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- PDB-4yud: Crystal structure of a RNA binding motif protein 39 (RBM39) from ... -

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Basic information

Entry
Database: PDB / ID: 4yud
TitleCrystal structure of a RNA binding motif protein 39 (RBM39) from Homo sapiens at 1.28 A resolution
ComponentsRNA-binding protein 39
KeywordsRNA BINDING PROTEIN / RNA recognition domain / RNP-1 / PF00076 family / 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


RS domain binding / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / centriolar satellite / RNA processing / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / microtubule cytoskeleton / nuclear speck ...RS domain binding / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / centriolar satellite / RNA processing / mRNA Splicing - Major Pathway / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.28 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 Homo sapiens at 1.28 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Source and taxonomy
Category: citation_author / entity_src_gen ...citation_author / entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_symm_contact
Item: _citation_author.name / _entity_src_gen.pdbx_alt_source_flag ..._citation_author.name / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 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 1.3Oct 25, 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


Theoretical massNumber of molelcules
Total (without water)10,3051
Polymers10,3051
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.574, 26.711, 35.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

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Components

#1: Protein RNA-binding protein 39 / CAPER alpha / Hepatocellular carcinoma protein 1 / RNA-binding motif protein 39 / RNA-binding ...CAPER alpha / Hepatocellular carcinoma protein 1 / RNA-binding motif protein 39 / RNA-binding region-containing protein 2 / Splicing factor HCC1


Mass: 10304.834 Da / Num. of mol.: 1 / Fragment: UNP residues 144-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM39, HCC1, RNPC2 / Plasmid: pET28TEVc / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21Gold(DE3) / References: UniProt: Q14498
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (RESIDUES 144-234) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE ...THIS CONSTRUCT (RESIDUES 144-234) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 1.96 Å3/Da / Density % sol: 37.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% polyethylene glycol 3350, 0.20M sodium fluoride, 1mM RNA-6b UAAUAA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.28→32.461 Å / Num. all: 20012 / Num. obs: 20012 / % possible obs: 92.2 % / Redundancy: 3.9 % / Rpim(I) all: 0.013 / Rrim(I) all: 0.027 / Rsym value: 0.023 / Net I/av σ(I): 19.625 / Net I/σ(I): 27.7 / Num. measured all: 77481
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
1.28-1.352.30.3550.2852.7452019480.2050.3550.2851363
1.35-1.433.20.2410.2033.8799125210.1260.2410.2035.185.9
1.43-1.534.30.1690.1495.21175527620.0790.1690.1498.699.7
1.53-1.654.20.1030.098.51071325680.0490.1030.0913.398.9
1.65-1.814.30.0630.05613.51029723960.0290.0630.05620.599.9
1.81-2.024.20.0360.03222.5901421660.0170.0360.03234.299
2.02-2.344.30.0260.02329.9826319440.0120.0260.02348.999.9
2.34-2.864.20.0210.01836.1679716310.010.0210.01859.999
2.86-4.0540.0170.01537.7520213070.0080.0170.01576.399
4.05-32.4613.80.0140.01345.129297690.0070.0140.01382.298.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
REFMAC5.5.0110refinement
XDSMarch 30, 2013data reduction
XSCALEMarch 30, 2013data scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CQ4

2cq4


Resolution: 1.28→32.461 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 1.825 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 1038 5.2 %RANDOM
Rwork0.1463 18936 --
obs0.1487 19974 92.11 %-
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: 91.12 Å2 / Biso mean: 21.6503 Å2 / Biso min: 9.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---0.89 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 1.28→32.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms666 0 0 117 783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022741
X-RAY DIFFRACTIONr_bond_other_d0.0030.02536
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9721011
X-RAY DIFFRACTIONr_angle_other_deg0.88731299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4555102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.95122.16237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.41315138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0281512
X-RAY DIFFRACTIONr_chiral_restr0.0960.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021845
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02163
X-RAY DIFFRACTIONr_mcbond_it2.9683461
X-RAY DIFFRACTIONr_mcbond_other1.5953185
X-RAY DIFFRACTIONr_mcangle_it4.455755
X-RAY DIFFRACTIONr_scbond_it4.7768280
X-RAY DIFFRACTIONr_scangle_it6.73711248
X-RAY DIFFRACTIONr_rigid_bond_restr2.00531277
X-RAY DIFFRACTIONr_sphericity_free8.263121
X-RAY DIFFRACTIONr_sphericity_bonded4.14531261
LS refinement shellResolution: 1.28→1.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 38 -
Rwork0.208 818 -
all-856 -
obs--54.91 %

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