1VC6	Translation Rna	date	Mar 04, 2004
title	Crystal Structure Of The Hepatitis Delta Virus Gemonic Ribozyme Product With C75u Mutaion, Cleaved In Imidazole And Mg2+ Solutions
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 0.247 R_Free 0.284
crystal cell	length a length b length c angle alpha angle beta angle gamma 109.159 109.159 190.603 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	MG	enzyme
related structures	by homologous chain: 1SJF, 1VBZ
Gene Ontology	Chain Function Process Component A nucleotide binding nucleic acid binding RNA binding protein binding snRNA binding mRNA splicing, via spliceoso... mRNA processing RNA splicing gene expression nucleus nucleoplasm spliceosomal complex ribonucleoprotein complex
Primary reference	A 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] (51 Kb) [Save to disk] Biological Unit Coordinates (1vc6.pdb1.gz) 47 Kb LPC: Ligand-Protein Contacts for 1VC6 CSU: Contacts of Structural Units for 1VC6 Likely Quarternary Molecular Structure file(s) for 1VC6 Structure Factors (109 Kb) Retrieve 1VC6 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1VC6 from S2C, [Save to disk] Re-refined 1vc6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1VC6 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 1VC6

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 1VC6, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1vc6a_, region A [Jmol] [rasmolscript] [script source] Fold representative 1vc6 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: [1vc6_A] [1vc6_B] SWISS-PROT database: [P09012] Domain organization of [SNRPA_HUMAN] by SWISSPFAM Domain found in 1VC6: [RRM ] by SMART Alignments of the sequence of 1VC6 with the sequences similar proteins can be viewed for 1VC6'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 1VC6

Community annotation for 1VC6 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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