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- PDB-5hy7: SF3B10-SF3B130 from Chaetomium thermophilum -

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Basic information

Entry
Database: PDB / ID: 5hy7
TitleSF3B10-SF3B130 from Chaetomium thermophilum
Components
  • Putative pre-mRNA splicing protein
  • YSF3
KeywordsPROTEIN BINDING / spliceosome / complex / WD40s / Hydrolase
Function / homology
Function and homology information


U2 snRNP / mRNA splicing, via spliceosome / nucleic acid binding / nucleus
Similarity search - Function
Splicing factor 3B, subunit 5 / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Splicing factor subunit / Putative pre-mRNA splicing protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.9 Å
AuthorsPonce-Salvatierra, A. / Schmitzova, J. / Pena, V.
CitationJournal: Mol.Cell / Year: 2016
Title: Molecular Architecture of SF3b and Structural Consequences of Its Cancer-Related Mutations.
Authors: Cretu, C. / Schmitzova, J. / Ponce-Salvatierra, A. / Dybkov, O. / De Laurentiis, E.I. / Sharma, K. / Will, C.L. / Urlaub, H. / Luhrmann, R. / Pena, V.
History
DepositionFeb 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative pre-mRNA splicing protein
D: YSF3
B: Putative pre-mRNA splicing protein
C: YSF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,14913
Polymers290,7884
Non-polymers3619
Water0
1
A: Putative pre-mRNA splicing protein
D: YSF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,5546
Polymers145,3942
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-47 kcal/mol
Surface area48660 Å2
MethodPISA
2
B: Putative pre-mRNA splicing protein
C: YSF3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,5947
Polymers145,3942
Non-polymers2005
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-53 kcal/mol
Surface area49350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.083, 197.083, 446.453
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Putative pre-mRNA splicing protein / Rse1


Mass: 134507.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0024090 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0S5A2
#2: Protein YSF3


Mass: 10886.376 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0012180 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0S133
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca

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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: 4.58 Å3/Da / Density % sol: 73.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: PEG 4000 8%, Calcium Chloride 0.1 M, Sodium Chloride 0.1 M, HEPES buffer pH 7.5 0.1 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→49.3 Å / Num. obs: 113522 / % possible obs: 100 % / Redundancy: 20.1 % / Rmerge(I) obs: 0.1671 / Net I/σ(I): 19.41
Reflection shellResolution: 2.9→3 Å / Redundancy: 20 % / Rmerge(I) obs: 3.8 / Mean I/σ(I) obs: 0.89 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.9→49.271 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.4
RfactorNum. reflection% reflection
Rfree0.2532 5676 5 %
Rwork0.2145 --
obs0.2164 113501 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19201 0 9 0 19210
Refine LS restraintsType: f_plane_restr / Dev ideal: 0.005 / Number: 3466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.9330.39621860.38653538X-RAY DIFFRACTION100
2.933-2.96750.35541850.35983513X-RAY DIFFRACTION100
2.9675-3.00360.40721850.3513523X-RAY DIFFRACTION100
3.0036-3.04170.40071870.34813553X-RAY DIFFRACTION100
3.0417-3.08170.36411880.33693563X-RAY DIFFRACTION100
3.0817-3.12390.36621860.32453543X-RAY DIFFRACTION100
3.1239-3.16850.36761860.31713526X-RAY DIFFRACTION100
3.1685-3.21580.32271860.32513545X-RAY DIFFRACTION100
3.2158-3.2660.34311870.3093539X-RAY DIFFRACTION100
3.266-3.31960.33531870.28583551X-RAY DIFFRACTION100
3.3196-3.37680.28391860.28943540X-RAY DIFFRACTION100
3.3768-3.43820.30341880.27633566X-RAY DIFFRACTION100
3.4382-3.50430.33271870.26973557X-RAY DIFFRACTION100
3.5043-3.57580.30691870.25793556X-RAY DIFFRACTION100
3.5758-3.65350.27771890.25093585X-RAY DIFFRACTION100
3.6535-3.73850.28251850.23413530X-RAY DIFFRACTION100
3.7385-3.83190.24631890.23433578X-RAY DIFFRACTION100
3.8319-3.93550.26091890.22173591X-RAY DIFFRACTION100
3.9355-4.05130.26811880.21633579X-RAY DIFFRACTION100
4.0513-4.1820.25621890.19853581X-RAY DIFFRACTION100
4.182-4.33130.22621880.18993588X-RAY DIFFRACTION100
4.3313-4.50470.21121910.17693611X-RAY DIFFRACTION100
4.5047-4.70950.19711890.16313598X-RAY DIFFRACTION100
4.7095-4.95760.21731900.16713611X-RAY DIFFRACTION100
4.9576-5.26790.19761920.18123639X-RAY DIFFRACTION100
5.2679-5.67410.23091910.18783647X-RAY DIFFRACTION100
5.6741-6.24410.25921930.19383653X-RAY DIFFRACTION100
6.2441-7.14520.21941950.19133708X-RAY DIFFRACTION100
7.1452-8.99330.22031980.18973755X-RAY DIFFRACTION100
8.9933-49.27780.2442090.19213958X-RAY DIFFRACTION100

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