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- PDB-2f9d: 2.5 angstrom resolution structure of the spliceosomal protein p14... -

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Basic information

Entry
Database: PDB / ID: 2f9d
Title2.5 angstrom resolution structure of the spliceosomal protein p14 bound to region of SF3b155
Components
  • Pre-mRNA branch site protein p14
  • Splicing factor 3B subunit 1
KeywordsRNA BINDING PROTEIN / p14 SF3bp14 SF3b155 SAP155 RRM
Function / homology
Function and homology information


U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / blastocyst formation / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / U2 snRNP ...U11/U12 snRNP / B-WICH complex / splicing factor binding / U12-type spliceosomal complex / blastocyst formation / RNA splicing, via transesterification reactions / 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 / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / 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 / : / PPP2R1A-like HEAT repeat / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...SF3B6, RNA recognition motif / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1-like / : / PPP2R1A-like HEAT repeat / 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 / MAD / Resolution: 2.5 Å
AuthorsSchellenberg, M.J. / Edwards, R.A. / Ritchie, D.B. / Glover, J.N.M. / 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 5, 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 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,9174
Polymers39,9174
Non-polymers00
Water1,20767
1
A: Pre-mRNA branch site protein p14
P: Splicing factor 3B subunit 1


Theoretical massNumber of molelcules
Total (without water)19,9582
Polymers19,9582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-10 kcal/mol
Surface area9480 Å2
MethodPISA
2
B: Pre-mRNA branch site protein p14
Q: Splicing factor 3B subunit 1


Theoretical massNumber of molelcules
Total (without water)19,9582
Polymers19,9582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-10 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.870, 115.227, 82.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13P
23Q

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEPHEPHE2AA20 - 8020 - 80
21ILEILEPHEPHE2BB20 - 8020 - 80
12ASNASNLEULEU2AA84 - 11284 - 112
22ASNASNLEULEU2BB84 - 11284 - 112
13ARGARGLEULEU4PC390 - 41518 - 43
23ARGARGLEULEU4QD390 - 41518 - 43

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

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Components

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


Mass: 14606.900 Da / Num. of mol.: 2
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: 5351.517 Da / Num. of mol.: 2 / Fragment: Residues: 373-415
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


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14-18% PEG3350, MOPS buffer, 0.2M sodium formate selenomethionine derivatized SF3b155 protein, pH 6, 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: 0.979547, 1.019859
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 25, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9795471
21.0198591
ReflectionNumber: 17097 / Rmerge(I) obs: 0.076 / Χ2: 1.033 / D res high: 2.5 Å / D res low: 100 Å / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.3910099.710.0310.971
4.275.3910010.0381.02
3.734.2710010.0491.002
3.393.7310010.0721.066
3.153.3910010.1161.068
2.963.1510010.1821.042
2.822.9610010.3221.067
2.692.8210010.4171.041
2.592.6999.910.5521.015
2.52.5995.610.3991.028
ReflectionResolution: 2.5→100 Å / Num. obs: 17097 / % possible obs: 99.5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 25.5
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.4 / % possible all: 95.6

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
12 wavelength10.97950.5-8.06
12 wavelength21.01990.54-2.84
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se19.6220.880.0680.0890.831
2Se600.0110.1290.0491.314
3Se16.3270.3990.1380.090.934
4Se30.5640.7610.2870.1690.988
Phasing dmFOM : 0.62 / FOM acentric: 0.62 / FOM centric: 0.67 / Reflection: 16104 / Reflection acentric: 14438 / Reflection centric: 1666
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-56.0420.910.920.88811592219
4.5-7.10.860.870.7923251976349
3.6-4.50.830.840.7828892562327
3.1-3.60.710.710.6828652591274
2.7-3.10.450.450.4648444488356
2.5-2.70.30.30.323702229141

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→76.25 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.918 / SU B: 16.022 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.382 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27562 858 5 %RANDOM
Rwork0.2214 ---
obs0.22403 16225 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.447 Å2
Baniso -1Baniso -2Baniso -3
1--4.8 Å20 Å20 Å2
2--4.63 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.5→76.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 0 67 2627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222618
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9793538
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1965302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32523.857140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.12415476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4681524
X-RAY DIFFRACTIONr_chiral_restr0.1340.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022034
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.21213
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21788
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6441.51570
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18222494
X-RAY DIFFRACTIONr_scbond_it1.74531194
X-RAY DIFFRACTIONr_scangle_it2.7184.51044
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
1A244tight positional0.050.05
2A116tight positional0.050.05
1A253medium positional0.530.5
2A137medium positional0.710.5
3P219medium positional0.70.5
1A244tight thermal0.110.5
2A116tight thermal0.170.5
1A253medium thermal0.672
2A137medium thermal0.532
3P219medium thermal1.382
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.487 47 -
Rwork0.33 1155 -
obs--95.02 %
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)
16.2341-1.01452.68582.0953-0.64613.9171-0.03230.15930.2839-0.0286-0.05570.02210.07230.10850.088-0.1581-0.0478-0.0127-0.09860.0268-0.113329.206131.55434.891
26.69091.2784-0.52232.63930.87232.8078-0.2129-0.1068-0.52340.14460.0317-0.27940.20950.3420.1812-0.13580.04090.02850.03310.02-0.03633.651122.211938.5014
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 125
2X-RAY DIFFRACTION2B13 - 125

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