2X04 Peptide Rna Binding Protein date Dec 04, 2009
title Crystal Structure Of The Pabc-Tnrc6c Complex
authors M.Jinek, M.R.Fabian, S.M.Coyle, N.Sonenberg, J.A.Doudna
compound source
Molecule: Polyadenylate-Binding Protein 1
Chain: A, B
Fragment: C-Terminal Domain (Pabc), Residues 456-530
Synonym: Poly(A)-Binding Protein 1, Pabp 1, Polya Binding Protein Pabp1;
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_type: Plasmid
Expression_system_plasmid: Pgex6p1

Molecule: Trinucleotide Repeat-Containing Gene 6c Protein
Chain: C, D
Fragment: Duf Domain, Residues 1382-1399
Synonym: Tnrc6c

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.163 R_Free 0.186
length a length b length c angle alpha angle beta angle gamma
37.110 72.230 37.040 90.00 119.76 90.00
method X-Ray Diffractionresolution 1.49 Å
ligand SO4 enzyme
A, B

Primary referenceStructural insights into the human GW182-PABC interaction in microRNA-mediated deadenylation., Jinek M, Fabian MR, Coyle SM, Sonenberg N, Doudna JA, Nat Struct Mol Biol. 2010 Jan 24. PMID:20098421
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (38 Kb) [Save to disk]
  • Biological Unit Coordinates (2x04.pdb1.gz) 18 Kb
  • Biological Unit Coordinates (2x04.pdb2.gz) 18 Kb
  • LPC: Ligand-Protein Contacts for 2X04
  • CSU: Contacts of Structural Units for 2X04
  • Structure Factors (189 Kb)
  • Retrieve 2X04 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2X04 from S2C, [Save to disk]
  • Re-refined 2x04 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2X04 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 2X04
  • 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 2X04, from MSDmotif at EBI
  • Fold representative 2x04 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2x04_C] [2x04_D] [2x04_B] [2x04] [2x04_A]
  • SWISS-PROT database: [P11940] [Q9HCJ0]
  • Domain organization of [PABP1_HUMAN] [TNR6C_HUMAN] by SWISSPFAM
  • Domain found in 2X04: [PolyA ] by SMART
  • Other resources with information on 2X04
  • Community annotation for 2X04 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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