2D1I: Human Atg4b

Structure of human Atg4b. Determined by X-ray diffraction at 2.0 Å resolution. Released 10 Jan 2006.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,724
Mol. weight: 89.53 kDa
Released: 10 Jan 2006

Explore 2D1I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2D1I contains 38 α-helices and 34 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: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	25	1
β-strand	26-28	3	1
β-strand	31-33	3	1
α-helix	39-48	10
β-strand	50	1	2
α-helix	51	1
β-strand	54-56	3	3
α-helix	58-60	3
α-helix	61-63	3
α-helix	74-91	18
α-helix	103-105	3
α-helix	106-113	8
α-helix	125-133	9
α-helix	142-144	3
α-helix	145-156	12
β-strand	165-168	4	1
β-strand	173-175	3	4
α-helix	176-183	8
β-strand	184	1	5
β-strand	219	1	5
α-helix	220-221	2
β-strand	222-229	8	1
α-helix	240-246	7
β-strand	252-257	6	1
β-strand	264-270	7	1
β-strand	273-277	5	1
β-strand	282-284	3	3
α-helix	285-286	2
α-helix	297-299	3
β-strand	300	1	2
α-helix	304-305	2
β-strand	306-309	4	1
α-helix	310-312	3
β-strand	316-323	8	1
α-helix	326-339	14
β-strand	350-352	3	4

Chain B: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	25	1
β-strand	26-28	3	6
β-strand	31-33	3	6
α-helix	39-48	10
β-strand	50	1	7
β-strand	55-56	2	8
α-helix	58-60	3
α-helix	74-91	18
α-helix	103-105	3
α-helix	106-113	8
α-helix	125-133	9
α-helix	142-144	3
α-helix	145-156	12
β-strand	165-168	4	6
β-strand	173-175	3	9
α-helix	176-183	8
β-strand	184	1	10
β-strand	219	1	10
β-strand	222-229	8	6
α-helix	237-239	3
α-helix	240-246	7
β-strand	252-257	6	6
β-strand	264-270	7	6
β-strand	273-277	5	6
β-strand	283-284	2	8
α-helix	285-287	3
α-helix	297-299	3
β-strand	300	1	7
α-helix	304-305	2
β-strand	306-309	4	6
α-helix	310-312	3
β-strand	316-323	8	6
α-helix	326-338	13
β-strand	350-352	3	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cysteine protease APG4B	A, B	protein	398	Homo sapiens	Q9Y4P1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2D1I_1 Cysteine protease APG4B (chains A, B)
GPLGSMDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDVASRLWFTYR
KNFPAIGGTGPTSDTGWGCMLRCGQMIFAQALVCRHLGRDWRWTQRKRQPDSYFSVLNAF
IDRKDSYYSIHQIAQMGVGEGKSIGQWYGPNTVAQVLKKLAVFDTWSSLAVHIAMDNTVV
MEEIRRLCRTSVPCAGATAFPADSDRHCNGFPAGAEVTNRPSPWRPLVLLIPLRLGLTDI
NEAYVETLKHCFMMPQSLGVIGGKPNSAHYFIGYVGEELIYLDPHTTQPAVEPTDGCFIP
DESFHCQHPPCRMSIAELDPSIAVGFFCKTEDDFNDWCQQVKKLSLLGGALPMFELVEQQ
PSHLACPDVLNLSLDSSDVERLERFFDSEDEDFEILSL

Primary citation

The Crystal Structure of Human Atg4b, a Processing and De-conjugating Enzyme for Autophagosome-forming Modifiers. Kumanomidou, T., Mizushima, T., Komatsu, M. et al. J Mol Biol (2006) 355:612-618. DOI 10.1016/j.jmb.2005.11.018 · 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
2Z0E 1.9 Å, The crystal structure of human Atg4B- LC3(1-124) complex
2ZZP 2.05 Å, The crystal structure of human Atg4B(C74S)- LC3(1-124) complex

Browse structure collections

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