2HYI	Hydrolase Rna Binding Protein Rna	date	Aug 06, 2006
title	Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna
authors	C.B.F.Andersen, H.Le Hir, G.R.Andersen
compound		source
Molecule: 5'-R(Upupupupupu)-3' Chain: F, L Fragment: Mrna Mimick Engineered: Yes		Synthetic: Yes
Molecule: Protein Mago Nashi Homolog Chain: A, G Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Magoh Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Rosetta Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28a
Molecule: Rna-Binding Protein 8a Chain: B, H Fragment: N-Terminal Deletion Mutant Synonym: Rna-Binding Motif Protein 8a, Ribonucleoprotein Rbm8a, Rna-Binding Protein Y14, Binder Of Ovca1- 1, Bov-1; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Rbm8a, Rbm8 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Rosetta Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28a
Molecule: Probable Atp-Dependent Rna Helicase Ddx48 Chain: C, I Synonym: Dead Box Protein 48, Eukaryotic Initiation Factor 4a-Like Nuk-34, Nuclear Matrix Protein 265, Hnmp 265, Eukaryotic Translation Initiation Factor 4a Isoform 3; Ec: 3.6.1.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ddx48, Eif4a3, Kiaa0111 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Rosetta Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28a
Molecule: Protein Casc3 Chain: D, J Fragment: Selor Fragment Synonym: Cancer Susceptibility Candidate Gene 3 Protein, Metastatic Lymph Node Protein 51, Mln 51 Protein, Barentsz Protein, Btz; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Casc3, Mln51 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Rosetta Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28a
symmetry	Space Group: C 1 2 1	R_factor 0.212 R_Free 0.231
crystal cell	length a length b length c angle alpha angle beta angle gamma 185.830 88.260 145.770 90.00 110.77 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	ANP, MG	enzyme	Hydrolase E.C.3.6.1 BRENDA
Gene Ontology	Chain Function Process Component A, G RNA binding protein binding nuclear-transcribed mRNA cat... mRNA splicing, via spliceoso... transcription from RNA polym... termination of RNA polymeras... mRNA processing mRNA export from nucleus regulation of translation transport RNA splicing gene expression RNA metabolic process mRNA metabolic process mRNA 3'-end processing mRNA transport nucleus nucleoplasm spliceosomal complex cytoplasm cytosol nuclear speck exon-exon junction complex catalytic step 2 spliceosome... C, I nucleotide binding nucleic acid binding RNA binding ATP-dependent RNA helicase a... helicase activity protein binding ATP binding ATP-dependent helicase activ... poly(A) RNA binding hydrolase activity nuclear-transcribed mRNA cat... nuclear-transcribed mRNA cat... nuclear-transcribed mRNA pol... mRNA splicing, via spliceoso... rRNA processing mRNA processing regulation of translation transport RNA splicing gene expression RNA metabolic process mRNA metabolic process negative regulation of trans... cytokine-mediated signaling ... positive regulation of trans... mRNA transport nucleus spliceosomal complex cytoplasm cytosol nuclear speck exon-exon junction complex catalytic step 2 spliceosome...
Primary reference	Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA., Andersen CB, Ballut L, Johansen JS, Chamieh H, Nielsen KH, Oliveira CL, Pedersen JS, Seraphin B, Le Hir H, Andersen GR, Science. 2006 Sep 29;313(5795):1968-72. Epub 2006 Aug 24. PMID:16931718

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (249 Kb) [Save to disk] Biological Unit Coordinates (2hyi.pdb1.gz) 125 Kb Biological Unit Coordinates (2hyi.pdb2.gz) 123 Kb LPC: Ligand-Protein Contacts for 2HYI CSU: Contacts of Structural Units for 2HYI Likely Quarternary Molecular Structure file(s) for 2HYI Structure Factors (852 Kb) Retrieve 2HYI in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2HYI from S2C, [Save to disk] Re-refined 2hyi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2HYI 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 2HYI

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 2HYI, from MSDmotif at EBI Fold representative 2hyi from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2hyi_A] [2hyi_B] [2hyi_C] [2hyi_D] [2hyi_F] [2hyi_G] [2hyi_H] [2hyi_I] [2hyi_J] [2hyi_L] SWISS-PROT database: [O15234] [P38919] [P61326] [Q9Y5S9] Belongs to the nuclear mrna exporter (mrna-e) family according to TCDB. Domain organization of [CASC3_HUMAN] [IF4A3_HUMAN] [MGN_HUMAN] [RBM8A_HUMAN] by SWISSPFAM Domains found in 2HYI: [Btz] [DEXDc] [HELICc] [RRM ] by SMART Alignments of the sequence of 2HYI with the sequences similar proteins can be viewed for 2HYI's classification [CASC3_HUMAN] [IF4A3_HUMAN] [MGN_HUMAN] [RBM8A_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 [CASC3_HUMAN] [IF4A3_HUMAN] [MGN_HUMAN] [RBM8A_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2HYI

Community annotation for 2HYI at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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