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- PDB-5ife: Crystal structure of the human SF3b core complex -

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Basic information

Entry
Database: PDB / ID: 5ife
TitleCrystal structure of the human SF3b core complex
Components
  • (Splicing factor 3B subunit ...) x 3
  • PHD finger-like domain-containing protein 5A
KeywordsSPLICING / pre-mRNA splicing / U2 snRNP / essential splicing factor
Function / homology
Function and homology information


U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / SAGA complex / U2 snRNP ...U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / SAGA complex / U2 snRNP / positive regulation of transcription by RNA polymerase III / U2-type prespliceosome / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / U2 snRNA binding / regulation of DNA repair / catalytic step 2 spliceosome / RNA splicing / mRNA Splicing - Major Pathway / stem cell differentiation / spliceosomal complex / B-WICH complex positively regulates rRNA expression / negative regulation of protein catabolic process / nuclear matrix / mRNA splicing, via spliceosome / nuclear speck / chromatin remodeling / mRNA binding / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Splicing factor 3B, subunit 5 / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / PHF5-like / PHF5-like protein / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Splicing factor 3B subunit 1-like / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term ...Splicing factor 3B, subunit 5 / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / PHF5-like / PHF5-like protein / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Splicing factor 3B subunit 1-like / 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 / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 3 / PHD finger-like domain-containing protein 5A / Splicing factor 3B subunit 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.1 Å
AuthorsCretu, C. / Dybkov, O. / De Laurentiis, E. / Will, C.L. / Luhrmann, R. / Pena, V.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
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 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Splicing factor 3B subunit 5
C: Splicing factor 3B subunit 1
D: PHD finger-like domain-containing protein 5A
A: Splicing factor 3B subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,5098
Polymers307,2744
Non-polymers2354
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15150 Å2
ΔGint-58 kcal/mol
Surface area86290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.055, 154.436, 210.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Splicing factor 3B subunit ... , 3 types, 3 molecules BCA

#1: Protein Splicing factor 3B subunit 5 / SF3b5 / Pre-mRNA-splicing factor SF3b 10 kDa subunit


Mass: 10149.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF3B5, SF3B10 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BWJ5
#2: Protein Splicing factor 3B subunit 1 / Pre-mRNA-splicing factor SF3b 155 kDa subunit / SF3b155 / Spliceosome-associated protein 155 / SAP 155


Mass: 146024.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF3B1, SAP155 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75533
#4: Protein Splicing factor 3B subunit 3 / Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein ...Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein 130 / SAP 130


Mass: 137791.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF3B3, KIAA0017, SAP130 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q15393

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Protein , 1 types, 1 molecules D

#3: Protein PHD finger-like domain-containing protein 5A / PHD finger-like domain protein 5A / Splicing factor 3B-associated 14 kDa protein / SF3b14b


Mass: 13308.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF5A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7RTV0

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K

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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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.05 M HEPES-NaOH pH=6.91-7.05, 40% Pentaerythritol propoxylate (5/4 PO/OH), 0.2M KCl
PH range: 6.91-7.05

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.918, 1.254, 1.282, 1.0
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9181
21.2541
31.2821
411
ReflectionResolution: 3.1→47.04 Å / Num. obs: 62814 / % possible obs: 99.9 % / Redundancy: 8.3 % / CC1/2: 0.995 / Net I/av σ(I): 1.2 / Net I/σ(I): 10.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
AutoSolphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.1→47.037 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 28.83
RfactorNum. reflection% reflection
Rfree0.2595 5928 4.95 %
Rwork0.2305 --
obs0.232 119805 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→47.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17099 0 4 0 17103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00217437
X-RAY DIFFRACTIONf_angle_d0.53923624
X-RAY DIFFRACTIONf_dihedral_angle_d13.65810579
X-RAY DIFFRACTIONf_chiral_restr0.0422682
X-RAY DIFFRACTIONf_plane_restr0.0043052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0998-3.1350.40141490.39173706X-RAY DIFFRACTION96
3.135-3.17190.39892180.3563798X-RAY DIFFRACTION100
3.1719-3.21060.37952070.33513760X-RAY DIFFRACTION100
3.2106-3.25120.34161900.34193782X-RAY DIFFRACTION100
3.2512-3.2940.33131690.32923862X-RAY DIFFRACTION100
3.294-3.33910.35291870.32943810X-RAY DIFFRACTION100
3.3391-3.38680.31621910.32923845X-RAY DIFFRACTION100
3.3868-3.43730.34572170.32023766X-RAY DIFFRACTION100
3.4373-3.4910.37841920.31023771X-RAY DIFFRACTION100
3.491-3.54820.29231950.29213765X-RAY DIFFRACTION100
3.5482-3.60940.31511900.27823888X-RAY DIFFRACTION100
3.6094-3.6750.31870.28293797X-RAY DIFFRACTION100
3.675-3.74560.32981710.27173822X-RAY DIFFRACTION100
3.7456-3.82210.31152040.26453769X-RAY DIFFRACTION100
3.8221-3.90510.27942040.26143849X-RAY DIFFRACTION100
3.9051-3.99590.28771970.24663748X-RAY DIFFRACTION100
3.9959-4.09580.2931630.24643840X-RAY DIFFRACTION100
4.0958-4.20650.28362130.22993839X-RAY DIFFRACTION100
4.2065-4.33020.25842190.21343749X-RAY DIFFRACTION100
4.3302-4.46980.22632100.19873791X-RAY DIFFRACTION100
4.4698-4.62950.23662210.18823755X-RAY DIFFRACTION100
4.6295-4.81460.21761900.1783851X-RAY DIFFRACTION100
4.8146-5.03350.24241630.18353828X-RAY DIFFRACTION100
5.0335-5.29860.23442000.19583801X-RAY DIFFRACTION100
5.2986-5.630.26561930.20993792X-RAY DIFFRACTION100
5.63-6.06390.27412340.21053769X-RAY DIFFRACTION100
6.0639-6.67260.24282060.21113818X-RAY DIFFRACTION100
6.6726-7.63460.23022120.20173763X-RAY DIFFRACTION100
7.6346-9.60530.15882180.16143791X-RAY DIFFRACTION100
9.6053-47.04250.18422180.17753752X-RAY DIFFRACTION99

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