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- PDB-2f9j: 3.0 angstrom resolution structure of a Y22M mutant of the spliceo... -

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Basic information

Entry
Database: PDB / ID: 2f9j
Title3.0 angstrom resolution structure of a Y22M mutant of the spliceosomal protein p14 bound to a region of SF3b155
Components
  • Pre-mRNA branch site protein p14
  • Splicing factor 3B subunit 1
KeywordsRNA BINDING PROTEIN / SF3bp14 SF3b155 SAP155 p14Y22M RRM
Function / homology
Function and homology information


U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / blastocyst formation / : / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly ...U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / RNA splicing, via transesterification reactions / blastocyst formation / : / 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 / precatalytic spliceosome / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / B-WICH complex positively regulates rRNA expression / mRNA splicing, via spliceosome / nuclear speck / chromatin remodeling / mRNA binding / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
SF3B6, RNA recognition motif / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / 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 ...SF3B6, RNA recognition motif / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / 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
Splicing factor 3B subunit 1 / Splicing factor 3B subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSchellenberg, M.J. / MacMillan, A.M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Crystal structure of a core spliceosomal protein interface
Authors: Schellenberg, M.J. / Edwards, R.A. / Ritchie, D.B. / Kent, O.A. / Golas, M.M. / Stark, H. / Glover, J.N.M. / Macmillan, A.M.
History
DepositionDec 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-mRNA branch site protein p14
P: Splicing factor 3B subunit 1
B: Pre-mRNA branch site protein p14
Q: Splicing factor 3B subunit 1


Theoretical massNumber of molelcules
Total (without water)37,9744
Polymers37,9744
Non-polymers00
Water19811
1
A: Pre-mRNA branch site protein p14
P: Splicing factor 3B subunit 1


Theoretical massNumber of molelcules
Total (without water)18,9872
Polymers18,9872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-12 kcal/mol
Surface area9110 Å2
MethodPISA
2
B: Pre-mRNA branch site protein p14
Q: Splicing factor 3B subunit 1


Theoretical massNumber of molelcules
Total (without water)18,9872
Polymers18,9872
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-10 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.271, 71.271, 102.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13P
23Q

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGASNASNAA12 - 8112 - 81
21ARGARGASNASNBC12 - 8112 - 81
12ARGARGGLUGLUAA85 - 11585 - 115
22ARGARGGLUGLUBC85 - 11585 - 115
13ASNASNLEULEUPB396 - 41517 - 36
23ASNASNLEULEUQD396 - 41517 - 36

NCS ensembles :
ID
1
2
3
Details2 biological units per ASU. Biological unit consists of one p14 molecule bound to one SF3b155 fragment

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Components

#1: Protein Pre-mRNA branch site protein p14 / SF3B 14 kDa subunit


Mass: 14574.924 Da / Num. of mol.: 2 / Mutation: Y22M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF3B14 / Plasmid: pMALc2x / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9Y3B4
#2: Protein/peptide Splicing factor 3B subunit 1 / Spliceosome associated protein 155 / SAP 155 / SF3b155 / Pre-mRNA splicing factor SF3b 155 kDa subunit


Mass: 4411.839 Da / Num. of mol.: 2 / Fragment: Residues: 381-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SF3B1, SAP155 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / References: UniProt: O75533
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.41 Å3/Da / Density % sol: 63.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 60% NaH2PO4/40% K2HPO4 0.5M beta-alanine, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 10288 / % possible obs: 99.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.059
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3-3.114.20.461100
3.11-3.234.20.3831100
3.23-3.384.20.2411100
3.38-3.564.20.138199.9
3.56-3.784.20.0891100
3.78-4.074.20.0671100
4.07-4.484.20.051100
4.48-5.134.20.0411100
5.13-6.464.20.0381100
6.46-1004.10.023198.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 2f9d

2f9d


Resolution: 3→71.25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.904 / SU B: 30.705 / SU ML: 0.329 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 4.152 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26586 488 4.8 %RANDOM
Rwork0.21906 ---
obs0.22128 9775 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.734 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å20 Å20 Å2
2--2.59 Å20 Å2
3----5.17 Å2
Refinement stepCycle: LAST / Resolution: 3→71.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 0 11 2428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222467
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.9853328
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1135286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6723.939132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.1715457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4011523
X-RAY DIFFRACTIONr_chiral_restr0.0990.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021909
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.21098
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21691
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4861.51490
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8722359
X-RAY DIFFRACTIONr_scbond_it1.00931105
X-RAY DIFFRACTIONr_scangle_it1.574.5969
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A280tight positional0.040.05
2A124tight positional0.030.05
3B80tight positional0.030.05
1A289medium positional0.490.5
2A147medium positional0.620.5
3B83medium positional0.90.5
1A280tight thermal0.050.5
2A124tight thermal0.030.5
3B80tight thermal0.10.5
1A289medium thermal0.362
2A147medium thermal0.182
3B83medium thermal0.342
LS refinement shellResolution: 3.002→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 34 -
Rwork0.277 716 -
obs--100 %
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)
14.8729-1.5274-3.4394.14853.2916.75270.1086-0.1217-0.34580.3132-0.34450.0392-0.0728-0.21550.2358-0.0734-0.0729-0.07590.06230.0438-0.2965.51666.7911.599
21.95860.13560.85153.04910.16544.8658-0.17750.1940.18680.0036-0.00380.097-0.68550.45780.18130.0251-0.0585-0.0385-0.0160.0429-0.240839.916941.857637.9701
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 125
2X-RAY DIFFRACTION2B13 - 125

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