5D7G Apoptosis date Aug 13, 2015
title Structure Of Human Atg5 E122d-Atg16l1 Complex At 3.0 Angstro
authors Y.Qiu, B.A.Schulman
compound source
Molecule: Autophagy Protein 5
Chain: A, C, E, G
Synonym: Apg5-Like,Apoptosis-Specific Protein
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Atg5, Apg5l, Asp
Expression_system: Baculovirus Expression Vector Pfastbac1-
Expression_system_taxid: 274590
Expression_system_cell_line: Hi5
Expression_system_vector_type: Baculovirus

Molecule: Autophagy-Related Protein 16-1
Chain: B, D, F, H
Fragment: Unp Residues 1-69
Synonym: Apg16-Like 1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Atg16l1, Apg16l, Unq9393pro34307
Expression_system: Baculovirus Expression Vector Pfastbac1-
Expression_system_taxid: 274590
Expression_system_cell_line: Hi5
Expression_system_vector_type: Baculovirus
symmetry Space Group: C 1 2 1
R_factor 0.198 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
217.114 84.478 151.849 90.00 133.81 90.00
method X-Ray Diffractionresolution 3.00 Å
Gene
Ontology
ChainFunctionProcessComponent
A, C, G, E


Primary referenceMutation in reduces autophagy and leads to ataxia with developmental delay., Kim M, Sandford E, Gatica D, Qiu Y, Liu X, Zheng Y, Schulman BA, Xu J, Semple I, Ro SH, Kim B, Mavioglu RN, Tolun A, Jipa A, Takats S, Karpati M, Li JZ, Yapici Z, Juhasz G, Lee JH, Klionsky DJ, Burmeister M, Elife. 2016 Jan 26;5. pii: e12245. doi: 10.7554/eLife.12245. PMID:26812546
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (199 Kb) [Save to disk]
  • Biological Unit Coordinates (5d7g.pdb1.gz) 98 Kb
  • Biological Unit Coordinates (5d7g.pdb2.gz) 97 Kb
  • CSU: Contacts of Structural Units for 5D7G
  • Structure Factors (709 Kb)
  • Retrieve 5D7G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D7G from S2C, [Save to disk]
  • Re-refined 5d7g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5D7G 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 5D7G
  • 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
  • Fold representative 5d7g from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5d7g_B] [5d7g_E] [5d7g_C] [5d7g_A] [5d7g_G] [5d7g_H] [5d7g] [5d7g_D] [5d7g_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5D7G
  • Community annotation for 5D7G at PDBWiki (http://pdbwiki.org)

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