4NAW Protein Transport Ligase date Oct 22, 2013
title Crystal Structure Of Human Atg12~Atg5-Atg16n In Complex With Fragment Of Atg3
authors Z.Metlagel, C.Otomo, G.Takaesu, T.Otomo
compound source
Molecule: Ubiquitin-Like Protein Atg12
Chain: A, E, I, M
Fragment: Unp Residues 52-140
Synonym: Autophagy-Related Protein 12, Apg12-Like
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apg12, Apg12l, Atg12
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacyc Duet-1

Molecule: Autophagy Protein 5
Chain: B, F, J, N
Synonym: Apg5-Like, Apoptosis-Specific Protein
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apg5l, Asp, Atg5
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacyc Duet-1

Molecule: Autophagy-Related Protein 16-1
Chain: C, G, K, O
Fragment: Unp Residues 11-43
Synonym: Apg16-Like 1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apg16l, Atg16l1, Unq9393pro34307
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

Molecule: Ubiquitin-Like-Conjugating Enzyme Atg3
Chain: D, H, L, P
Fragment: Unp Residues 140-170
Synonym: Autophagy-Related Protein 3, Apg3-Like, Hapg3, Pro 96;
Ec: 6.3.2.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apg3, Apg3l, Atg3
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet
symmetry Space Group: P 21 21 21
R_factor 0.172 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.584 120.097 189.466 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand NA, SO4 enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, M, I, E


F, J, N, B


Primary referenceStructural basis of ATG3 recognition by the autophagic ubiquitin-like protein ATG12., Metlagel Z, Otomo C, Takaesu G, Otomo T, Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):18844-9. doi:, 10.1073/pnas.1314755110. Epub 2013 Nov 4. PMID:24191030
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (856 Kb) [Save to disk]
  • Biological Unit Coordinates (4naw.pdb1.gz) 214 Kb
  • Biological Unit Coordinates (4naw.pdb2.gz) 214 Kb
  • Biological Unit Coordinates (4naw.pdb3.gz) 213 Kb
  • Biological Unit Coordinates (4naw.pdb4.gz) 213 Kb
  • LPC: Ligand-Protein Contacts for 4NAW
  • CSU: Contacts of Structural Units for 4NAW
  • Structure Factors (513 Kb)
  • Retrieve 4NAW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NAW from S2C, [Save to disk]
  • Re-refined 4naw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NAW 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 4NAW
  • 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 4NAW, from MSDmotif at EBI
  • Fold representative 4naw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4naw_C] [4naw_F] [4naw_A] [4naw_B] [4naw_O] [4naw_N] [4naw_K] [4naw_G] [4naw_I] [4naw_E] [4naw_J] [4naw] [4naw_P] [4naw_L] [4naw_H] [4naw_D] [4naw_M]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4NAW
  • Community annotation for 4NAW at PDBWiki (http://pdbwiki.org)

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