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- PDB-3ue2: Crystal structure of a RNA binding domain of poly-U binding splic... -

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Basic information

Entry
Database: PDB / ID: 3ue2
TitleCrystal structure of a RNA binding domain of poly-U binding splicing factor 60KDa (PUF60) from Homo sapiens at 1.23 A resolution
ComponentsPoly(U)-binding-splicing factor PUF60
KeywordsRNA BINDING PROTEIN / RNA RECOGNITION MOTIF / RRM / RNA BINDING DOMAIN / SPLICING / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


alternative mRNA splicing, via spliceosome / mRNA splice site recognition / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Major Pathway / cell junction / cadherin binding / ribonucleoprotein complex / apoptotic process / DNA binding / RNA binding ...alternative mRNA splicing, via spliceosome / mRNA splice site recognition / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Major Pathway / cell junction / cadherin binding / ribonucleoprotein complex / apoptotic process / DNA binding / RNA binding / nucleoplasm / identical protein binding
Similarity search - Function
Poly-U binding splicing factor, PUF60-like / PUF60, RNA recognition motif 1 / PUF60, RNA recognition motif 2 / PUF60, RNA recognition motif 3 / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...Poly-U binding splicing factor, PUF60-like / PUF60, RNA recognition motif 1 / PUF60, RNA recognition motif 2 / PUF60, RNA recognition motif 3 / RNA recognition motif domain, eukaryote / RNA recognition motif / 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
Poly(U)-binding-splicing factor PUF60
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.23 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a RNA binding domain of poly-U binding splicing factor 60KDa (PUF60) from Homo sapiens at 1.23 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology
History
DepositionOct 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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: Poly(U)-binding-splicing factor PUF60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7203
Polymers13,5281
Non-polymers1922
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.640, 49.995, 55.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Poly(U)-binding-splicing factor PUF60 / 60 kDa poly(U)-binding-splicing factor / FUSE-binding protein-interacting repressor / FBP- ...60 kDa poly(U)-binding-splicing factor / FUSE-binding protein-interacting repressor / FBP-interacting repressor / Ro-binding protein 1 / RoBP1 / Siah-binding protein 1 / Siah-BP1


Mass: 13527.543 Da / Num. of mol.: 1 / Fragment: RNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BC008875, FIR, PUF60, ROBPI, SIAHBP1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9UHX1
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (RESIDUES 443-559) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE ...THIS CONSTRUCT (RESIDUES 443-559) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. RESIDUE NUMBERING IS BASED ON ISOFORM 1 OF UNIPROTKB Q9UHX1.

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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: 1.87 Å3/Da / Density % sol: 34.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.4 M ammonium sulfate, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537,0.9796,0.9794
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 9, 2011 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97961
30.97941
ReflectionResolution: 1.23→29.553 Å / Num. all: 30048 / Num. obs: 30048 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rsym value: 0.08 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.23-1.263.40.6121.3751521980.612100
1.26-1.33.40.5081.5724021190.508100
1.3-1.333.40.4371.7712020780.437100
1.33-1.383.40.3452.2697420390.345100
1.38-1.423.50.3032.5670219400.30399.9
1.42-1.473.40.243.2662319290.24100
1.47-1.533.40.1983.3626018250.198100
1.53-1.593.40.1564.7609417710.156100
1.59-1.663.40.135.7588117110.13100
1.66-1.743.40.116.6559416330.1199.9
1.74-1.833.40.098530815520.0999.9
1.83-1.943.40.0739.7495114550.07399.8
1.94-2.083.40.06510.3474014000.06599.8
2.08-2.253.30.0679.9428612810.06799.5
2.25-2.463.30.0679.6392412000.06799.5
2.46-2.753.10.0649.9338310810.06499.1
2.75-3.183.20.0610.230939640.0699.1
3.18-3.893.50.04214.929178340.04299.7
3.89-5.53.40.04115.522786620.04199.3
5.5-29.5533.10.05112.111733760.05196.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.20data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.23→29.553 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.06 / SU B: 1.52 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.042
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.SULFATE (SO4) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1601 1520 5.1 %RANDOM
Rwork0.1341 ---
obs0.1355 29999 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 84.76 Å2 / Biso mean: 16.2176 Å2 / Biso min: 4.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2---0.41 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.23→29.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms932 0 10 189 1131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221068
X-RAY DIFFRACTIONr_bond_other_d0.0030.02752
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9651457
X-RAY DIFFRACTIONr_angle_other_deg0.92631847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1555146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32324.65558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92115215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1341510
X-RAY DIFFRACTIONr_chiral_restr0.1080.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021228
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02221
X-RAY DIFFRACTIONr_mcbond_it2.7512637
X-RAY DIFFRACTIONr_mcbond_other1.5042260
X-RAY DIFFRACTIONr_mcangle_it3.85541045
X-RAY DIFFRACTIONr_scbond_it5.4086431
X-RAY DIFFRACTIONr_scangle_it7.4058398
X-RAY DIFFRACTIONr_rigid_bond_restr2.33131820
X-RAY DIFFRACTIONr_sphericity_free11.8223195
X-RAY DIFFRACTIONr_sphericity_bonded5.64931794
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 110 -
Rwork0.221 2082 -
all-2192 -
obs--99.91 %

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