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- PDB-6en4: SF3b core in complex with a splicing modulator -

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Basic information

Entry
Database: PDB / ID: 6en4
TitleSF3b core in complex with a splicing modulator
Components
  • (Splicing factor 3B subunit ...) x 3
  • PHD finger-like domain-containing protein 5A
KeywordsSPLICING / Protein complex / splicing modulator
Function / homology
Function and homology information


U11/U12 snRNP / B-WICH complex / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / splicing factor binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / SAGA complex / U2 snRNP ...U11/U12 snRNP / B-WICH complex / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / splicing factor binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / SAGA complex / U2 snRNP / U2-type prespliceosome / positive regulation of transcription by RNA polymerase III / precatalytic spliceosome / regulation of RNA splicing / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / positive regulation of transcription by RNA polymerase I / U2 snRNA binding / regulation of DNA repair / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / spliceosomal complex / mRNA splicing, via spliceosome / negative regulation of protein catabolic process / B-WICH complex positively regulates rRNA expression / nuclear matrix / nuclear speck / chromatin remodeling / mRNA binding / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / 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 / : / PPP2R1A-like HEAT repeat ...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 / : / PPP2R1A-like HEAT repeat / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-BGZ / 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 / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsCretu, C. / Pena, V.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Mol. Cell / Year: 2018
Title: Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds.
Authors: Cretu, C. / Agrawal, A.A. / Cook, A. / Will, C.L. / Fekkes, P. / Smith, P.G. / Luhrmann, R. / Larsen, N. / Buonamici, S. / Pena, V.
History
DepositionOct 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)254,0568
Polymers253,3234
Non-polymers7334
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15900 Å2
ΔGint-66 kcal/mol
Surface area85290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.067, 154.568, 210.207
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 ABC

#1: 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: 135018.984 Da / Num. of mol.: 1 / Mutation: internal deletion 1068-1085
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
#2: Protein Splicing factor 3B subunit 5 / SF3b5 / Pre-mRNA-splicing factor SF3b 10 kDa subunit


Mass: 10018.173 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
#3: Protein Splicing factor 3B subunit 1 / Pre-mRNA-splicing factor SF3b 155 kDa subunit / SF3b155 / Spliceosome-associated protein 155 / SAP 155


Mass: 96615.734 Da / Num. of mol.: 1 / Mutation: deletion 1-452
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

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Protein , 1 types, 1 molecules D

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


Mass: 11670.525 Da / Num. of mol.: 1 / Mutation: deletion 99-110
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-BGZ / [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{S})-6-methyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] ethanoate


Mass: 536.697 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H48O8

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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: 3.4 Å3/Da / Density % sol: 63.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 50 mM HEPES-NaOH, pH 7-7.4, 200 mM KCl, and 38-39% (v/v) pentaerythritol propoxylate (5/4 PO/OH)
PH range: 7.0-7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.08→48.79 Å / Num. obs: 64636 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 1 / Net I/σ(I): 16.85
Reflection shellResolution: 3.08→3.19 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6273 / CC1/2: 0.556 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFE

5ife


Resolution: 3.08→48.79 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2655 --
Rwork0.2325 --
obs-64404 100 %
Refinement stepCycle: LAST / Resolution: 3.08→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17205 0 41 0 17246

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