2Z0E: Human Atg4B- LC3(1-124) complex

The crystal structure of human Atg4B- LC3(1-124) complex. Determined by X-ray diffraction at 1.9 Å resolution. Released 22 May 2007.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Rattus norvegicus
Chains: 2
Atoms: 3,584
Mol. weight: 55.04 kDa
Released: 22 May 2007

Explore 2Z0E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2Z0E contains 23 α-helices and 24 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 18 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	14-18	5
β-strand	26-28	3	1
β-strand	31-33	3	1
α-helix	39-48	10
β-strand	54-56	3	2
α-helix	58-60	3
β-strand	68	1	2
α-helix	74-91	18
α-helix	103-105	3
α-helix	106-113	8
α-helix	125-133	9
β-strand	143	1	3
α-helix	145-156	12
β-strand	165-168	4	1
β-strand	173-175	3	4
α-helix	176-183	8
α-helix	220-221	2
β-strand	222-229	8	1
α-helix	237-245	9
β-strand	252-259	8	1
β-strand	262-270	9	1
β-strand	273-277	5	1
β-strand	282-284	3	2
α-helix	285-286	2
α-helix	297-299	3
α-helix	305	1
β-strand	306-309	4	1
α-helix	310-312	3
β-strand	316-323	8	1
α-helix	326-337	12
α-helix	338-341	4
β-strand	350-352	3	4

Chain B: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	13-26	14
β-strand	30-37	8	5
α-helix	45-47	3
β-strand	51-55	5	5
β-strand	59	1	6
α-helix	60-70	11
β-strand	80-82	3	5
β-strand	83	1	7
β-strand	86	1	7
β-strand	94	1	6
α-helix	95-102	8
β-strand	109-114	6	5
β-strand	119	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cysteine protease ATG4B	A	protein	357	Homo sapiens	Q9Y4P1 (AlphaFold model)
Microtubule-associated proteins 1A/1B light chain 3B	B	protein	129	Rattus norvegicus	Q62625 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2Z0E_1 Cysteine protease ATG4B (chains A)
GPHMDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDVASRLWFTYRKN
FPAIGGTGPTSDTGWGCMLRCGQMIFAQALVCRHLGRDWRWTQRKRQPDSYFSVLNAFID
RKDSYYSIHQIAQMGVGEGKSIGQWYGPNTVAQVLKKLAVFDTWSSLAVHIAMDNTVVME
EIRRLCRTSVPCAGATAFPADSDRHCNGFPAGAEVTNRPSPWRPLVLLIPLRLGLTDINE
AYVETLKHCFMMPQSLGVIGGKPNSAHYFIGYVGEELIYLDPATTQPAVEPTDGCFIPDE
SFHCQHPPCRMSIAELDPSIAVGFFCKTEDDFNDWCQQVKKLSLLGGALPMFELVEQ

Sequence of entity 2 (B), FASTA

>2Z0E_2 Microtubule-associated proteins 1A/1B light chain 3B (chains B)
GPLGSMPSEKTFKQRRSFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVP
DHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYESERDEDGFLYMVYAS
QETFGTALA

Primary citation

The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy. Satoo, K., Noda, N.N., Kumeta, H. et al. EMBO J (2009) 28:1341-1350. DOI 10.1038/emboj.2009.80 · PubMed

Other PDB entries of the same protein (UniProt Q9Y4P1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5LXI 1.44 Å, GABARAP-L1 ATG4B LIR Complex
5LXH 1.58 Å, GABARAP-L1 ATG4B LIR Complex
2CY7 1.9 Å, The crystal structure of human Atg4B
2Z0D 1.9 Å, The crystal structure of human Atg4B- LC3(1-120) complex
2D1I 2.0 Å, Structure of human Atg4b
2ZZP 2.05 Å, The crystal structure of human Atg4B(C74S)- LC3(1-124) complex

Browse structure collections

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