6FQ3 Rna Binding Protein date Feb 13, 2018
title Crystal Structure Of Danio Rerio Lin41 Filamin-Nhl Domains I With Lin-29a 5'Utr 13mer Rna
authors P.Kumari, F.Aeschimann, D.Gaidatzis, J.J.Keusch, P.Ghosh, A.Neagu K.Pachulska-Wieczorek, J.M.Bujnicki, H.Gut, H.Grosshans, R.Cios
compound source
Molecule: E3 Ubiquitin-Protein Ligase Trim71
Chain: A
Synonym: Protein Lin-41 Homolog,Ring-Type E3 Ubiquitin Tran Trim71,Tripartite Motif-Containing Protein 71;
Ec: 2.3.2.27
Engineered: Yes
Other_details: Fragment Of Lin41 Encompassing Filamin-Nhl D (Residues 435-824);
Organism_scientific: Danio Rerio
Organism_common: Zebrafish
Organism_taxid: 7955
Gene: Trim71, Lin41
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9

Molecule: Rna (5'-R(Gpgpapgpupcpcpapapcpupcpc)
Chain: B
Engineered: Yes
Other_details: Fragment Of Lin-29a 5'Utr

Organism_scientific: Caenorhabditis Elegans
Organism_taxid: 6239
Expression_system: Synthetic Construct
Expression_system_taxid: 32630
symmetry Space Group: P 31 2 1
R_factor 0.158 R_Free 0.180
crystal
cell
length a length b length c angle alpha angle beta angle gamma
101.850 101.850 109.890 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.90 Å
ligand CL enzyme Transferase E.C.2.3.2.27 BRENDA
Primary referenceEvolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition., Kumari P, Aeschimann F, Gaidatzis D, Keusch JJ, Ghosh P, Neagu A, Pachulska-Wieczorek K, Bujnicki JM, Gut H, Grosshans H, Ciosk R, Nat Commun. 2018 Apr 19;9(1):1549. doi: 10.1038/s41467-018-03920-7. PMID:29674686
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (148 Kb) [Save to disk]
  • Biological Unit Coordinates (6fq3.pdb1.gz) 143 Kb
  • LPC: Ligand-Protein Contacts for 6FQ3
  • CSU: Contacts of Structural Units for 6FQ3
  • Structure Factors (407 Kb)
  • Retrieve 6FQ3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6FQ3 from S2C, [Save to disk]
  • View 6FQ3 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 6FQ3
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6fq3_A] [6fq3_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6FQ3
  • Community annotation for 6FQ3 at PDBWiki (http://pdbwiki.org)

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