1SJ3	Translation Rna	date	Mar 02, 2004
title	Hepatitis Delta Virus Gemonic Ribozyme Precursor, With Mg2+
authors	A.Ke, K.Zhou, F.Ding, J.H.Cate, J.A.Doudna
compound		source
Molecule: Precursor Form Of The Hepatitis Delta Virus Riboz Chain: R Engineered: Yes Mutation: Yes		Organism_scientific: Hepatitis Delta Virus Organism_taxid: 12475 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Dh5alpha Expression_system_vector_type: Plasmid Expression_system_plasmid: Puc19-Pt3 Other_details: C75u In Vitro Transcription
Molecule: Small Nuclear Ribonucleoprotein A Chain: P Fragment: Rna Binding Domain Synonym: U1 Snrnp Protein A; U1a Protein; U1-A; Small Nucle Ribonucleoprotein Polypeptide A; Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Snrpa Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Other_details: Y31h, Q36r
symmetry	Space Group: H 3 2	R_factor 0.255 R_Free 0.282
crystal cell	length a length b length c angle alpha angle beta angle gamma 108.731 108.731 191.726 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	MG	enzyme
related structures	by homologous chain: 1CX0, 1M5O
Gene Ontology	Chain Function Process Component P 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] (53 Kb) [Save to disk] Biological Unit Coordinates (1sj3.pdb1.gz) 48 Kb LPC: Ligand-Protein Contacts for 1SJ3 CSU: Contacts of Structural Units for 1SJ3 Likely Quarternary Molecular Structure file(s) for 1SJ3 Structure Factors (222 Kb) Retrieve 1SJ3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1SJ3 from S2C, [Save to disk] Re-refined 1sj3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1SJ3 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 1SJ3

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 1SJ3, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1sj3p_, region P [Jmol] [rasmolscript] [script source] Fold representative 1sj3 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: [1sj3_P] [1sj3_R] SWISS-PROT database: [P09012] Domain organization of [SNRPA_HUMAN] by SWISSPFAM Domain found in 1SJ3: [RRM ] by SMART Alignments of the sequence of 1SJ3 with the sequences similar proteins can be viewed for 1SJ3'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 1SJ3

Community annotation for 1SJ3 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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