2Z0E Hydrolase Structural Protein date May 07, 2007
title The Crystal Structure Of Human Atg4b- Lc3(1-124) Complex
authors K.Satoo, N.N.Noda, F.Inagaki
compound source
Molecule: Cysteine Protease Atg4b
Chain: A
Fragment: Residues (-2)-354
Synonym: Hsatg4b, Autophagy-Related Protein 4 Homolog B, Hapg4b, Autophagin-1, Autophagy-Related Cysteine Endopeptidase 1, Aut-Like 1 Cysteine Endopeptidase;
Ec: 3.4.22.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p

Molecule: Microtubule-Associated Proteins 1a1b Light Chain 3b;
Chain: B
Synonym: Lc3, Microtubule-Associated Protein 1 Light Chain Beta, Map1amap1b Lc3 B, Map1a1b Light Chain 3 B, Map1 Light Chain 3-Like Protein 2, Autophagy-Related Protein Lc3 B, Autophagy-Related Ubiquitin-Like Modifier Lc3 B;
Engineered: Yes

Organism_scientific: Rattus Norvegicus
Organism_common: Norway Rat
Organism_taxid: 10116
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p
symmetry Space Group: P 21 21 21
R_factor 0.200 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.850 90.883 102.472 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand
enzyme Hydrolase E.C.3.4.22 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy., Satoo K, Noda NN, Kumeta H, Fujioka Y, Mizushima N, Ohsumi Y, Inagaki F, EMBO J. 2009 May 6;28(9):1341-50. Epub 2009 Mar 26. PMID:19322194
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (2z0e.pdb1.gz) 73 Kb
  • CSU: Contacts of Structural Units for 2Z0E
  • Likely Quarternary Molecular Structure file(s) for 2Z0E
  • Structure Factors (233 Kb)
  • Retrieve 2Z0E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Z0E from S2C, [Save to disk]
  • Re-refined 2z0e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Z0E 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 2Z0E
  • 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
  • 3D motif for 2Z0E, from MSDmotif at EBI
  • Fold representative 2z0e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2z0e_B] [2z0e_A] [2z0e]
  • SWISS-PROT database: [Q9Y4P1] [Q62625]
  • Belongs to the autophagy-related phagophore-formation transporter (apt) family according to TCDB.
  • Domain organization of [ATG4B_HUMAN] [MLP3B_RAT] by SWISSPFAM
  • Other resources with information on 2Z0E
  • Community annotation for 2Z0E at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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