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- PDB-1vc5: Crystal Structure of the Wild Type Hepatitis Delta Virus Gemonic ... -

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Basic information

Entry
Database: PDB / ID: 1vc5
TitleCrystal Structure of the Wild Type Hepatitis Delta Virus Gemonic Ribozyme Precursor, in EDTA solution
Components
  • Hepatitis Delta virus ribozyme
  • U1 small nuclear ribonucleoprotein A
KeywordsTRANSLATION/RNA / HDV / ribozyme / RNA / U1A / precursor / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsKe, A. / Zhou, K. / Ding, F. / Cate, J.H.D. / 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.D. / Doudna, J.A.
History
DepositionMar 4, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)36,0114
Polymers35,9652
Non-polymers462
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.488, 109.488, 187.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: RNA chain Hepatitis Delta virus ribozyme /


Mass: 24466.537 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 protein A / U1A protein / U1-A


Mass: 11498.472 Da / Num. of mol.: 1 / Fragment: U1A_RBD(residues 1-100) / Mutation: Y31H/Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pETR / Production host: Escherichia coli (E. coli) / References: UniProt: P09012
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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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: 3.43 Å3/Da / Density % sol: 63.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: EDTA, NaCl, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1EDTAEthylenediaminetetraacetic acid11
2NaClSodium chloride11
3MPD11
4Sodium Cacodylate11
5Spermine-HCl11
6EDTAEthylenediaminetetraacetic acid12
7NaClSodium chloride12
8MPD12
9Sodium Cacodylate12

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 2003 / Details: graphite
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 3.4→80 Å / Num. all: 6744 / Num. obs: 6322 / % possible obs: 93.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2
Reflection shellResolution: 3.4→3.486 Å / % possible all: 81.5

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→20 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.808 / SU B: 44.423 / SU ML: 0.708 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.723 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.32706 322 5.4 %RANDOM
Rwork0.30486 ---
all0.31 6744 --
obs0.30601 5636 96.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.392 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å2-1.17 Å20 Å2
2---2.34 Å20 Å2
3---3.51 Å2
Refine analyzeLuzzati coordinate error obs: 0.71 Å
Refinement stepCycle: LAST / Resolution: 3.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms759 1489 2 0 2250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212435
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9372.7013623
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.815594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0460.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.021286
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1290.2870
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4690.294
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6860.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it3.6321.5476
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.312767
X-RAY DIFFRACTIONr_scbond_it7.1231959
X-RAY DIFFRACTIONr_scangle_it10.3224.52856
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.486 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.26 15
Rwork0.349 351
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)
110.0424-2.3842-0.803210.4840.09077.21110.28-0.1306-0.9151-0.4155-0.296-0.72960.54030.00990.0160.4783-0.07870.18350.0402-0.06830.303238.8639-19.328457.3292
22.0138-1.81060.90939.0146-2.24740.0484-0.4611-0.24941.1281-0.57980.1708-0.7482-0.2629-0.02620.29031.48990.02640.07880.7294-0.12311.042434.469618.558342.2666
30000000000000000.8257000.825700.825739.7612-0.9744.2455
40000000000000000.8257000.825700.825749.754725.450136.1556
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB4 - 984 - 98
2X-RAY DIFFRACTION2BA101 - 1724 - 75
3X-RAY DIFFRACTION3BC2011
4X-RAY DIFFRACTION4BD2021

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