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- PDB-4pr6: A Second Look at the HDV Ribozyme Structure and Dynamics. -

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Basic information

Entry
Database: PDB / ID: 4pr6
TitleA Second Look at the HDV Ribozyme Structure and Dynamics.
Components
  • HDV RIBOZYME SELF-CLEAVED
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA BINDING PROTEIN/RNA / Base Sequence / Binding Sites / Catalysis / Cloning / Molecular / Computer Graphics / Escherichia coli / Hepatitis Delta Virus / Models / Molecular Sequence Data / Nucleic Acid Conformation / RNA / Catalytic / Viral / RNA-Binding Proteins / Ribonucleoprotein / U1 Small Nuclear / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / 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 ...U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / 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) / RNA (> 100) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsKapral, G.J. / Jain, S. / Noeske, J. / Doudna, J.A. / Richardson, D.C. / Richardson, J.S.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.
Authors: Kapral, G.J. / Jain, S. / Noeske, J. / Doudna, J.A. / Richardson, D.C. / Richardson, J.S.
History
DepositionMar 5, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionOct 29, 2014ID: 1CX0
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: HDV RIBOZYME SELF-CLEAVED
A: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,96218
Polymers57,5732
Non-polymers38916
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-111 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.350, 109.350, 190.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-245-

HOH

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Components

#1: RNA chain HDV RIBOZYME SELF-CLEAVED


Mass: 46404.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcription
#2: Protein U1 small nuclear ribonucleoprotein A / U1 snRNP A / U1-A / U1A


Mass: 11168.391 Da / Num. of mol.: 1 / Fragment: RNA BINDING DOMAIN, UNP residues 101-244 / Mutation: Y31H, Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Plasmid: T7 expression plasmid (A1-98 Y31H, Q36R) / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P09012
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.91 Å3/Da / Density % sol: 35.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG MME 2000, LITHIUM SULPHATE, SPERMINE, TRIS, COBALT HEXAMMINE, MAGNESIUM CHLORIDE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9209 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9209 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 19773 / Num. obs: 18903 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.84 % / Biso Wilson estimate: 47.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 25.9
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.84 % / Rmerge(I) obs: 0.041 / % possible all: 96.5

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→18.577 Å / SU ML: 0.38 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.11 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 1863 9.86 %RANDOM
Rwork0.1985 ---
obs0.2028 18903 95.67 %-
all-18903 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.8 Å2
Baniso -1Baniso -2Baniso -3
1--9.57 Å21.53 Å20 Å2
2---9.57 Å20 Å2
3---19.15 Å2
Refinement stepCycle: LAST / Resolution: 2.3→18.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms771 1532 16 83 2402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052555
X-RAY DIFFRACTIONf_angle_d0.6783806
X-RAY DIFFRACTIONf_dihedral_angle_d12.6431198
X-RAY DIFFRACTIONf_chiral_restr0.027486
X-RAY DIFFRACTIONf_plane_restr0.003210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0.022

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.36210.39911530.3514129697
2.3621-2.43150.3541640.3272127897
2.4315-2.50980.33541440.3124128596
2.5098-2.59930.36111510.2776131397
2.5993-2.70310.29521350.269131696
2.7031-2.82570.33471300.2601134197
2.8257-2.97410.30571160.2707134397
2.9741-3.15960.30791370.2331133598
3.1596-3.40220.26121550.2112132898
3.4022-3.7420.22751390.189135097
3.742-4.27770.20971420.1647132896
4.2777-5.36780.17691580.144129795
5.3678-18.57760.20471390.1583121884

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