1VBX Translation Rna date Mar 03, 2004
title Crystal Structure Of The Hepatitis Delta Virus Gemonic Ribozyme Precursor, With C75u Mutaion, In Edta Solution
authors A.Ke, K.Zhou, F.Ding, J.H.D.Cate, J.A.Doudna
compound source
Molecule: Hepatitis Delta Virus Ribozyme
Chain: B
Engineered: Yes
Mutation: Yes
Synthetic: Yes
Other_details: Rna Occurs From Hapatitis Delta Virus Pathogen, In Vitro Transcription With Puc19;

Molecule: U1 Small Nuclear Ribonucleoprotein A
Chain: A
Fragment: U1a_rbd(Residues 1-100)
Synonym: U1 Snrnp Protein A, U1a Protein, U1-A
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet
symmetry Space Group: H 3 2
R_factor 0.252 R_Free 0.285
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.581 108.581 189.996 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
related structures by homologous chain: 1M5P, 1SJF
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA conformational switch controls hepatitis delta virus ribozyme catalysis., Ke A, Zhou K, Ding F, Cate JH, Doudna JA, Nature 2004 May 13;429(6988):201-5. PMID:15141216
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (1vbx.pdb1.gz) 47 Kb
  • CSU: Contacts of Structural Units for 1VBX
  • Likely Quarternary Molecular Structure file(s) for 1VBX
  • Structure Factors (130 Kb)
  • Retrieve 1VBX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VBX from S2C, [Save to disk]
  • Re-refined 1vbx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VBX 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 1VBX
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1VBX, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vbxa_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1vbx 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: [1vbx_B] [1vbx] [1vbx_A]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM
  • Domain found in 1VBX: [RRM ] by SMART
  • Other resources with information on 1VBX
  • Community annotation for 1VBX 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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