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- PDB-4oz1: Crystal structure of human CAPERalpha UHM bound to SF3b155 ULM5 -

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Basic information

Entry
Database: PDB / ID: 4oz1
TitleCrystal structure of human CAPERalpha UHM bound to SF3b155 ULM5
Components
  • RNA-binding protein 39
  • Splicing factor 3B subunit 1
KeywordsTRANSCRIPTION / U2AF homology motif / UHM / protein-peptide complex / pre-mRNA splicing factor
Function / homology
Function and homology information


RS domain binding / U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / U1 snRNP binding / RNA splicing, via transesterification reactions / regulation of mRNA splicing, via spliceosome / U2-type spliceosomal complex / U2-type precatalytic spliceosome ...RS domain binding / U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / U1 snRNP binding / RNA splicing, via transesterification reactions / regulation of mRNA splicing, via spliceosome / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2 snRNP / positive regulation of transcription by RNA polymerase III / U2-type prespliceosome / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / centriolar satellite / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / B-WICH complex positively regulates rRNA expression / mRNA processing / mRNA splicing, via spliceosome / microtubule cytoskeleton / nuclear speck / chromatin remodeling / mRNA binding / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / RNA recognition motif domain, eukaryote / RNA recognition motif / Splicing factor 3B subunit 1-like / RRM (RNA recognition motif) domain / RNA recognition motif ...Splicing factor, RBM39-like / Splicing factor RBM39, linker / linker between RRM2 and RRM3 domains in RBM39 protein / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / RNA recognition motif domain, eukaryote / RNA recognition motif / Splicing factor 3B subunit 1-like / 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 / Armadillo-like helical / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / LYSINE / Splicing factor 3B subunit 1 / RNA-binding protein 39
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.74 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 1.2Jan 14, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...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_entity_src_syn / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _symmetry.Int_Tables_number
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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
C: Splicing factor 3B subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8496
Polymers26,6273
Non-polymers2223
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-23 kcal/mol
Surface area12020 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

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#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: Protein/peptide Splicing factor 3B subunit 1


Mass: 1306.470 Da / Num. of mol.: 1 / Fragment: 333-342 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75533

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Non-polymers , 4 types, 305 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 1.92 Å3/Da / Density % sol: 35.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8 M sodium phosphate, 0.8 M potassium phosphate, 0.1 M HEPES pH 7.5

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→34 Å / Num. obs: 37595 / % possible obs: 97.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 11.37 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.1
Reflection shellResolution: 1.74→1.84 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.2 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PROTEUM PLUSdata collection
PROTEUM PLUSdata scaling
PDB_EXTRACT3.14data extraction
PHENIXrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.74→33.989 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 16.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1805 3769 10.03 %Random selection
Rwork0.1434 33826 --
obs0.1472 37595 94.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71 Å2 / Biso mean: 17.9033 Å2 / Biso min: 4.74 Å2
Refinement stepCycle: final / Resolution: 1.74→33.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 24 303 2076
Biso mean--34.99 26.36 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011856
X-RAY DIFFRACTIONf_angle_d1.2992545
X-RAY DIFFRACTIONf_chiral_restr0.06285
X-RAY DIFFRACTIONf_plane_restr0.009335
X-RAY DIFFRACTIONf_dihedral_angle_d14.156656
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.74-1.7620.26191110.2405930104170
1.762-1.78520.24881230.23491041116480
1.7852-1.80970.24921160.21011110122683
1.8097-1.83550.25951290.21731109123886
1.8355-1.86290.24471380.19271210134890
1.8629-1.8920.24611310.1971174130591
1.892-1.9230.20981390.1871252139193
1.923-1.95620.24961400.18821251139194
1.9562-1.99180.19971380.1661232137096
1.9918-2.03010.21331350.15671305144096
2.0301-2.07150.17681460.14471248139497
2.0715-2.11650.18711430.1511291143498
2.1165-2.16580.171360.13781305144199
2.1658-2.21990.17721580.14321281143998
2.2199-2.27990.18361460.13151313145999
2.2799-2.3470.14631400.13661307144799
2.347-2.42270.19281580.13071268142699
2.4227-2.50930.19361380.13651330146899
2.5093-2.60970.17691390.13021322146199
2.6097-2.72850.23631330.13413261459100
2.7285-2.87220.16291610.134413041465100
2.8722-3.05210.1791320.133413161448100
3.0521-3.28760.14891460.123413371483100
3.2876-3.61810.15081430.115813081451100
3.6181-4.14080.14691400.110913231463100
4.1408-5.2140.12651630.107813141477100
5.214-33.99590.17651470.168413191466100
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)
12.1086-1.60941.31592.6381-1.46232.59520.10310.1764-0.0538-0.1614-0.15470.09240.3010.13950.03130.1028-0.00750.01720.0566-0.00290.08975.8429-55.4622100.5807
20.60410.6505-0.55567.1154-5.39384.08860.02780.01750.0557-0.00010.02090.0583-0.0546-0.102-0.12070.0591-0.0019-0.00660.05540.00590.0836-2.2132-50.0555106.2485
31.08130.4187-0.64131.8931-1.50734.86340.01720.04740.0304-0.03960.0198-0.0563-0.06920.0663-0.03620.02980.006-0.00050.0317-0.00340.06116.3046-54.0977107.9351
47.40722.50387.18181.5982.32338.1003-0.04220.1466-0.0935-0.11990.11540.0501-0.0410.0596-0.08030.1397-0.00070.01910.04770.00060.10443.9528-62.0912101.4117
54.0557-2.73032.38274.5872-0.32176.54460.0829-0.4180.09860.22710.0129-0.5129-0.38870.3363-0.01470.0931-0.039-0.02910.1034-0.00350.160218.2856-51.4556110.3019
68.44662.9851-4.60019.77513.44036.0987-0.0843-0.49980.14220.33950.0916-0.3979-0.39460.7620.00880.1072-0.0263-0.03250.12960.00170.138515.5866-45.558112.0465
74.64463.05442.27393.6670.27628.7723-0.0099-0.51150.28160.03460.11480.0749-0.3064-0.2712-0.13970.17320.00160.00780.0877-0.01510.10513.3827-45.0699118.5196
82.7865-0.13141.00055.5217-2.83255.9414-0.0826-0.21050.04480.10710.18290.2301-0.1074-0.2540.00040.0520.00530.0070.0825-0.01740.054924.868-49.298495.4755
97.8052-4.1758-4.41043.62865.12367.9777-0.2811-0.4488-0.13850.30040.4081-0.18010.36140.15-0.0330.11810.0064-0.03410.11540.03960.150136.7371-64.4729100.74
107.425-6.18446.76695.5343-5.02527.09490.25760.1257-0.2022-0.1193-0.05950.10460.38050.2202-0.14120.12060.02560.0090.0946-0.01590.059427.4368-60.015588.6463
112.94080.0461.15151.8525-0.71843.01-0.0361-0.11910.03970.16880.0059-0.14740.0170.18760.01130.06850.0153-0.00260.0597-0.01660.056626.6302-50.490.8666
122.77243.1654-1.74926.9046-2.69242.2884-0.0572-0.01290.09710.13620.16320.2880.0179-0.1152-0.07480.07120.0228-0.00540.0891-0.00910.040724.1868-49.117295.4114
131.72180.89551.09043.82533.77534.3994-0.06730.2635-0.038-0.20970.2203-0.1825-0.1290.5237-0.07060.06880.00940.00340.1659-0.01150.086732.7703-50.289681.5014
143.2138-2.8633.17784.8626-3.57585.1058-0.11760.1703-0.73990.44990.01750.41640.8736-0.16730.00670.30610.03540.04540.25770.03410.228521.0394-65.337796.7429
150.85770.57171.77293.99728.854320.2311-0.22380.5548-0.39150.263-0.7223-0.7569-0.1548-0.51730.32790.08250.13370.22150.03190.6091-2.899-63.593116.5648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 412 through 435 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 436 through 450 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 451 through 485 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 486 through 501 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 502 through 508 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 509 through 513 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 514 through 522 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 414 through 427 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 428 through 435 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 436 through 450 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 451 through 485 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 486 through 508 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 509 through 523 )B0
14X-RAY DIFFRACTION14chain 'C' and (resid 335 through 342 )C0
15X-RAY DIFFRACTION15chain 'F' and (resid 2 through 2 )A603

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