2XB2 Hydrolase date Apr 03, 2010
title Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery
authors G.Buchwald, J.Ebert, C.Basquin, J.Sauliere, U.Jayachandran, F.Bono, H.Le Hir, E.Conti
compound source
Molecule: Eukaryotic Initiation Factor 4a-III
Chain: A, X
Synonym: Eif4aiii, 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, Nmp 265;
Ec: 3.6.1.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector: Petmcn

Molecule: Rna Poly-U-Ribonucleotide
Chain: E, R
Other_details: 15 Poly-U Synthetic Construct

Synthetic: Yes

Molecule: Regulator Of Nonsense Transcripts 3b
Chain: G, U
Fragment: C-Terminal Ejc Binding Region, Residues 411-470
Synonym: Upf3b, Nonsense Mrna Reducing Factor 3b, Up-Frameshift Suppressor 3 Homolog B, Up-Frameshift Suppressor 3 Homolog On Chromosome X, Hupf3p-X;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector: Pec

Molecule: Putative Regulator Of Nonsense Transcripts 3b
Chain: F

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector: Pec

Molecule: Rna-Binding Protein 8a
Chain: D, Z
Fragment: Rrm, Residues 66-155
Synonym: Rna-Binding Motif Protein 8a, Y14, Ribonucleoprotein Rbm8a, Rna-Binding Protein Y14, Binder Of Ovca1-1, Bov-1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector: Petmcn

Molecule: Protein Mago Nashi Homolog
Chain: C, Y
Synonym: Mago
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector: Petmcn

Molecule: Protein Casc3
Chain: T, S
Fragment: Selor Domain, Residues 137-286
Synonym: Barentsz, Cancer Susceptibility Candidate Gene 3 Protein, Metastatic Lymph Node Gene 51 Protein, Mln 51, Btz;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector: Petmcn
symmetry Space Group: P 41 21 2
R_factor 0.2204 R_Free 0.2604
crystal
cell
length a length b length c angle alpha angle beta angle gamma
134.800 134.800 227.250 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.40 Å
ligand ANP, MG enzyme Hydrolase E.C.3.6.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, X

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

  • catalytic step 2 spliceosome...
  • Primary referenceInsights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex., Buchwald G, Ebert J, Basquin C, Sauliere J, Jayachandran U, Bono F, Le Hir H, Conti E, Proc Natl Acad Sci U S A. 2010 May 17. PMID:20479275
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (224 Kb) [Save to disk]
  • Biological Unit Coordinates (2xb2.pdb1.gz) 110 Kb
  • Biological Unit Coordinates (2xb2.pdb2.gz) 110 Kb
  • Biological Unit Coordinates (2xb2.pdb3.gz) 5 Kb
  • LPC: Ligand-Protein Contacts for 2XB2
  • CSU: Contacts of Structural Units for 2XB2
  • Structure Factors (246 Kb)
  • Retrieve 2XB2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XB2 from S2C, [Save to disk]
  • Re-refined 2xb2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XB2 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 2XB2
  • 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 2XB2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1q2xb2, region B:134-357 [Jmol] [rasmolscript] [script source]
        - Domain d1w2xb2, region B:1815-2189 [Jmol] [rasmolscript] [script source]
        - Domain d1n2xb2, region B:8-114,B:216-292 [Jmol] [rasmolscript] [script source]
  • Fold representative 2xb2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xb2_Z] [2xb2_Y] [2xb2_S] [2xb2_D] [2xb2_C] [2xb2_T] [2xb2] [2xb2_F] [2xb2_X] [2xb2_G] [2xb2_E] [2xb2_A] [2xb2_U] [2xb2_R]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2XB2: [Btz] [DEXDc] [HELICc] [RRM ] by SMART
  • Other resources with information on 2XB2
  • Community annotation for 2XB2 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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