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- PDB-3s6e: Crystal structure of a RNA binding motif protein 39 (RBM39) from ... -

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Basic information

Entry
Database: PDB / ID: 3s6e
TitleCrystal structure of a RNA binding motif protein 39 (RBM39) from Mus musculuS at 0.95 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 / Initiation of Nuclear Envelope (NE) Reformation / RND3 GTPase cycle / RS domain binding / RAC3 GTPase cycle / RAC2 GTPase cycle / RHOD GTPase cycle / mRNA Splicing - Major Pathway / RND2 GTPase cycle ...Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / Initiation of Nuclear Envelope (NE) Reformation / RND3 GTPase cycle / RS domain binding / RAC3 GTPase cycle / RAC2 GTPase cycle / RHOD GTPase cycle / mRNA Splicing - Major Pathway / RND2 GTPase cycle / RND1 GTPase cycle / RAC1 GTPase cycle / RHOG GTPase cycle / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / centriolar satellite / RNA splicing / mRNA processing / nuclear speck / protein-containing complex / RNA binding
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
CITRIC ACID / RNA-binding protein 39
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.95 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a RNA binding motif protein 39 (RBM39) from Mus musculus at 0.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionMay 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Oct 21, 2015Group: Database references / Structure summary
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.5Feb 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

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein 39
B: RNA-binding protein 39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8045
Polymers25,4282
Non-polymers3763
Water6,954386
1
A: RNA-binding protein 39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8062
Polymers12,7141
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-binding protein 39
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9983
Polymers12,7141
Non-polymers2842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.701, 55.139, 84.601
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY AND CRYSTAL PACKING ANALYSIS SUPPORT THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT 300 OLIGOMERIZATION STATE IN SOLUTION.

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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: 12713.939 Da / Num. of mol.: 2 / Fragment: sequence database 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...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: 2.05 Å3/Da / Density % sol: 40 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.95369,0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 5, 2011
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953691
20.979151
ReflectionResolution: 0.95→28.2 Å / Num. all: 131023 / Num. obs: 131023 / % possible obs: 99.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 6.707 Å2 / Rsym value: 0.063 / Net I/σ(I): 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
0.95-0.974.10.671.93850292920.6796.7
0.97-14.60.5372.74250292410.53798.4
1-1.034.60.393.74175190310.3998.6
1.03-1.064.60.3024.84085188160.30299
1.06-1.14.70.2316.23972385320.23199.2
1.1-1.144.70.188.13855582830.1899.5
1.14-1.184.70.1489.43779080840.14899.7
1.18-1.234.70.13210.43650077560.13299.9
1.23-1.284.70.12211.23531074830.122100
1.28-1.344.80.11412.13386371290.114100
1.34-1.424.80.10113.63261968290.101100
1.42-1.54.80.07915.43091664360.079100
1.5-1.6150.07217.53029561010.072100
1.61-1.735.50.07320.53135356620.073100
1.73-1.96.40.07224.93363452380.072100
1.9-2.1280.0631.83831047810.06100
2.12-2.458.50.05136.23601842250.051100
2.45-38.50.05240.93057136090.052100
3-4.2580.049592289728450.049100
4.25-28.27.20.04760.71179816500.04799.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 0.95→28.2 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.981 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 0.453 / SU ML: 0.011 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018
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.CITRATE (CIT) FROM THE CRYSTALLIZATION SOLUTION AND GLYCEROL (GOL) FROM THE CRYOPROTECTANT SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1315 6590 5 %RANDOM
Rwork0.1191 ---
obs0.1197 130918 99.2 %-
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: 42.53 Å2 / Biso mean: 11.9317 Å2 / Biso min: 3.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.56 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 0.95→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 25 386 2129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222065
X-RAY DIFFRACTIONr_bond_other_d0.0020.021333
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.9572882
X-RAY DIFFRACTIONr_angle_other_deg1.22233349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7775303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77925.97892
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88215343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.95154
X-RAY DIFFRACTIONr_chiral_restr0.1130.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212410
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02386
X-RAY DIFFRACTIONr_mcbond_it1.99721283
X-RAY DIFFRACTIONr_mcbond_other1.1072500
X-RAY DIFFRACTIONr_mcangle_it2.90432124
X-RAY DIFFRACTIONr_scbond_it2.8832782
X-RAY DIFFRACTIONr_scangle_it4.073722
X-RAY DIFFRACTIONr_rigid_bond_restr1.42333398
X-RAY DIFFRACTIONr_sphericity_free9.3033447
X-RAY DIFFRACTIONr_sphericity_bonded4.41833311
LS refinement shellResolution: 0.95→0.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 450 -
Rwork0.311 8765 -
all-9215 -
obs--95.68 %

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