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- PDB-4j5o: Room temperature crystal structure of a RNA binding motif protein... -

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Basic information

Entry
Database: PDB / ID: 4j5o
TitleRoom temperature crystal structure of a RNA binding motif protein 39 (Rbm39) from Mus musculus at 1.11 A resolution
ComponentsRNA-binding protein 39
KeywordsRNA BINDING PROTEIN / Ferredoxin-like / 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


Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / RND3 GTPase cycle / Initiation of Nuclear Envelope (NE) Reformation / RAC3 GTPase cycle / RAC2 GTPase cycle / RS domain binding / RHOD GTPase cycle / mRNA Splicing - Major Pathway / RAC1 GTPase cycle ...Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / RND3 GTPase cycle / Initiation of Nuclear Envelope (NE) Reformation / RAC3 GTPase cycle / RAC2 GTPase cycle / RS domain binding / RHOD GTPase cycle / mRNA Splicing - Major Pathway / RAC1 GTPase cycle / RND2 GTPase cycle / RND1 GTPase cycle / RHOG GTPase cycle / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / centriolar satellite / RNA splicing / mRNA processing / microtubule cytoskeleton / nuclear speck / protein-containing complex / RNA binding / nucleoplasm
Similarity search - Function
Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / 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 ...Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / 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
RNA-binding protein 39
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.11 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Room temperature crystal structure of a RNA binding motif protein 39 (Rbm39) from Mus musculus at 1.11 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionFeb 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: 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 1.4Sep 20, 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: RNA-binding protein 39
B: RNA-binding protein 39


Theoretical massNumber of molelcules
Total (without water)25,1472
Polymers25,1472
Non-polymers00
Water3,315184
1
A: RNA-binding protein 39


Theoretical massNumber of molelcules
Total (without water)12,5731
Polymers12,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-binding protein 39


Theoretical massNumber of molelcules
Total (without water)12,5731
Polymers12,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.617, 52.829, 85.652
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA-binding protein 39 / Coactivator of activating protein 1 and estrogen receptors / Coactivator of AP-1 and ERs / RNA- ...Coactivator of activating protein 1 and estrogen receptors / Coactivator of AP-1 and ERs / RNA-binding motif protein 39 / RNA-binding region-containing protein 2 / Transcription coactivator CAPER


Mass: 12573.253 Da / Num. of mol.: 2 / Fragment: UNP residues 418-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: BC030493, Caper, Rbm39, Rnpc2 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8VH51
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 418-530 OF THE TARGET SEQUENCE. NUMBERING IS BASED ON ISOFORM 1 OF UNIPROTKB Q8VH51.

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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: 2.01 Å3/Da / Density % sol: 38.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20.00% polyethylene glycol 6000, 0.1M sodium citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 296 K / Ambient temp details: room temperature
Crystal support: loop mounted and sealed with a MiTeGen MicroRT polyester capillary
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.11→28.551 Å / Num. obs: 75696 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 10.629 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs
1.11-1.1457.951.0162.2170083368
1.14-1.1778.45.90.8192.8264584473
1.17-1.292.16.90.6793.5352305081
1.2-1.2498.59.50.6344.5504565328
1.24-1.2899.510.60.5485.6552575232
1.28-1.3399.610.40.4566.4525685067
1.33-1.3899.7100.3727.3487294886
1.38-1.4399.810.80.2989.2511054748
1.43-1.599.810.60.22111.4479324538
1.5-1.5799.810.10.16813.7440564367
1.57-1.6699.710.50.13216.8437504159
1.66-1.7699.810.90.10720.3424663907
1.76-1.8899.810.70.07826.4398733710
1.88-2.0399.3100.0632.7347323456
2.03-2.2299.811.10.0542.4353263190
2.22-2.4899.810.80.04447.5315112917
2.48-2.8798.69.90.04150.6251102528
2.87-3.5198.5110.03662.4236642158
3.51-4.9796.510.50.03369.9174151666
4.97-28.5592.510.40.03367.39542917

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
REFMACrefinement
XSCALEMarch 15, 2012data scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3s6e

3s6e


Resolution: 1.11→28.551 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.983 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 0.743 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1289 3786 5 %RANDOM
Rwork0.1126 ---
obs0.1134 75639 93.85 %-
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: 57.61 Å2 / Biso mean: 17.5736 Å2 / Biso min: 7.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.11→28.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 0 184 1860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222048
X-RAY DIFFRACTIONr_bond_other_d0.0020.021308
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9442863
X-RAY DIFFRACTIONr_angle_other_deg1.11833289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2495299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09426.49597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72415340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.869153
X-RAY DIFFRACTIONr_chiral_restr0.0940.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212415
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02380
X-RAY DIFFRACTIONr_mcbond_it2.52631283
X-RAY DIFFRACTIONr_mcbond_other1.4833499
X-RAY DIFFRACTIONr_mcangle_it3.86852130
X-RAY DIFFRACTIONr_scbond_it4.4798765
X-RAY DIFFRACTIONr_scangle_it6.42711699
X-RAY DIFFRACTIONr_rigid_bond_restr1.5532.83356
X-RAY DIFFRACTIONr_sphericity_free9.3323.5187
X-RAY DIFFRACTIONr_sphericity_bonded4.643.53267
LS refinement shellResolution: 1.11→1.139 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 168 -
Rwork0.205 3192 -
all-3360 -
obs--56.99 %

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