1VC5 Translation Rna date Mar 04, 2004
title Crystal Structure Of The Wild Type Hepatitis Delta Virus Gemonic Ribozyme Precursor, 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
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: Petr
symmetry Space Group: H 3 2
R_factor 0.305 R_Free 0.327
crystal
cell
length a length b length c angle alpha angle beta angle gamma
109.488 109.488 187.580 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.40 Å
ligand NA enzyme
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] (104 Kb) [Save to disk]
  • Biological Unit Coordinates (1vc5.pdb1.gz) 98 Kb
  • LPC: Ligand-Protein Contacts for 1VC5
  • CSU: Contacts of Structural Units for 1VC5
  • Likely Quarternary Molecular Structure file(s) for 1VC5
  • Structure Factors (60 Kb)
  • Retrieve 1VC5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VC5 from S2C, [Save to disk]
  • Re-refined 1vc5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VC5 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 1VC5
  • 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 1VC5, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vc5a_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1vc5 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: [1vc5_B] [1vc5_A] [1vc5]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM
  • Domain found in 1VC5: [RRM ] by SMART
  • Alignments of the sequence of 1VC5 with the sequences similar proteins can be viewed for 1VC5's classification [SNRPA_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [SNRPA_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1VC5
  • Community annotation for 1VC5 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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