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- PDB-7sn6: U2AF65 UHM BOUND TO SF3B155 ULM5 -

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Basic information

Entry
Database: PDB / ID: 7sn6
TitleU2AF65 UHM BOUND TO SF3B155 ULM5
Components
  • Splicing factor 3B subunit 1
  • Splicing factor U2AF 65 kDa subunit
KeywordsPEPTIDE BINDING PROTEIN / U2AF HOMOLOGY MOTIF / UHM / PRE-MRNA SPLICING FACTOR / PROTEIN BINDING / PHOSPHORYLATION / PROTEIN-PEPTIDE COMPLEX / SPLICING
Function / homology
Function and homology information


U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / mRNA 3'-end processing / C2H2 zinc finger domain binding ...U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / mRNA 3'-end processing / C2H2 zinc finger domain binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / commitment complex / U2-type prespliceosome assembly / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2 snRNP / RNA Polymerase II Transcription Termination / U2-type prespliceosome / positive regulation of transcription by RNA polymerase III / molecular function inhibitor activity / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / Protein hydroxylation / negative regulation of mRNA splicing, via spliceosome / catalytic step 2 spliceosome / negative regulation of protein ubiquitination / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / B-WICH complex positively regulates rRNA expression / mRNA processing / nuclear speck / chromatin remodeling / mRNA binding / nucleolus / enzyme binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
U2 snRNP auxilliary factor, large subunit, splicing factor / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1-like / : / PPP2R1A-like HEAT repeat / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...U2 snRNP auxilliary factor, large subunit, splicing factor / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1-like / : / PPP2R1A-like HEAT repeat / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Splicing factor 3B subunit 1 / Splicing factor U2AF 65 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLoerch, S. / Jenkins, J.L. / Kielkopf, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM070503-15 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: A UHM-ULM interface with unusual structural features contributes to U2AF2 and SF3B1 association for pre-mRNA splicing.
Authors: Galardi, J.W. / Bela, V.N. / Jeffery, N. / He, X. / Glasser, E. / Loerch, S. / Jenkins, J.L. / Pulvino, M.J. / Boutz, P.L. / Kielkopf, C.L.
History
DepositionOct 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Splicing factor U2AF 65 kDa subunit
B: Splicing factor U2AF 65 kDa subunit
C: Splicing factor 3B subunit 1
D: Splicing factor 3B subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4985
Polymers28,4384
Non-polymers601
Water1,27971
1
A: Splicing factor U2AF 65 kDa subunit
C: Splicing factor 3B subunit 1


Theoretical massNumber of molelcules
Total (without water)14,2192
Polymers14,2192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Splicing factor U2AF 65 kDa subunit
D: Splicing factor 3B subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2793
Polymers14,2192
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.163, 63.156, 49.387
Angle α, β, γ (deg.)90.000, 94.370, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Splicing factor U2AF 65 kDa subunit / U2 auxiliary factor 65 kDa subunit / hU2AF(65) / hU2AF65 / U2 snRNP auxiliary factor large subunit


Mass: 12095.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: U2AF2, U2AF65 / Plasmid: PGEX-6P / Production host: Escherichia coli (E. coli) / References: UniProt: P26368
#2: Protein/peptide Splicing factor 3B subunit 1 / Pre-mRNA-splicing factor SF3b 155 kDa subunit / SF3b155 / Spliceosome-associated protein 155 / SAP 155


Mass: 2123.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75533
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 15% V/V 2-PROPANOL, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.8→37.97 Å / Num. obs: 21337 / % possible obs: 98.4 % / Redundancy: 3.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.023 / Net I/σ(I): 16.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 3 / Num. unique obs: 1256 / CC1/2: 0.92 / Rpim(I) all: 0.304

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSNovember 3, 2014data reduction
Aimless0.5.8data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FXW

4fxw


Resolution: 1.8→37.97 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2169 2008 9.43 %
Rwork0.1798 19297 -
obs0.1834 21305 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.97 Å2 / Biso mean: 51.521 Å2 / Biso min: 21.87 Å2
Refinement stepCycle: final / Resolution: 1.8→37.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 12 71 1858
Biso mean--86.77 46.92 -
Num. residues----230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.850.25181430.25041368151197
1.85-1.90.3171560.25661373152998
1.9-1.950.29861280.23061362149098
1.95-2.010.29471350.2121347148297
2.01-2.090.28651590.20571370152998
2.09-2.170.24611280.20361401152999
2.17-2.270.26131490.20161366151599
2.27-2.390.21591470.19511377152499
2.39-2.540.2391410.19771371151298
2.54-2.730.23421350.19551404153998
2.73-3.010.24411520.19231380153299
3.01-3.440.20911390.1831392153199
3.44-4.340.18931440.14871373151797
4.34-37.970.18391520.16291413156598
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1616-0.8107-0.70043.5298-2.31932.03210.26220.31950.0876-0.17720.1270.1684-0.12040.1655-0.00190.29240.07550.00630.33920.0240.340411.0533-28.163217.9197
21.40310.2283-0.74210.87070.33081.13750.13770.3246-0.7868-0.19940.04450.27221.3871-0.743-0.00160.4325-0.0636-0.06690.39440.02270.50625.0478-37.397318.4014
33.0172-0.12070.00973.97741.02992.21320.51170.52590.0601-0.1552-0.10420.6706-0.6881-0.45160.03290.26320.1038-0.03370.39410.07090.41865.4489-26.525716.6419
40.45180.32850.53672.00890.12250.67330.1351-0.2156-0.21220.93690.20140.317-0.1875-0.1320.05480.34790.09890.09780.29780.07820.30439.9014-29.704231.0164
50.4418-0.1328-0.09580.6283-0.20740.52420.31370.32490.0862-0.3645-0.39450.23231.21950.1874-0.00320.4420.1421-0.0310.336-0.03310.29418.7557-36.202618.9839
60.1251-0.19040.14070.8254-0.0470.21250.19420.38470.02130.2160.21210.8776-0.9513-0.03530.00950.41150.0650.10430.32760.04280.368513.5012-23.123526.0575
71.2766-0.6023-1.23231.0392.7917.6820.1372-0.53140.18160.6840.80270.5594-1.7471-0.94750.11690.62090.3490.31950.67450.28740.68734.6083-17.293822.8236
82.50721.5131-0.65271.35990.17230.88360.2643-0.1825-0.45760.02750.04310.27960.41590.076300.45510.13530.01550.4736-0.00260.320725.978-32.76519.5395
91.5947-0.4453-0.64942.69450.06811.6558-0.27870.36270.7876-0.3601-0.1034-0.3163-0.41530.2133-0.00360.42530.03220.01930.44640.02630.470327.1092-23.3998-2.5552
100.813-1.18210.40451.7172-0.58880.2027-0.4378-0.06890.26050.2136-0.2243-0.63460.2458-0.0531-0.0440.3952-0.0140.06910.6313-0.02280.376235.6279-28.78895.4805
110.7716-0.1538-0.83063.3534-0.49691.57550.0708-0.4051-0.1377-0.02320.0437-0.05580.74190.0837-0.00120.32940.10920.03090.35120.02310.302426.2002-34.6313-1.7
121.09150.0705-0.2532.56-0.72280.59630.1782-0.7252-0.05940.63470.38170.1424-0.2524-0.17980.04760.54130.1811-0.14420.5974-0.12340.391932.3755-28.57515.7404
130.72090.5981.8290.99260.58366.4413-0.2403-0.48930.26740.79690.18480.6775-0.2703-0.8989-0.00610.57040.2060.03580.25370.02060.327619.6245-21.61377.7993
140.78680.75750.33880.95030.05830.46590.23210.1248-0.2136-0.1391-0.0638-0.82580.5871-0.23120.01730.51130.17750.06050.42070.03790.416929.2164-38.5858.3142
153.9438-3.30751.94833.1994-0.62193.3726-0.6105-0.7145-0.4070.1859-0.05662.51060.776-1.54220.09750.6480.0849-0.11940.5046-0.16740.767427.1947-42.75821.798
160.01520.0751-0.09870.6958-0.61710.6846-0.15640.3336-0.3575-0.16070.104-0.04410.94820.8678-0.00060.6710.0964-0.01750.4299-0.04070.50117.3284-41.346522.4144
171.2703-0.43221.26910.68510.82696.2394-0.5677-0.34440.9147-0.27780.0873-0.9629-2.50021.37180.03340.7450.0944-0.13110.487-0.05930.621526.0364-16.30097.0245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 372 through 391 )A372 - 391
2X-RAY DIFFRACTION2chain 'A' and (resid 392 through 408 )A392 - 408
3X-RAY DIFFRACTION3chain 'A' and (resid 409 through 431 )A409 - 431
4X-RAY DIFFRACTION4chain 'A' and (resid 432 through 449 )A432 - 449
5X-RAY DIFFRACTION5chain 'A' and (resid 450 through 459 )A450 - 459
6X-RAY DIFFRACTION6chain 'A' and (resid 460 through 465 )A460 - 465
7X-RAY DIFFRACTION7chain 'A' and (resid 466 through 475 )A466 - 475
8X-RAY DIFFRACTION8chain 'B' and (resid 371 through 385 )B371 - 385
9X-RAY DIFFRACTION9chain 'B' and (resid 386 through 408 )B386 - 408
10X-RAY DIFFRACTION10chain 'B' and (resid 409 through 416 )B409 - 416
11X-RAY DIFFRACTION11chain 'B' and (resid 417 through 438 )B417 - 438
12X-RAY DIFFRACTION12chain 'B' and (resid 439 through 449 )B439 - 449
13X-RAY DIFFRACTION13chain 'B' and (resid 450 through 459 )B450 - 459
14X-RAY DIFFRACTION14chain 'B' and (resid 460 through 470 )B460 - 470
15X-RAY DIFFRACTION15chain 'B' and (resid 471 through 475 )B471 - 475
16X-RAY DIFFRACTION16chain 'C' and (resid 335 through 346 )C335 - 346
17X-RAY DIFFRACTION17chain 'D' and (resid 335 through 343 )D335 - 343

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