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 Rb 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 Isofor Dependent Rna Helicase Eif4a-3, Atp-Dependent Rna Helicase Dead Box Protein 48, Eukaryotic Initiation Factor 4a-Like N 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, Me Lymph Node Protein 51, Protein Mln 51, Protein Barentsz, Bt
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 Diffractionresolution 2.30 Å
ligand ADP, AF3, MG enzyme Hydrolase E.C.3.6.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E

  • catalytic step 2 spliceosome...
  • D, I


    G, B


    H, C

  • catalytic step 2 spliceosome...
  • Primary referenceMechanism 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] (482 Kb) [Save to disk]
  • Biological Unit Coordinates (3ex7.pdb1.gz) 236 Kb
  • Biological Unit Coordinates (3ex7.pdb2.gz) 242 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.
  • Visual 3D analysis of 3EX7
  • 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 3EX7, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ex7_A] [3ex7_I] [3ex7] [3ex7_C] [3ex7_B] [3ex7_G] [3ex7_J] [3ex7_E] [3ex7_H] [3ex7_D] [3ex7_F]
  • 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
  • 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, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science