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 Diffractionresolution 2.30 Å
ligand ANP, MG enzyme Hydrolase E.C.3.6.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, G

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

  • catalytic step 2 spliceosome...
  • H, B


    Primary referenceStructure 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 (840 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.
  • 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] [2hyi_L] [2hyi_H] [2hyi_J] [2hyi_B] [2hyi_I] [2hyi_F] [2hyi_A] [2hyi_D] [2hyi_C] [2hyi_G]
  • 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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