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- PDB-1sj3: Hepatitis Delta Virus Gemonic Ribozyme Precursor, with Mg2+ Bound -

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Basic information

Entry
Database: PDB / ID: 1sj3
TitleHepatitis Delta Virus Gemonic Ribozyme Precursor, with Mg2+ Bound
Components
  • precursor form of the Hepatitis Delta virus ribozyme
  • small nuclear ribonucleoprotein A
KeywordsTRANSLATION/RNA / HDV / ribozyme / RNA / U1A / precurosr / TRANSLATION-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) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHepatitis delta virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKe, A. / Zhou, K. / Ding, F. / Cate, J.H. / Doudna, J.A.
CitationJournal: Nature / Year: 2004
Title: A Conformational Switch controls hepatitis delta virus ribozyme catalysis
Authors: Ke, A. / Zhou, K. / Ding, F. / Cate, J.H. / Doudna, J.A.
History
DepositionMar 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: precursor form of the Hepatitis Delta virus ribozyme
P: small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0154
Polymers35,9662
Non-polymers492
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.731, 108.731, 191.726
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settingtrigonal
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11R-36-

HOH

21P-126-

HOH

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Components

#1: RNA chain precursor form of the Hepatitis Delta virus ribozyme


Mass: 24467.521 Da / Num. of mol.: 1 / Mutation: C75U
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis delta virus / Genus: Deltavirus / Description: C75U in vitro transcription / Plasmid: pUC19-pT3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
#2: Protein small nuclear ribonucleoprotein A / U1 snRNP protein A / U1A protein / U1-A / small nuclear ribonucleoprotein polypeptide A


Mass: 11498.472 Da / Num. of mol.: 1 / Fragment: RNA binding domain / Mutation: Y31H, Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Y31H, Q36R; / Gene: SNRPA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09012
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.31 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: NaCl, MgCl2, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaCl11
2MgCl211
3MPD11
4Sodium Cacodylate11
5Spermine-HCl11
6NaCl12
7MgCl212
8MPD12

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9892 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 29, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9892 Å / Relative weight: 1
ReflectionResolution: 2.2→34 Å / Num. all: 22445 / Num. obs: 21056 / % possible obs: 0.938 % / Observed criterion σ(I): 2.5 / Biso Wilson estimate: 30.2 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→31.39 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2862606.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2159 10.3 %RANDOM
Rwork0.255 ---
all0.2551 22445 --
obs0.255 21056 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.6652 Å2 / ksol: 0.393894 e/Å3
Displacement parametersBiso mean: 68.8 Å2
Baniso -1Baniso -2Baniso -3
1--10.05 Å2-2.53 Å20 Å2
2---10.05 Å20 Å2
3---20.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.2→31.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms762 1552 2 37 2353
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d28.5
X-RAY DIFFRACTIONc_improper_angle_d1.61
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.742
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.662.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 344 10.6 %
Rwork0.346 2910 -
obs--88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-MULTI-ENDO.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4ION.PARAM

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