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- PDB-4fxw: Structure of phosphorylated SF1 complex with U2AF65-UHM domain -

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Basic information

Entry
Database: PDB / ID: 4fxw
TitleStructure of phosphorylated SF1 complex with U2AF65-UHM domain
Components
  • Splicing factor 1
  • Splicing factor U2AF 65 kDa subunit
KeywordsPROTEIN BINDING / UHM / pre-mRNA splicing factor / phosphorylation
Function / homology
Function and homology information


U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / negative regulation of mRNA splicing, via spliceosome / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination ...U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / negative regulation of mRNA splicing, via spliceosome / mRNA 3'-end processing / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / U2-type prespliceosome / molecular function inhibitor activity / spliceosomal complex assembly / mRNA 3'-splice site recognition / Protein hydroxylation / negative regulation of protein ubiquitination / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / spliceosomal complex / negative regulation of smooth muscle cell proliferation / mRNA splicing, via spliceosome / mRNA processing / transcription corepressor activity / nuclear speck / ribosome / mRNA binding / enzyme binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / U2 snRNP auxilliary factor, large subunit, splicing factor / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / RRM (RNA recognition motif) domain ...Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / : / KHDC4/BBP-like, KH-domain type I / KH domain-containing BBP-like / U2 snRNP auxilliary factor, large subunit, splicing factor / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / K Homology domain / K homology RNA-binding domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Splicing factor U2AF 65 kDa subunit / Splicing factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.29 Å
AuthorsWang, W. / Bauer, W.J. / Wedekind, J.E. / Kielkopf, C.L.
CitationJournal: Structure / Year: 2013
Title: Structure of Phosphorylated SF1 Bound to U2AF(65) in an Essential Splicing Factor Complex.
Authors: Wang, W. / Maucuer, A. / Gupta, A. / Manceau, V. / Thickman, K.R. / Bauer, W.J. / Kennedy, S.D. / Wedekind, J.E. / Green, M.R. / Kielkopf, C.L.
History
DepositionJul 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 1
C: Splicing factor U2AF 65 kDa subunit
D: Splicing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0417
Polymers53,7534
Non-polymers2883
Water1,00956
1
A: Splicing factor U2AF 65 kDa subunit
B: Splicing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0694
Polymers26,8762
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-16 kcal/mol
Surface area12520 Å2
MethodPISA
2
C: Splicing factor U2AF 65 kDa subunit
D: Splicing factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9723
Polymers26,8762
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-17 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.800, 116.100, 130.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-218-

HOH

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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: 12236.441 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) / Strain (production host): BL21 Rosetta / References: UniProt: P26368
#2: Protein Splicing factor 1 / Mammalian branch point-binding protein / BBP / mBBP / Transcription factor ZFM1 / Zinc finger gene ...Mammalian branch point-binding protein / BBP / mBBP / Transcription factor ZFM1 / Zinc finger gene in MEN1 locus / Zinc finger protein 162


Mass: 14639.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF1, ZFM1, ZNF162 / Plasmid: pGEX-6p / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q15637
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Lithium sulfate, 20% PEG 3350 and 0.1 M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9219, 0.9794, 0.9793
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 19, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.92191
20.97941
30.97931
ReflectionResolution: 2.29→50 Å / Num. obs: 50161 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.062 / Χ2: 1.583 / Net I/σ(I): 28.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.29-2.3330.61926891.392199.7
2.33-2.383.10.51126170.985199.5
2.38-2.423.20.38126391.002199.7
2.42-2.483.30.30926261.024199.5
2.48-2.533.30.27226451.0671100
2.53-2.63.40.23726451.0351100
2.6-2.673.40.20726281.081100
2.67-2.753.40.16826041.156199.8
2.75-2.833.40.1226771.4291100
2.83-2.943.40.10426481.2451100
2.94-3.055.60.13526501.281100
3.05-3.195.80.11826561.5851100
3.19-3.365.80.09426491.71100
3.36-3.575.80.07826421.921100
3.57-3.855.80.07126422.0291100
3.85-4.235.80.06726462.092199.9
4.23-4.855.80.05726332.3471100
4.85-6.15.80.0526441.6681100
6.1-505.10.03925551.584195.5
1.5391

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
Web-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.29→34.56 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.645 / SU ML: 0.39 / σ(F): 0 / Phase error: 39.51 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.2807 3951 8.74 %
Rwork0.2484 --
obs0.2513 45220 89.42 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.436 Å2 / ksol: 0.282 e/Å3
Displacement parametersBiso max: 262.19 Å2 / Biso mean: 105.0561 Å2 / Biso min: 37.01 Å2
Baniso -1Baniso -2Baniso -3
1-47.6199 Å2-0 Å2-0 Å2
2---27.4242 Å2-0 Å2
3----20.1957 Å2
Refinement stepCycle: LAST / Resolution: 2.29→34.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3273 0 15 56 3344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033429
X-RAY DIFFRACTIONf_angle_d0.6564670
X-RAY DIFFRACTIONf_chiral_restr0.044502
X-RAY DIFFRACTIONf_plane_restr0.004623
X-RAY DIFFRACTIONf_dihedral_angle_d14.2631329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.31790.46041080.43481175128368
2.3179-2.34730.49771100.44431200131074
2.3473-2.37820.41611250.41571271139677
2.3782-2.41070.40541220.43551287140978
2.4107-2.44520.41681220.40911264138678
2.4452-2.48170.40421160.37281291140778
2.4817-2.52040.36891310.41951371150284
2.5204-2.56170.37131200.3671360148081
2.5617-2.60590.47161270.37751356148383
2.6059-2.65330.49631380.38631395153385
2.6533-2.70430.35541370.36121379151685
2.7043-2.75940.30351480.36131432158086
2.7594-2.81940.43371330.35781489162290
2.8194-2.8850.35761360.35511511164791
2.885-2.95710.34291520.32851519167192
2.9571-3.0370.28871460.32511557170395
3.037-3.12630.37891520.33641584173696
3.1263-3.22710.44681590.32751615177498
3.2271-3.34240.34081520.29861625177798
3.3424-3.47610.33751560.27991609176599
3.4761-3.63410.24691600.25341613177398
3.6341-3.82550.30131560.24281609176599
3.8255-4.06480.26191620.22731660182299
4.0648-4.37810.24821610.18721616177799
4.3781-4.81770.18841600.17416381798100
4.8177-5.51240.18821520.189616511803100
5.5124-6.93580.24451560.216216541810100
6.9358-34.56410.25171540.18321538169294
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)
15.7791-1.336-4.94954.80093.25495.17320.3806-0.1704-0.00540.72580.285-0.0512-0.33391.50310.03560.4530.0611-0.0670.3803-0.07520.366526.964518.491370.393
21.52861.5142-4.97817.2057-0.83962.00030.69990.67480.7253-1.98190.5347-0.3716-0.9374-4.6439-0.01991.56240.5064-0.15641.12680.13951.052814.018626.062958.3606
38.0253-1.2039-3.54662.88690.83763.9972-0.41760.3981-0.43270.4228-0.93441.31971.6438-1.57210.34550.8799-0.1042-0.03230.8069-0.24520.959914.497913.717667.9908
45.4017-1.49965.30222.06281.08999.2118-0.93221.48231.9312-0.5606-0.63751.3142-3.46330.04920.48641.30340.5685-0.21010.7933-0.01151.008717.709830.928266.1291
51.8161-1.4102-2.4365.98712.80754.9138-0.04410.0509-0.49680.2102-0.0617-0.05811.31420.81060.16730.76040.2395-0.12690.6958-0.08380.597225.31515.362271.2547
61.5304-0.4224-0.97666.84664.10142.81561.6940.5054-0.56720.5836-0.52140.2158-1.19080.33160.13030.97660.0346-0.15930.6106-0.13010.692322.05627.74377.7332
76.4541-3.7666-2.74517.34427.07929.79360.07531.1711-1.34240.69310.7296-0.57651.00131.6588-0.55450.97730.2302-0.06080.95080.08130.608930.618113.886762.24
86.39210.31684.79036.52220.18763.86650.17580.41920.404-0.66180.3072-0.6909-0.03173.1576-0.6750.7562-0.1630.16261.0464-0.08790.70634.391522.842857.3961
98.8675-7.07364.04047.9608-1.36964.84760.8708-2.3148-2.7096-0.50921.12040.80032.1978-0.426-0.31271.4853-0.0732-0.02610.92310.04260.911516.561115.524743.6781
102.3037-0.48213.789-0.0841-0.38227.29580.2781-0.28730.12840.0304-0.1908-0.2646-0.48320.7077-0.03271.1388-0.1245-0.05530.6403-0.05280.447723.782926.293141.2128
115.2361-1.981-0.15686.2204-1.47042.4810.3922.42772.0564-0.22811.90140.3180.82420.572-1.78112.06380.32460.24511.6015-0.19480.611842.494131.964353.2983
127.6235-2.3465-2.59958.75137.98169.7620.15680.34190.2436-1.9521-1.76410.79020.5742-0.45840.78860.92360.13190.01450.4860.08430.459421.185347.437380.6612
135.1759-0.8791-5.10152.3832-0.12295.45751.59740.04412.53983.21780.3931-0.62290.4833-0.732-2.65851.9853-0.2193-0.31070.74020.12931.506826.622165.091182.6551
144.4356-2.82050.32055.8179-4.59135.3942-0.4959-0.33850.96771.64610.715-1.7346-1.62120.4529-0.11511.1025-0.1878-0.34140.88510.04661.074632.667553.692787.8539
158.36192.2559-1.95074.74163.13323.71120.25870.75060.6751-1.0369-1.0009-1.0582-1.76661.02340.31541.1716-0.03740.05440.74110.15650.890728.506254.241477.3896
167.6391-3.15431.41837.4591-5.47514.1881.48690.6644-0.8919-3.0364-1.981-0.70970.07321.18450.74631.0970.0637-0.01380.73860.21870.82928.180545.1279.9747
174.3035-5.9904-5.43898.59987.25356.86270.03390.2091-0.183-0.7205-0.1671.0729-0.7315-0.1524-0.03230.73940.16880.02980.4070.08020.503523.389938.607686.3635
189.922-2.69681.95534.3155-5.66077.7963-0.2634-0.0175-0.27811.0943-0.16290.8133-1.13510.31640.45080.80080.01320.01840.6045-0.10090.648418.989553.159391.6841
196.21642.5475-5.4284.5417-1.51695.2802-0.64470.9987-0.0132-2.7998-0.5697-0.01110.2496-0.07060.7911.32150.184-0.03910.91190.0760.587224.252246.133572.9576
207.3498-0.3701-0.78697.5629-1.03724.24250.57280.4411-0.3286-0.002-0.61251.55620.3342-0.28550.36670.95290.0841-0.29170.3791-0.19560.824112.103453.363587.0556
218.51330.8854-0.24797.27171.82276.5201-0.7023-0.3204-0.9864-0.26830.7127-0.70051.71260.4550.18710.93080.00090.19410.3705-0.04420.403218.078374.0854103.6968
227.0856-1.09522.16087.2591-1.4428.45790.62161.1594-0.4894-1.3343-0.75072.5199-0.2518-0.14850.44471.04630.2229-0.36230.5247-0.28541.48797.740667.106986.717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 371:385)A371 - 385
2X-RAY DIFFRACTION2chain 'A' and (resseq 386:391)A386 - 391
3X-RAY DIFFRACTION3chain 'A' and (resseq 392:416)A392 - 416
4X-RAY DIFFRACTION4chain 'A' and (resseq 417:430)A417 - 430
5X-RAY DIFFRACTION5chain 'A' and (resseq 431:470)A431 - 470
6X-RAY DIFFRACTION6chain 'A' and (resseq 471:475)A471 - 475
7X-RAY DIFFRACTION7chain 'B' and (resseq 20:45)B20 - 45
8X-RAY DIFFRACTION8chain 'B' and (resseq 46:66)B46 - 66
9X-RAY DIFFRACTION9chain 'B' and (resseq 67:83)B67 - 83
10X-RAY DIFFRACTION10chain 'B' and (resseq 84:118)B84 - 118
11X-RAY DIFFRACTION11chain 'B' and (resseq 119:128)B119 - 128
12X-RAY DIFFRACTION12chain 'C' and (resseq 371:385)C371 - 385
13X-RAY DIFFRACTION13chain 'C' and (resseq 386:391)C386 - 391
14X-RAY DIFFRACTION14chain 'C' and (resseq 392:408)C392 - 408
15X-RAY DIFFRACTION15chain 'C' and (resseq 409:430)C409 - 430
16X-RAY DIFFRACTION16chain 'C' and (resseq 431:438)C431 - 438
17X-RAY DIFFRACTION17chain 'C' and (resseq 439:449)C439 - 449
18X-RAY DIFFRACTION18chain 'C' and (resseq 450:459)C450 - 459
19X-RAY DIFFRACTION19chain 'C' and (resseq 460:475)C460 - 475
20X-RAY DIFFRACTION20chain 'D' and (resseq 19:67)D19 - 67
21X-RAY DIFFRACTION21chain 'D' and (resseq 68:96)D68 - 96
22X-RAY DIFFRACTION22chain 'D' and (resseq 97:132)D97 - 132

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