3EX7	Hydrolase Rna Binding Protein Rna	date	Oct 16, 2008
title	The Crystal Structure Of Ejc In Its Transition State
authors	G.R.Andersen, K.H.Nielsen
compound		source
Molecule: Protein Mago Nashi Homolog Chain: A, E 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 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet30
Molecule: Rna-Binding Protein 8a Chain: B, G Fragment: Unp Residues 51-174 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 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet30
Molecule: Eukaryotic Initiation Factor 4a-III Chain: C, H Synonym: Eukaryotic Translation Initiation Factor 4a Isoform 3, Atp-Dependent Rna Helicase Eif4a-3, Atp- Dependent Rna Helicase Ddx48, Dead Box Protein 48, Eukaryotic Initiation Factor 4a-Like Nuk-34, Nuclear Matrix Protein 265, Hnmp 265; Ec: 3.6.1.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Eif4a3 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet30
Molecule: Protein Casc3 Chain: D, I Fragment: Unp Residues 138-283 Synonym: Cancer Susceptibility Candidate Gene 3 Protein, Metastatic Lymph Node Protein 51, Protein Mln 51, Protein Barentsz, Btz; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Casc3 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet30
Molecule: Rna (5'-R(Upupupupupu)-3') Chain: F, J Engineered: Yes		Synthetic: Yes Other_details: Poly Uracil (Sigma)
symmetry	Space Group: C 1 2 1	R_factor 0.206 R_Free 0.251
crystal cell	length a length b length c angle alpha angle beta angle gamma 182.040 100.750 145.880 90.00 112.08 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	ADP, AF3, MG	enzyme	Hydrolase E.C.3.6.1 BRENDA
Gene Ontology	Chain Function Process Component A, E 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... H, C 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	Mechanism of ATP turnover inhibition in the EJC., Nielsen KH, Chamieh H, Andersen CB, Fredslund F, Hamborg K, Le Hir H, Andersen GR, RNA. 2008 Nov 25. PMID:19033377

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (495 Kb) [Save to disk] Biological Unit Coordinates (3ex7.pdb1.gz) 242 Kb Biological Unit Coordinates (3ex7.pdb2.gz) 248 Kb LPC: Ligand-Protein Contacts for 3EX7 CSU: Contacts of Structural Units for 3EX7 Likely Quarternary Molecular Structure file(s) for 3EX7 Structure Factors (870 Kb) Retrieve 3EX7 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3EX7 from S2C, [Save to disk] Re-refined 3ex7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3EX7 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 3EX7

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 3EX7, from MSDmotif at EBI Fold representative 3ex7 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ex7_A] [3ex7_B] [3ex7_C] [3ex7_D] [3ex7_E] [3ex7_F] [3ex7_G] [3ex7_H] [3ex7_I] [3ex7_J] 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 3EX7: [Btz] [DEXDc] [HELICc] [RRM ] by SMART Alignments of the sequence of 3EX7 with the sequences similar proteins can be viewed for 3EX7'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 3EX7

Community annotation for 3EX7 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2010 Bioinformatics Unit Weizmann Institute of Science

---