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- PDB-4n0t: Core structure of the U6 small nuclear ribonucleoprotein at 1.7 A... -

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Basic information

Entry
Database: PDB / ID: 4n0t
TitleCore structure of the U6 small nuclear ribonucleoprotein at 1.7 Angstrom resolution
Components
  • U4/U6 snRNA-associated-splicing factor PRP24
  • U6 snRNA
KeywordsRNA BINDING PROTEIN/RNA / spliceosomal ribonucleoprotein complex / annealing U6 and U4 snRNA / nucleus / 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMontemayor, E.J. / Curran, E.C. / Liao, H. / Andrews, K.L. / Treba, C.N. / Butcher, S.E. / Brow, D.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Core structure of the U6 small nuclear ribonucleoprotein at 1.7- angstrom resolution.
Authors: Montemayor, E.J. / Curran, E.C. / Liao, H.H. / Andrews, K.L. / Treba, C.N. / Butcher, S.E. / Brow, D.A.
History
DepositionOct 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Sep 20, 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_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,5283
Polymers66,4322
Non-polymers961
Water12,538696
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-30 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.782, 71.370, 82.081
Angle α, β, γ (deg.)90.00, 109.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 43246.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: PRP24, YM8156.10C, YMR268C / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) STAR pLysS / References: UniProt: P49960
#2: RNA chain U6 snRNA


Mass: 23184.857 Da / Num. of mol.: 1 / Mutation: A62G, U100C, U101C / Source method: obtained synthetically
Details: In vitro transcription using a cloned plasmid template
References: GenBank: BK006945.2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 274 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM lithium sulfate, 100 mM sodium citrate, pH 5.5, 20 % PEG 1,000, VAPOR DIFFUSION, SITTING DROP, temperature 274K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2013
RadiationMonochromator: diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Net I/σ(I): 15.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.9 / % possible all: 97

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GHP

2ghp


Resolution: 1.7→26.25 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 4690 3.22 %random
Rwork0.1836 ---
obs0.1845 145765 99.6 %-
all-146350 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→26.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 1389 5 696 5024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064547
X-RAY DIFFRACTIONf_angle_d1.0256444
X-RAY DIFFRACTIONf_dihedral_angle_d14.6731932
X-RAY DIFFRACTIONf_chiral_restr0.066780
X-RAY DIFFRACTIONf_plane_restr0.005583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6961-1.71530.35741250.28764407X-RAY DIFFRACTION91
1.7153-1.73550.26391600.26684644X-RAY DIFFRACTION100
1.7355-1.75670.2991740.25754744X-RAY DIFFRACTION100
1.7567-1.77890.29341630.25734679X-RAY DIFFRACTION100
1.7789-1.80230.29541430.24864673X-RAY DIFFRACTION100
1.8023-1.8270.31311640.2364761X-RAY DIFFRACTION100
1.827-1.85310.28011520.23614693X-RAY DIFFRACTION100
1.8531-1.88070.23541660.22974772X-RAY DIFFRACTION100
1.8807-1.91010.29241490.22254708X-RAY DIFFRACTION100
1.9101-1.94140.30111540.22214704X-RAY DIFFRACTION100
1.9414-1.97490.27911460.22284754X-RAY DIFFRACTION100
1.9749-2.01080.22861390.20784779X-RAY DIFFRACTION100
2.0108-2.04950.28391720.20114687X-RAY DIFFRACTION100
2.0495-2.09130.21711500.20224707X-RAY DIFFRACTION100
2.0913-2.13670.23291700.19944700X-RAY DIFFRACTION100
2.1367-2.18640.23391530.19434698X-RAY DIFFRACTION100
2.1864-2.24110.20641430.19764730X-RAY DIFFRACTION100
2.2411-2.30160.27611670.19824769X-RAY DIFFRACTION100
2.3016-2.36930.25021710.19824687X-RAY DIFFRACTION100
2.3693-2.44570.27571480.19314660X-RAY DIFFRACTION100
2.4457-2.53310.22631670.19444725X-RAY DIFFRACTION100
2.5331-2.63440.22031540.18774777X-RAY DIFFRACTION100
2.6344-2.75420.26211550.19544686X-RAY DIFFRACTION100
2.7542-2.89920.22141560.18854719X-RAY DIFFRACTION100
2.8992-3.08060.21831560.18964732X-RAY DIFFRACTION100
3.0806-3.3180.18731670.17824694X-RAY DIFFRACTION100
3.318-3.65110.17691480.15984758X-RAY DIFFRACTION100
3.6511-4.17760.15561630.14634703X-RAY DIFFRACTION100
4.1776-5.25640.14561540.14224737X-RAY DIFFRACTION100
5.2564-26.25360.18871610.174588X-RAY DIFFRACTION98
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)
11.21580.30340.60612.1167-0.09091.0197-1.187-0.5455-1.11910.3563-0.53820.55912.4537-0.4932-0.51582.5628-0.8308-0.02981.0351.08941.279610.9912-17.697477.8594
23.84660.20372.62784.8488-1.76312.19090.47050.05430.46280.3073-0.87350.93411.0874-0.4980.35061.1673-0.21990.41050.83-0.2791.1203-2.1565-31.291449.5011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and ((resseq 30:36))) or (chain 'B' and ((resseq 97:100)))
2X-RAY DIFFRACTION2(chain 'B' and ((resseq 63:70))) or (chain 'B' and ((resseq 77:86)))

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