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- PDB-4oz0: Crystal structure of human CAPERalpha U2AF homology motif (apo-state) -

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Basic information

Entry
Database: PDB / ID: 4oz0
TitleCrystal structure of human CAPERalpha U2AF homology motif (apo-state)
ComponentsRNA-binding protein 39
KeywordsTRANSCRIPTION / U2AF homology motif / UHM / protein-peptide complex / pre-mRNA splicing factor
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLoerch, S. / Kielkopf, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM070503 United States
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Cancer-relevant splicing factor CAPER alpha engages the essential splicing factor SF3b155 in a specific ternary complex.
Authors: Loerch, S. / Maucuer, A. / Manceau, V. / Green, M.R. / Kielkopf, C.L.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software / struct_keywords / symmetry
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _symmetry.Int_Tables_number
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)25,3563
Polymers25,3212
Non-polymers351
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-17 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.653, 52.410, 85.141
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 / Hepatocellular carcinoma protein 1 / RNA-binding motif protein 39 / RNA-binding region-containing ...Hepatocellular carcinoma protein 1 / RNA-binding motif protein 39 / RNA-binding region-containing protein 2 / Splicing factor HCC1


Mass: 12660.332 Da / Num. of mol.: 2 / Fragment: 417-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPER, CAPERalpha, FSAP59, HCC1, RBM39, RNPC2 / Variant: isoform B / Plasmid: pGEX-6p / Details (production host): TEV site / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q14498
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M tri-sodium acetate pH 4.5, 0.1 M Bis-Tris pH 5.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jan 3, 2013
RadiationMonochromator: Cu KA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→42.65 Å / Num. obs: 17820 / % possible obs: 95.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 6.95 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 12.4
Reflection shellResolution: 2.2→2.29 Å / Redundancy: 1.59 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 3.4 / % possible all: 80.8

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Processing

Software
NameVersionClassification
PROTEUM PLUSdata collection
PROTEUM PLUSdata scaling
PDB_EXTRACT3.14data extraction
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S6E

3s6e


Resolution: 2.2→42.571 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1772 9.94 %Random Selection
Rwork0.1958 16048 --
obs0.1985 17820 90.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.04 Å2 / Biso mean: 15.0619 Å2 / Biso min: 3.7 Å2
Refinement stepCycle: final / Resolution: 2.2→42.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 1 189 1878
Biso mean--18.5 16.72 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041758
X-RAY DIFFRACTIONf_angle_d0.8942408
X-RAY DIFFRACTIONf_chiral_restr0.036272
X-RAY DIFFRACTIONf_plane_restr0.004316
X-RAY DIFFRACTIONf_dihedral_angle_d12.545618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.25950.2683930.245686595864
2.2595-2.3260.24851170.21721094121178
2.326-2.4010.25691330.21711117125084
2.401-2.48680.23941280.21161211133987
2.4868-2.58640.23611400.22231171131188
2.5864-2.70410.32921160.21311214133089
2.7041-2.84660.26711540.20631319147397
2.8466-3.02490.21771480.199913641512100
3.0249-3.25840.20511450.197213611506100
3.2584-3.58620.20151430.18181310145398
3.5862-4.10470.20231360.17681319145596
4.1047-5.17010.16051660.142413441510100
5.1701-42.57850.22361530.208313591512100

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