5D94 Protein Binding Peptide date Aug 18, 2015
title Crystal Structure Of Lc3-Lir Peptide Complex
authors K.Takagi, T.Mizushima, T.Johansen
compound source
Molecule: Microtubule-Associated Proteins 1a1b Light Chain
Chain: A
Synonym: Autophagy-Related Protein Lc3 B,Autophagy-Related Like Modifier Lc3 B,Map1 Light Chain 3-Like Protein 2,Map1a Light Chain 3 B,Map1amap1b Lc3 B,Microtubule-Associated Pr Light Chain 3 Beta;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Map1lc3b, Map1alc3
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Peptide From Fyve And Coiled-Coil Domain-Containi 1;
Chain: B
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.175 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.724 39.162 42.756 90.00 115.05 90.00
method X-Ray Diffractionresolution 1.53 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceFYCO1 Contains a C-terminally Extended, LC3A/B-preferring LC3-Interacting Region (LIR) Motif Required for Efficient Maturation of Autophagosomes During Basal Autophagy., Olsvik HL, Lamark T, Takagi K, Bowitz Larsen K, Evjen G, Overvatn A, Mizushima T, Johansen T, J Biol Chem. 2015 Oct 14. pii: jbc.M115.686915. PMID:26468287
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk]
  • Biological Unit Coordinates (5d94.pdb1.gz) 26 Kb
  • CSU: Contacts of Structural Units for 5D94
  • Structure Factors (322 Kb)
  • Retrieve 5D94 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D94 from S2C, [Save to disk]
  • Re-refined 5d94 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5D94 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 5D94
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5d94_A] [5d94_B] [5d94]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5D94
  • Community annotation for 5D94 at PDBWiki (http://pdbwiki.org)

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