1RK8	Translation	date	Nov 21, 2003
title	Structure Of The Cytosolic Protein Pym Bound To The Mago-Y14 The Exon Junction Complex
authors	F.Bono, J.Ebert, T.Guettler, E.Izaurralde, E.Conti
compound		source
Molecule: Cg8781-Pa Protein Chain: A Fragment: Rbd Domain Synonym: Cg8781-Pa Engineered: Yes		Organism_scientific: Drosophila Melanogaster Organism_common: Fruit Fly Organism_taxid: 7227 Gene: Tsu Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid
Molecule: Mago Nashi Protein Chain: B Fragment: Full-Length Synonym: Cg9401-Pa Engineered: Yes		Organism_scientific: Drosophila Melanogaster Organism_common: Fruit Fly Organism_taxid: 7227 Gene: Mago,Mgn,Cg9401 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid
Molecule: Within The Bgcn Gene Intron Protein Chain: C Fragment: N-Terminal Domain (Residues 1-58) Synonym: Pym Protein; Cg30176-Pa Engineered: Yes		Organism_scientific: Drosophila Melanogaster Organism_common: Fruit Fly Organism_taxid: 7227 Gene: Wibg,Pym,Cg30176cg10330 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid
symmetry	Space Group: P 43 21 2	R_factor 0.235 R_Free 0.249
crystal cell	length a length b length c angle alpha angle beta angle gamma 106.357 106.357 58.139 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.90 Å
ligand	CA	enzyme
note	1RK8 is a representative structure
related structures	by homologous chain: 1OO0, 1P27
Gene Ontology	Chain Function Process Component A catalytic step 2 spliceosome... B C
Primary reference	Molecular insights into the interaction of PYM with the Mago-Y14 core of the exon junction complex., Bono F, Ebert J, Unterholzner L, Guttler T, Izaurralde E, Conti E, EMBO Rep 2004 Mar;5(3):304-10. Epub 2004 Feb 13. PMID:14968132

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk] Biological Unit Coordinates (1rk8.pdb1.gz) 43 Kb LPC: Ligand-Protein Contacts for 1RK8 CSU: Contacts of Structural Units for 1RK8 Likely Quarternary Molecular Structure file(s) for 1RK8 Structure Factors (241 Kb) Retrieve 1RK8 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1RK8 from S2C, [Save to disk] Re-refined 1rk8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1RK8 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 1RK8

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 3D motif for 1RK8, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1rk8a_, region A [Jmol] [rasmolscript] [script source]     - Domain d1rk8b_, region B [Jmol] [rasmolscript] [script source]     - Domain d1rk8c_, region C [Jmol] [rasmolscript] [script source] 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: [1rk8] [1rk8_A] [1rk8_C] [1rk8_B] SWISS-PROT database: [P49028] [Q9V535] [P82804] Domain organization of [MGN_DROME] [RBM8A_DROME] [WIBG_DROME] by SWISSPFAM Domains found in 1RK8: [Mago-bind] [RRM ] by SMART

Other resources with information on 1RK8

Community annotation for 1RK8 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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