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- PDB-4z2x: Crystal structure of a RNA binding domain of a U2 small nuclear r... -

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Basic information

Entry
Database: PDB / ID: 4z2x
TitleCrystal structure of a RNA binding domain of a U2 small nuclear ribonucleoprotein auxiliary factor 2 (U2AF) from mouse at 2.15 A resolution
ComponentsSplicing factor U2AF 65 kDa subunit
KeywordsRNA BINDING PROTEIN / Canonical RNA binding protein / RNA 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


mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Transport of Mature mRNA derived from an Intron-Containing Transcript / Protein hydroxylation / mRNA Splicing - Major Pathway / U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / Prp19 complex / C2H2 zinc finger domain binding ...mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Transport of Mature mRNA derived from an Intron-Containing Transcript / Protein hydroxylation / mRNA Splicing - Major Pathway / U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / Prp19 complex / C2H2 zinc finger domain binding / commitment complex / U2-type prespliceosome / molecular function inhibitor activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of protein ubiquitination / positive regulation of RNA splicing / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / nuclear speck / enzyme binding / nucleus
Similarity search - Function
U2 snRNP auxilliary factor, large subunit, splicing factor / 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
Splicing factor U2AF 65 kDa subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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 a U2 small nuclear ribonucleoprotein auxiliary factor 2 (U2AF) from mouse at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionMar 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Source and taxonomy
Category: citation_author / entity_src_gen / pdbx_struct_oper_list
Item: _citation_author.name / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: 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 U2AF 65 kDa subunit
B: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)24,0672
Polymers24,0672
Non-polymers00
Water84747
1
A: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)12,0341
Polymers12,0341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Splicing factor U2AF 65 kDa subunit


Theoretical massNumber of molelcules
Total (without water)12,0341
Polymers12,0341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.130, 90.260, 37.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Splicing factor U2AF 65 kDa subunit / U2 auxiliary factor 65 kDa subunit / U2 snRNP auxiliary factor large subunit


Mass: 12033.667 Da / Num. of mol.: 2 / Fragment: RNA binding domain (UNP residues 371-475)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: U2af2, U2af65 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21Gold(DE3) / References: UniProt: P26369
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTALLIZATION CONTAINED TWO DIFFERENT CONSTRUCTS OF UNIPROTKB P26369. THE TAGS WERE REMOVED ...THE CRYSTALLIZATION CONTAINED TWO DIFFERENT CONSTRUCTS OF UNIPROTKB P26369. THE TAGS WERE REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 368-471 OF THE TARGET SEQUENCE OF THE FIRST CONSTRUCT AND RESIDUES 85-94 OF THE SECOND CONSTRUCT. HOWEVER, THE CRYSTAL STRUCTURE CONSISTS OF RESIDUES FROM THE LARGER CONSTRUCT. THE SEQUENCE NUMBERING IS BASED ON THE UNIPROTKB ID P26369 ISOFORM THAT MATCHES THE CANONICAL HUMAN ISOFORM FROM UNIPROT ID P26368.

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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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium thiocyanate, 20% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97879 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 2.15→37.9 Å / Num. obs: 11422 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.782 % / Biso Wilson estimate: 35.62 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.113 / Net I/σ(I): 12.09 / Num. measured all: 43198
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
2.15-2.210.7420.951.832658598431.093198.1
2.21-2.270.7380.8252.131158047960.94999
2.27-2.330.8020.7012.330497957910.80999.5
2.33-2.40.8470.5812.828847717630.67299
2.4-2.480.8750.4783.326747527370.55798
2.48-2.570.9050.3893.827127397300.4598.8
2.57-2.670.9230.3694.327146926880.42499.4
2.67-2.780.9560.2635.926266786730.30399.3
2.78-2.90.970.27.725346556530.22999.7
2.9-3.040.9820.1519.923626246220.17499.7
3.04-3.210.9850.1251121086065930.14697.9
3.21-3.40.9940.08216.320715635490.09497.5
3.4-3.630.9960.05722.920845405350.06699.1
3.63-3.930.9980.04926.319485085000.05798.4
3.93-4.30.9980.0429.617234654570.04698.3
4.3-4.810.9990.03134.113804253950.03692.9
4.81-5.550.9990.03433.214003803720.03997.9
5.55-6.80.9990.0429.711923293220.04697.9
6.8-9.620.9990.028388552742520.03392
9.6210.01654.75021671510.01990.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
MOLREPphasing
BUSTER2.10.0refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3v4m

3v4m


Resolution: 2.15→37.9 Å / Cor.coef. Fo:Fc: 0.9378 / Cor.coef. Fo:Fc free: 0.9046 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS)
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 545 4.78 %RANDOM
Rwork0.2088 ---
obs0.211 11397 98.38 %-
Displacement parametersBiso max: 139.08 Å2 / Biso mean: 46.7017 Å2 / Biso min: 22.07 Å2
Baniso -1Baniso -2Baniso -3
1-5.5028 Å20 Å20 Å2
2--1.8899 Å20 Å2
3----7.3927 Å2
Refine analyzeLuzzati coordinate error obs: 0.336 Å
Refinement stepCycle: LAST / Resolution: 2.15→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1655 0 0 47 1702
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d801SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes52HARMONIC2
X-RAY DIFFRACTIONt_gen_planes245HARMONIC5
X-RAY DIFFRACTIONt_it1706HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion211SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1923SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1706HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg2312HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion2.72
LS refinement shellResolution: 2.15→2.35 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 113 4.21 %
Rwork0.2322 2573 -
all0.2329 2686 -
obs--98.38 %
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)
17.05561.751-1.90792.4137-1.02391.93590.06430.2116-0.1628-0.05790.03370.08640.0372-0.118-0.0979-0.1506-0.0166-0.0174-0.11660.00130.006324.8997-13.1404-1.797
25.39920.05040.46384.3977-0.93420.7933-0.0982-0.4769-0.06020.44250.18920.15540.0046-0.1191-0.091-0.1070.0179-0.0135-0.06720.0188-0.084825.0765-33.290813.2621
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|372-475 }
2X-RAY DIFFRACTION2{ B|372-475 }

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