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- PDB-5tf6: Structure and conformational plasticity of the U6 small nuclear r... -

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Basic information

Entry
Database: PDB / ID: 5tf6
TitleStructure and conformational plasticity of the U6 small nuclear ribonucleoprotein core
Components
  • U4/U6 snRNA-associated-splicing factor PRP24
  • U6 snRNA
KeywordsRNA BINDING PROTEIN/RNA / ribonucleoprotein / spliceosome / snRNP / U6 / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


U6 snRNP / snRNA binding / spliceosomal complex assembly / spliceosomal tri-snRNP complex assembly / U6 snRNA binding / spliceosomal complex / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA binding / nucleus
Similarity search - Function
Occluded RNA-recognition motif / Prp24, RNA recognition motif1 / Prp24, RNA recognition motif2 / : / Occluded RNA-recognition motif / LSM-interacting domain / Lsm interaction motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif ...Occluded RNA-recognition motif / Prp24, RNA recognition motif1 / Prp24, RNA recognition motif2 / : / Occluded RNA-recognition motif / LSM-interacting domain / Lsm interaction 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 / RNA (> 10) / U4/U6 snRNA-associated-splicing factor PRP24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsMontemayor, E.J. / Brow, D.A. / Butcher, S.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM065166 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118131 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118075 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core.
Authors: Montemayor, E.J. / Didychuk, A.L. / Liao, H. / Hu, P. / Brow, D.A. / Butcher, S.E.
History
DepositionSep 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_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 / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U4/U6 snRNA-associated-splicing factor PRP24
B: U6 snRNA
C: U4/U6 snRNA-associated-splicing factor PRP24
D: U6 snRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,62918
Polymers132,8314
Non-polymers79814
Water13,493749
1
A: U4/U6 snRNA-associated-splicing factor PRP24
B: U6 snRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8419
Polymers66,4162
Non-polymers4257
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-19 kcal/mol
Surface area29650 Å2
MethodPISA
2
C: U4/U6 snRNA-associated-splicing factor PRP24
D: U6 snRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7889
Polymers66,4162
Non-polymers3727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-18 kcal/mol
Surface area26190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.921, 84.446, 255.142
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 / RNA chain , 2 types, 4 molecules ACBD

#1: Protein U4/U6 snRNA-associated-splicing factor PRP24 / U4/U6 snRNP protein


Mass: 43246.758 Da / Num. of mol.: 2 / Fragment: UNP residues 34-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PRP24, YMR268C, YM8156.10C / Plasmid: pET3a
Details (production host): mutated to contain a C-terminal 6-his tag
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P49960
#2: RNA chain U6 snRNA


Mass: 23168.857 Da / Num. of mol.: 2 / Mutation: U100C,U101C / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1039022925

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Non-polymers , 4 types, 763 molecules

#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 3.17 Å3/Da / Density % sol: 61.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1 M lithium chloride, 100 mM sodium MES, 64 mM hydrochloric acid, 25% PEG 8,000, 20% glycerol, 1 mM MnCl2, 400 mM potassium chloride, 10 mM HEPES acid, 10 mM Tris base, 2 mM MgCl2, 1 mM TCEP-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→49.1 Å / Num. obs: 141843 / % possible obs: 99.71 % / Redundancy: 12.1 % / Biso Wilson estimate: 50.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.67

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→49.1 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.17
RfactorNum. reflection% reflection
Rfree0.2316 3782 2.67 %
Rwork0.185 --
obs0.1863 141843 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 261.01 Å2 / Biso mean: 69.6255 Å2 / Biso min: 26.98 Å2
Refinement stepCycle: final / Resolution: 2.3→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5922 2630 39 750 9341
Biso mean--69.7 57.86 -
Num. residues----856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0159023
X-RAY DIFFRACTIONf_angle_d1.77112754
X-RAY DIFFRACTIONf_chiral_restr0.1091539
X-RAY DIFFRACTIONf_plane_restr0.011172
X-RAY DIFFRACTIONf_dihedral_angle_d18.2343830
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 (%)
2.3-2.32910.37751270.33314787491492
2.3291-2.35980.31261320.32314830496295
2.3598-2.39210.30481420.30035132527499
2.3921-2.42630.32131440.281551465290100
2.4263-2.46250.31481410.266250945235100
2.4625-2.5010.32371400.257451455285100
2.501-2.5420.33841450.25151815326100
2.542-2.58580.31851390.236551475286100
2.5858-2.63280.31741390.237550975236100
2.6328-2.68350.31551420.249851455287100
2.6835-2.73820.36851450.241751685313100
2.7382-2.79780.3021420.229751325274100
2.7978-2.86280.31291390.205951295268100
2.8628-2.93440.22151410.211151415282100
2.9344-3.01380.29491410.200251475288100
3.0138-3.10240.2811380.192651105248100
3.1024-3.20260.22371450.192851475292100
3.2026-3.3170.24691410.197451205261100
3.317-3.44980.25171420.182851375279100
3.4498-3.60670.16531380.170351425280100
3.6067-3.79680.21881400.16551535293100
3.7968-4.03460.22171420.171851795321100
4.0346-4.34590.21971420.149450795221100
4.3459-4.78290.17291410.147251805321100
4.7829-5.47430.21591350.15651405275100
5.4743-6.8940.18371390.166951275266100
6.894-49.11140.17231400.15951265266100

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