2Z0D	Hydrolase Structural Protein	date	May 07, 2007
title	The Crystal Structure Of Human Atg4b- Lc3(1-120) 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, Ha Autophagin-1, Autophagy-Related Cysteine Endopeptidase 1, A 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 Chain: B Synonym: Lc3, Microtubule-Associated Protein 1 Light Chain Map1amap1b Lc3 B, Map1a1b Light Chain 3 B, Map1 Light Cha Protein 2, Autophagy-Related Protein Lc3 B, Autophagy-Relat 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 0.192 R_Free 0.227
crystal cell	length a length b length c angle alpha angle beta angle gamma 47.475 91.812 102.594 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.90 Å
ligand		enzyme	Hydrolase E.C.3.4.22 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	The 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] (78 Kb) [Save to disk] Biological Unit Coordinates (2z0d.pdb1.gz) 73 Kb CSU: Contacts of Structural Units for 2Z0D Likely Quarternary Molecular Structure file(s) for 2Z0D Structure Factors (265 Kb) Retrieve 2Z0D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2Z0D from S2C, [Save to disk] Re-refined 2z0d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2Z0D 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 2Z0D

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 3D motif for 2Z0D, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2z0d] [2z0d_A] [2z0d_B] 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 2Z0D

Community annotation for 2Z0D at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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