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
  • Alignments of the sequence of 2XB2 with the sequences similar proteins can be viewed for 2XB2's classification 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 at ProtoMap. Click on the Cluster number.
  • 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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