1M5P	Translation Rna	date	Jul 09, 2002
title	Transition State Stabilization By A Catalytic Rna
authors	P.B.Rupert, A.Massey, S.T.Sigurdsson, A.R.Ferre-D'Amare
compound		source
Molecule: Rna Inhibitor Substrate Chain: A, D Engineered: Yes Other_details: First Fragment		Synthetic: Yes Other_details: This Sequence Occurs Naturally In Satellite Tobacco Ringspot Virus;
Molecule: Rna Inhibitor Substrate Chain: M, P Engineered: Yes Other_details: Second Fragment		Synthetic: Yes Other_details: This Sequence Occurs Naturally In Satellite Tobacco Ringspot Virus;
Molecule: Rna Hairpin Ribozyme Chain: B, E Engineered: Yes		Synthetic: Yes Other_details: This Sequence Occurs Naturally In Satellite Tobacco Ringspot Virus;
Molecule: U1 Small Nuclear Ribonucleoprotein A Chain: C, F Fragment: U1a Rna Binding Domain Synonym: U1 Snrnp A Protein; U1 Snrnp-Specific Protein A Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Snrpa Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid
symmetry	Space Group: C 1 2 1	R_factor 0.223 R_Free 0.280
crystal cell	length a length b length c angle alpha angle beta angle gamma 259.800 44.300 102.400 90.00 107.00 90.00
method	X-Ray Diffraction	resolution	2.60 Å
ligand	5CG, CA	enzyme
related structures	by homologous chain: 1VBX, 1VC0
Gene Ontology	Chain Function Process Component F, C 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	Transition state stabilization by a catalytic RNA., Rupert PB, Massey AP, Sigurdsson ST, Ferre-D'Amare AR, Science 2002 Nov 15;298(5597):1421-4. Epub 2002 Oct 10. PMID:12376595

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (134 Kb) [Save to disk] Biological Unit Coordinates (1m5p.pdb1.gz) 65 Kb Biological Unit Coordinates (1m5p.pdb2.gz) 65 Kb LPC: Ligand-Protein Contacts for 1M5P CSU: Contacts of Structural Units for 1M5P Likely Quarternary Molecular Structure file(s) for 1M5P Structure Factors (364 Kb) Retrieve 1M5P in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1M5P from S2C, [Save to disk] Re-refined 1m5p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1M5P 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 1M5P

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 1M5P, from MSDmotif at EBI Structure summary from SCOR (Structural Classification of RNA) Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1m5pc_, region C [Jmol] [rasmolscript] [script source]     - Domain d1m5pf_, region F [Jmol] [rasmolscript] [script source] Fold representative 1m5p 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: [1m5p_A] [1m5p_B] [1m5p_C] [1m5p_D] [1m5p_E] [1m5p_F] [1m5p_M] [1m5p_P] SWISS-PROT database: [P09012] Domain organization of [SNRPA_HUMAN] by SWISSPFAM Domain found in 1M5P: [RRM ] by SMART Alignments of the sequence of 1M5P with the sequences similar proteins can be viewed for 1M5P'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 1M5P

Community annotation for 1M5P at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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