4ZDV Protein Transport date Apr 19, 2015
title Crystal Structure Of Lc3 In Complex With Fam134b Lir
authors A.Khaminets, P.Grumati, I.Dikic, M.Akutsu
compound source
Molecule: Microtubule-Associated Proteins 1a1b Light Chain
Chain: A
Synonym: Autophagy-Related Protein Lc3 A,Autophagy-Related Like Modifier Lc3 A,Map1 Light Chain 3-Like Protein 1,Map1a Light Chain 3 A,Map1amap1b Lc3 A,Microtubule-Associated Pr Light Chain 3 Alpha;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Map1lc3a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 42 21 2
R_factor 0.184 R_Free 0.223
length a length b length c angle alpha angle beta angle gamma
62.170 62.170 74.410 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å

Primary referenceRegulation of endoplasmic reticulum turnover by selective autophagy., Khaminets A, Heinrich T, Mari M, Grumati P, Huebner AK, Akutsu M, Liebmann L, Stolz A, Nietzsche S, Koch N, Mauthe M, Katona I, Qualmann B, Weis J, Reggiori F, Kurth I, Hubner CA, Dikic I, Nature. 2015 Jun 3. doi: 10.1038/nature14498. PMID:26040720
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (4zdv.pdb1.gz) 48 Kb
  • CSU: Contacts of Structural Units for 4ZDV
  • Structure Factors (874 Kb)
  • Retrieve 4ZDV in mmCIF format [Save to disk]
  • Re-refined 4zdv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4ZDV 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 4ZDV
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4ZDV, from MSDmotif at EBI
  • Fold representative 4zdv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4zdv_A] [4zdv]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4ZDV
  • Community annotation for 4ZDV at PDBWiki (http://pdbwiki.org)

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