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- PDB-3cgr: X-ray structure containing the pseudouridylated U2 snRNA and intr... -

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Basic information

Entry
Database: PDB / ID: 3cgr
TitleX-ray structure containing the pseudouridylated U2 snRNA and intron branch site consensus sequences
Components
  • RNA (5'-R(*CP*GP*CP*AP*CP*UP*AP*AP*CP*CP*GP*CP*G)-3')
  • RNA (5'-R(*GP*CP*GP*CP*GP*GP*(PSU)P*AP*GP*UP*GP*C)-3')
KeywordsRNA / RNA double helix / Branchpoint sequence / BPS / U2 snRNA / pseudouridine / pre-mRNA splicing
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,0953
Polymers7,9992
Non-polymers961
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-5.9 kcal/mol
Surface area4780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.98, 40.47, 32.21
Angle α, β, γ (deg.)90.00, 95.20, 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*GP*(PSU)P*AP*GP*UP*GP*C)-3')


Mass: 3883.360 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*AP*CP*UP*AP*AP*CP*CP*GP*CP*G)-3')


Mass: 4115.534 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2ammonium sulfate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorDetector: CCD / Date: Jan 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 5193 / Num. obs: 4759 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rsym value: 0.119 / Net I/σ(I): 12
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.486 / % possible all: 83.2

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Processing

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

Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 172 -random
Rwork0.2379 ---
all0.2415 4759 --
obs0.2415 4627 93.1 %-
Displacement parametersBiso mean: 26.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.57 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 529 5 81 615
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.96

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