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- PDB-3cgp: X-ray structure of a pseudouridine-containing yeast spliceosomal ... -

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Basic information

Entry
Database: PDB / ID: 3cgp
TitleX-ray structure of a pseudouridine-containing yeast spliceosomal U2 snRNA-intron branch site duplex bound to iodide ions
Components
  • RNA (5'-R(*CP*GP*CP*UP*AP*CP*UP*AP*AP*CP*GP*CP*G)-3')
  • RNA (5'-R(*GP*CP*GP*CP*GP*(PSU)P*AP*GP*UP*AP*GP*C)-3')
KeywordsRNA / RNA double helix / Branchpoint sequence / BPS / U2 snRNA / pseudouridine / pre-mRNA splicing
Function / homologyIODIDE ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsLin, Y. / Kielkopf, C.L.
CitationJournal: Biochemistry / Year: 2008
Title: X-ray structures of U2 snRNA-branchpoint duplexes containing conserved pseudouridines.
Authors: Lin, Y. / Kielkopf, C.L.
History
DepositionMar 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq / struct_site
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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*GP*CP*GP*CP*GP*(PSU)P*AP*GP*UP*AP*GP*C)-3')
B: RNA (5'-R(*CP*GP*CP*UP*AP*CP*UP*AP*AP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4616
Polymers7,9842
Non-polymers4774
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-4.3 kcal/mol
Surface area4950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.30, 40.79, 32.55
Angle α, β, γ (deg.)90.00, 94.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain RNA (5'-R(*GP*CP*GP*CP*GP*(PSU)P*AP*GP*UP*AP*GP*C)-3')


Mass: 3867.360 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Central nucleotides of this sequence are highly conserved in yeast U2 snRNA
#2: RNA chain RNA (5'-R(*CP*GP*CP*UP*AP*CP*UP*AP*AP*CP*GP*CP*G)-3')


Mass: 4116.518 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Central nucleotides of this sequence are highly conserved in yeast pre-mRNAs
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1M ammonium sulfate, 0.2M sodium iodide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2sodium iodide11
3ammonium sulfate12
4sodium iodide12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.57→20 Å / Num. all: 12574 / Num. obs: 12181 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.043 / Net I/σ(I): 24.3
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 3 % / Mean I/σ(I) obs: 9.7 / Rsym value: 0.122 / % possible all: 92.5

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Processing

Software
NameClassification
CBASSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: our previously solved RNA duplex

Resolution: 1.57→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 857 -random
Rwork0.2012 ---
all0.2024 12181 --
obs0.2024 11922 95.4 %-
Displacement parametersBiso mean: 21.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 1.57→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 528 8 158 694
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.85

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