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

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Basic information

Entry
Database: PDB / ID: 4prf
TitleA Second Look at the HDV Ribozyme Structure and Dynamics.
Components
  • Hepatitis Delta virus ribozyme
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA BINDING PROTEIN/RNA / HDV / ribozyme / RNA / U1A / precursor / TRANSLATION-RNA COMPLEX / 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
STRONTIUM ION / RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.395 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: 1VC7
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Feb 28, 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_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

Downloads & links

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Assembly

Deposited unit
B: Hepatitis Delta virus ribozyme
A: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1414
Polymers35,9662
Non-polymers1752
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-79 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.944, 108.944, 191.754
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-217-

HOH

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Components

#1: RNA chain Hepatitis Delta virus ribozyme /


Mass: 24467.521 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA occurs from Hapatitis Delta Virus pathogen, in vitro transcription with pUc19
#2: Protein U1 small nuclear ribonucleoprotein A / U1 snRNP A / U1-A / U1A


Mass: 11498.472 Da / Num. of mol.: 1 / Fragment: U1A_RBD, UNP residues 98-173 / Mutation: Y31H, Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P09012
#3: Chemical ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: SrCl2, NaCl, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0781, 0.9787, 0.9795, 0.9797
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 16, 2003
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07811
20.97871
30.97951
40.97971
ReflectionResolution: 2.395→50 Å / Num. all: 17315 / % possible obs: 93.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.56
Reflection shellResolution: 2.4→2.46 Å / % possible all: 75

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Processing

Software
NameVersionClassification
SOLVEphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.395→35.528 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 854 5.07 %RANDOM
Rwork0.198 ---
obs0.2005 16844 96 %-
all-17315 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.395→35.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms759 1577 2 42 2380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042566
X-RAY DIFFRACTIONf_angle_d0.6443828
X-RAY DIFFRACTIONf_dihedral_angle_d13.771200
X-RAY DIFFRACTIONf_chiral_restr0.029493
X-RAY DIFFRACTIONf_plane_restr0.004205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.395-2.54520.36821430.31392364X-RAY DIFFRACTION86
2.5452-2.74170.34181480.29392621X-RAY DIFFRACTION96
2.7417-3.01750.32581280.25772681X-RAY DIFFRACTION97
3.0175-3.45380.25281460.19982715X-RAY DIFFRACTION99
3.4538-4.35020.22221650.17212740X-RAY DIFFRACTION99
4.3502-35.53180.21961240.1732869X-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)
12.0653-1.3092-0.13591.3412-0.18063.3235-0.0769-0.0281-0.4372-0.12840.0523-0.21790.20140.0433-0.00010.45050.00380.07880.3729-0.01860.491639.274944.217790.9949
20.9015-0.48340.10614.1578-1.32531.0061-0.20570.09560.64950.02360.1023-0.3835-0.7865-0.1345-0.12061.20470.0936-0.06510.50020.00120.722534.726881.57975.9757
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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