1DRZ Rna Binding Protein Rna date Sep 01, 1998
title U1a Spliceosomal Proteinhepatitis Delta Virus Genomic Ribozyme Complex
authors A.R.Ferre-D'Amare, K.Zhou, J.A.Doudna
compound source
Molecule: Rna (Hepatitis Delta Virus Genomic Ribozyme)
Chain: B
Fragment: Ribozyme Domain
Synonym: Hdv Ribozyme, Delta Ribozyme
Engineered: Yes
Other_details: Rna Is The Product Of Self-Cleavage. Nucleotides 146 - 159 Inclusive Are An Engineered Cognate Binding Site For The U1a Protein;
Organism_scientific: Hepatitis Delta Virus
Organism_taxid: 12475
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pdu9
Other_details: Rna Produced By In Vitro Run-Off Transcription With Bacteriophage T7 Rna Polymerase From Plasmid Dna Linearized With Restriction Enzyme Bsai. T7 Transcript;

Molecule: Protein (U1 Small Ribonucleoprotein A)
Chain: A
Fragment: Rna Binding Domain
Synonym: U1a-Rbd, U1snrnp
Engineered: Yes
Mutation: Yes
Other_details: Selenomethionyl Protein

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834
Expression_system_plasmid: T7
Other_details: (A1-98 Y31h Q36r) T7 Plasmid Expressed In E. Coli Strain B834 Grown In Minimal Medium Supplemented With Selenomethionine;
symmetry Space Group: H 3 2
R_factor 0.281 R_Free 0.284
length a length b length c angle alpha angle beta angle gamma
109.350 109.350 190.680 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand MG, MSE, SO4 enzyme
related structures by homologous chain: 1A9N, 1CX0

Primary referenceCrystal structure of a hepatitis delta virus ribozyme., Ferre-D'Amare AR, Zhou K, Doudna JA, Nature 1998 Oct 8;395(6702):567-74. PMID:9783582
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (1drz.pdb1.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 1DRZ
  • CSU: Contacts of Structural Units for 1DRZ
  • Likely Quarternary Molecular Structure file(s) for 1DRZ
  • Retrieve 1DRZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DRZ from S2C, [Save to disk]
  • View 1DRZ in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1DRZ
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1DRZ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1drza_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1drz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1drz_A] [1drz_B] [1drz]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM
  • Domain found in 1DRZ: [RRM ] by SMART
  • Other resources with information on 1DRZ
  • Community annotation for 1DRZ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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