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- PDB-1jmt: X-ray Structure of a Core U2AF65/U2AF35 Heterodimer -

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Basic information

Entry
Database: PDB / ID: 1jmt
TitleX-ray Structure of a Core U2AF65/U2AF35 Heterodimer
Components
  • SPLICING FACTOR U2AF 35 KDA SUBUNIT
  • SPLICING FACTOR U2AF 65 KDA SUBUNIT
KeywordsRNA BINDING PROTEIN / RRM / RNA SPLICING / PROLINE / PPII HELIX / PEPTIDE RECOGNITION
Function / homology
Function and homology information


U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA 3'-end processing / mRNA 3'-end processing / RNA export from nucleus / 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 / mRNA 3'-end processing / mRNA 3'-end processing / RNA export from nucleus / 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 / Protein hydroxylation / negative regulation of mRNA splicing, via spliceosome / Cajal body / mRNA export from nucleus / negative regulation of protein ubiquitination / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / nuclear speck / enzyme binding / RNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
U2 auxiliary factor small subunit / U2 snRNP auxilliary factor, large subunit, splicing factor / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / RNA recognition motif domain, eukaryote / RNA recognition motif / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / RRM (RNA recognition motif) domain / RNA recognition motif ...U2 auxiliary factor small subunit / U2 snRNP auxilliary factor, large subunit, splicing factor / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / RNA recognition motif domain, eukaryote / RNA recognition motif / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / 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 / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HEXANE-1,6-DIOL / Splicing factor U2AF 65 kDa subunit / Splicing factor U2AF 35 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsKielkopf, C.L. / Rodionova, N.A. / Green, M.R. / Burley, S.K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: A novel peptide recognition mode revealed by the X-ray structure of a core U2AF35/U2AF65 heterodimer.
Authors: Kielkopf, C.L. / Rodionova, N.A. / Green, M.R. / Burley, S.K.
History
DepositionJul 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPLICING FACTOR U2AF 35 KDA SUBUNIT
B: SPLICING FACTOR U2AF 65 KDA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6574
Polymers15,4212
Non-polymers2362
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-1 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.520, 49.740, 92.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number16
Space group name H-MP222

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Components

#1: Protein SPLICING FACTOR U2AF 35 KDA SUBUNIT / U2 SNRNP AUXILIARY FACTOR SMALL SUBUNIT


Mass: 12039.095 Da / Num. of mol.: 1 / Mutation: C67S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q01081
#2: Protein/peptide SPLICING FACTOR U2AF 65 KDA SUBUNIT / U2 SNRNP AUXILIARY FACTOR LARGE SUBUNIT


Mass: 3382.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P26368
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: PEG mme5000, sodium acetate, 1,6-hexanediol, MES, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1500 mMsodium acetate1reservoir
2100 mMMES1reservoir
315 %(w/v)PEG5000 MME1reservoir
45 %(w/v)1,6-hexanediol1reservoir
50.5 mMTCEP1reservoir
645 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.979
SYNCHROTRONCHESS F220.9793,0.9791,0.9649
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDNov 14, 2000
BRANDEIS - B42CCDDec 14, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) crystalsSINGLE WAVELENGTHMx-ray1
2Si(111) crystalsMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97931
30.97911
40.96491
ReflectionResolution: 2.2→19.34 Å / Num. all: 9935 / Num. obs: 9935 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Redundancy: 4 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 21
Reflection shellResolution: 2.2→2.34 Å / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 40388
Reflection shell
*PLUS
% possible obs: 98.3 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 5.6

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.36 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2041662.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 693 7 %RANDOM
Rwork0.226 ---
obs0.226 9935 97.4 %-
all-9935 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 156.287 Å2 / ksol: 0.666393 e/Å3
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--7.46 Å20 Å2
3----7.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms999 0 16 118 1133
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it3.491.5
X-RAY DIFFRACTIONc_mcangle_it5.12
X-RAY DIFFRACTIONc_scbond_it5.22
X-RAY DIFFRACTIONc_scangle_it7.352.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 113 7 %
Rwork0.257 1506 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HEZ.PARAMHEZ.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.273 / % reflection Rfree: 7 % / Rfactor Rwork: 0.257

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