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
crystal cell	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 Diffraction	resolution	2.30 Å
ligand	MG, MSE, SO4	enzyme
related structures	by homologous chain: 1A9N, 1CX0
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	Crystal 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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] SWISS-PROT database: [P09012] Domain organization of [SNRPA_HUMAN] by SWISSPFAM Domain found in 1DRZ: [RRM ] by SMART Alignments of the sequence of 1DRZ with the sequences similar proteins can be viewed for 1DRZ'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 1DRZ

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

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