarity search - Function
SPF45, RNA recognition motif / Splicing factor 45 / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif ...SPF45, RNA recognition motif / Splicing factor 45 / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCorsini, L. / Basquin, J. / Hothorn, M. / Sattler, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: U2AF-homology motif interactions are required for alternative splicing regulation by SPF45.
Authors: Corsini, L. / Bonna, S. / Basquin, J. / Hothorn, M. / Scheffzek, K. / Valcarcel, J. / Sattler, M.
History
DepositionApr 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Splicing factor 45


Theoretical massNumber of molelcules
Total (without water)11,6901
Polymers11,6901
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.900, 90.200, 99.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Splicing factor 45 / / 45 kDa-splicing factor / RNA-binding motif protein 17


Mass: 11690.481 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM17, SPF45 / Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 BL21(DE3) pLysS / References: UniProt: Q96I25
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.05 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% PEG 3,350, 0.2 M MgCl2, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 1, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. all: 9819 / Num. obs: 9819 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.57 % / Biso Wilson estimate: 46.5 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.053 / Net I/σ(I): 20.13
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 4.67 / Num. unique all: 719 / Rsym value: 0.44 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UHM domain homology model based on PDB-ID 1o0p

1o0p


Resolution: 2→19.58 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.956 / SU B: 12.328 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / ESU R: 0.169 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24348 488 5 %RANDOM
Rwork0.23143 ---
all0.23204 9294 --
obs0.23204 9294 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.965 Å2
Baniso -1Baniso -2Baniso -3
1-3.65 Å20 Å20 Å2
2---0.39 Å20 Å2
3----3.27 Å2
Refinement stepCycle: LAST / Resolution: 2→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms761 0 0 30 791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022771
X-RAY DIFFRACTIONr_bond_other_d0.0010.02528
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9821037
X-RAY DIFFRACTIONr_angle_other_deg0.88231286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.614599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96424.06232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49915133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.04155
X-RAY DIFFRACTIONr_chiral_restr0.0660.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02158
X-RAY DIFFRACTIONr_nbd_refined0.1960.2136
X-RAY DIFFRACTIONr_nbd_other0.1860.2518
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2369
X-RAY DIFFRACTIONr_nbtor_other0.0810.2424
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.226
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.26
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0640.22
X-RAY DIFFRACTIONr_mcbond_it0.721.5642
X-RAY DIFFRACTIONr_mcbond_other0.1181.5207
X-RAY DIFFRACTIONr_mcangle_it0.8182788
X-RAY DIFFRACTIONr_scbond_it1.3913320
X-RAY DIFFRACTIONr_scangle_it1.9124.5249
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 32 -
Rwork0.357 669 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 15.6378 Å / Origin y: -6.1278 Å / Origin z: -11.5434 Å
111213212223313233
T-0.1143 Å20.1558 Å20.0131 Å2--0.2062 Å2-0.0514 Å2---0.2934 Å2
L7.0967 °2-1.4879 °2-2.0088 °2-10.7401 °2-1.0198 °2--10.6791 °2
S-0.6095 Å °-0.5825 Å °-0.2448 Å °1.0327 Å °0.4732 Å °0.0056 Å °-0.5017 Å °0.3891 Å °0.1363 Å °

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