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- PDB-1drz: U1A SPLICEOSOMAL PROTEIN/HEPATITIS DELTA VIRUS GENOMIC RIBOZYME C... -

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Basic information

Entry
Database: PDB / ID: 1drz
TitleU1A SPLICEOSOMAL PROTEIN/HEPATITIS DELTA VIRUS GENOMIC RIBOZYME COMPLEX
Components
  • PROTEIN (U1 SMALL RIBONUCLEOPROTEIN A)
  • RNA (HEPATITIS DELTA VIRUS GENOMIC RIBOZYME)
KeywordsRNA BINDING PROTEIN/RNA / CATALYTIC RNA / RIBOZYME / RNA-BINDING PROTEIN / U1A / HDV / 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) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHepatitis delta virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsFerre-D'Amare, A.R. / Zhou, K. / Doudna, J.A.
CitationJournal: Nature / Year: 1998
Title: Crystal structure of a hepatitis delta virus ribozyme.
Authors: Ferre-D'Amare, A.R. / Zhou, K. / Doudna, J.A.
History
DepositionSep 1, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: RNA (HEPATITIS DELTA VIRUS GENOMIC RIBOZYME)
A: PROTEIN (U1 SMALL RIBONUCLEOPROTEIN A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8427
Polymers34,5762
Non-polymers2655
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Cell settingtrigonal
Space group name H-MH32

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Components

#1: RNA chain RNA (HEPATITIS DELTA VIRUS GENOMIC RIBOZYME) / HDV RIBOZYME / DELTA RIBOZYME


Mass: 23179.793 Da / Num. of mol.: 1 / Fragment: RIBOZYME DOMAIN
Source method: isolated from a genetically manipulated source
Details: RNA IS THE PRODUCT OF SELF-CLEAVAGE. NUCLEOTIDES 146 - 159 INCLUSIVE ARE AN ENGINEERED COGNATE BINDING SITE FOR THE U1A PROTEIN
Source: (gene. exp.) Hepatitis delta virus / Genus: Deltavirus
Description: RNA PRODUCED BY IN VITRO RUN-OFF TRANSCRIPTION WITH BACTERIOPHAGE T7 RNA POLYMERASE FROM PLASMID DNA LINEARIZED WITH RESTRICTION ENZYME BSAI. T7 TRANSCRIPT
Plasmid: PDU9 / Production host: Escherichia coli (E. coli)
#2: Protein PROTEIN (U1 SMALL RIBONUCLEOPROTEIN A) / U1A-RBD / U1SNRNP


Mass: 11396.701 Da / Num. of mol.: 1 / Fragment: RNA BINDING DOMAIN / Mutation: Y31H, Q36R
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONYL PROTEIN / Source: (gene. exp.) Homo sapiens (human)
Description: (A1-98 Y31H Q36R) T7 PLASMID EXPRESSED IN E. COLI STRAIN B834 GROWN IN MINIMAL MEDIUM SUPPLEMENTED WITH SELENOMETHIONINE;
Plasmid: T7 / 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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 67 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMprotein1drop
21.25 mM1dropMgCl2
312.5-14 %(w/v)mPEG20001reservoir
4100 mMTris-HCl1reservoir
5200-250 mM1reservoirLi2SO4
64 mMspermine-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9761, 0.9794, 0.9792, 1.1390
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 15, 1998 / Details: MIRROR
RadiationMonochromator: SI / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97611
20.97941
30.97921
41.1391
ReflectionResolution: 2.9→41.3 Å / Num. all: 17817 / Num. obs: 17817 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 47.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 21.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 5.2 / % possible all: 97.6
Reflection
*PLUS
Num. measured all: 55889
Reflection shell
*PLUS
% possible obs: 97.6 %

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Processing

Software
NameVersionClassification
SOLVEphasing
SHARPphasing
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 2082995.34 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1861 9.8 %RANDOM
Rwork0.281 ---
obs0.281 18903 95.6 %-
all-18903 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.3 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso mean: 76.2 Å2
Baniso -1Baniso -2Baniso -3
1--10 Å20.08 Å20 Å2
2---10 Å20 Å2
3---20.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms802 1532 13 19 2366
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.441
X-RAY DIFFRACTIONc_mcangle_it0.81
X-RAY DIFFRACTIONc_scbond_it0.482
X-RAY DIFFRACTIONc_scangle_it0.732
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 295 9.4 %
Rwork0.426 2841 -
obs--96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 76.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.93
X-RAY DIFFRACTIONc_mcbond_it1
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it1
X-RAY DIFFRACTIONc_scangle_it2
LS refinement shell
*PLUS
Rfactor Rfree: 0.399 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.426

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