4GDK: Human Atg12~Atg5 Conjugate

Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1. Determined by X-ray diffraction at 2.7 Å resolution. Released 5 Dec 2012.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,547
Mol. weight: 94.9 kDa
Released: 5 Dec 2012

Explore 4GDK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4GDK contains 43 α-helices and 47 β-strands across 6 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: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	54-61	8	1
α-helix	66-68	3
β-strand	72-76	5	1
β-strand	80	1	2
α-helix	81-91	11
β-strand	101-104	4	1
β-strand	108	1	1
β-strand	115	1	2
α-helix	116-123	8
β-strand	125	1	1
β-strand	128-134	7	1

Chain B: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9
β-strand	15-22	8	3
α-helix	31-34	4
β-strand	35-40	6	3
α-helix	45-48	4
α-helix	50-57	8
α-helix	62-64	3
β-strand	69-72	4	3
β-strand	75-76	2	3
α-helix	83-91	9
α-helix	95	1
β-strand	98-103	6	3
α-helix	118-137	20
α-helix	147-158	12
α-helix	162-169	8
α-helix	171-173	3
β-strand	187-190	4	4
β-strand	198-199	2	4
β-strand	206	1	5
α-helix	211	1
β-strand	212	1	5
α-helix	213	1
β-strand	214	1	6
α-helix	215-222	8
α-helix	224-226	3
β-strand	236-239	4	4
β-strand	240	1	7
β-strand	243	1	7
β-strand	250	1	6
α-helix	251-257	7
β-strand	265-271	7	4
α-helix	272-273	2

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	12-25	14
α-helix	26-30	5
α-helix	31-41	11

Chain D: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	55-61	7	8
α-helix	66-68	3
β-strand	72-75	4	8
β-strand	80	1	9
α-helix	81-91	11
β-strand	101-104	4	8
β-strand	108	1	8
β-strand	115	1	9
α-helix	116-123	8
β-strand	125	1	10
β-strand	128	1	10
β-strand	129-134	6	8

Chain E: 15 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9
β-strand	15-22	8	11
α-helix	31-34	4
β-strand	35-40	6	11
α-helix	45-48	4
α-helix	50-57	8
β-strand	69-72	4	11
β-strand	75-76	2	11
α-helix	83-90	8
α-helix	95	1
β-strand	98-103	6	11
α-helix	118-137	20
α-helix	140-143	4
α-helix	147-158	12
α-helix	162-169	8
α-helix	170-173	4
β-strand	187-191	5	12
β-strand	199	1	12
β-strand	206	1	13
α-helix	211	1
β-strand	212	1	13
α-helix	213	1
β-strand	214	1	14
α-helix	215-222	8
β-strand	236-239	4	12
β-strand	240	1	15
β-strand	243	1	15
β-strand	250	1	14
α-helix	251-257	7
β-strand	265-271	7	12

Chain F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-27	16
α-helix	29-41	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like protein ATG12	A, D	protein	91	Homo sapiens	O94817 (AlphaFold model)
Autophagy protein 5	B, E	protein	275	Homo sapiens	Q9H1Y0 (AlphaFold model)
Autophagy-related protein 16-1	C, F	protein	36	Homo sapiens	Q676U5 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>4GDK_1 Ubiquitin-like protein ATG12 (chains A, D)
GSKKKIDILLKAVGDTPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFA
PSPDQEVGTLYECFGSDGKLVLHYCKSQAWG

Sequence of entity 2 (B, E), FASTA

>4GDK_2 Autophagy protein 5 (chains B, E)
MTDDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVM
RQEDISEIWFEYEGTPLKWHYPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDA
IEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQNDRFDQFWAINRKLMEYPAEEN
GFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIDPEDGEKKNQVMI
HGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPTD

Sequence of entity 3 (C, F), FASTA

>4GDK_3 Autophagy-related protein 16-1 (chains C, F)
SHMPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLL

Primary citation

Structure of the human ATG12~ATG5 conjugate required for LC3 lipidation in autophagy. Otomo, C., Metlagel, Z., Takaesu, G. et al. Nat Struct Mol Biol (2013) 20:59-66. DOI 10.1038/nsmb.2431 · PubMed

Other PDB entries of the same protein (UniProt O94817 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4NAW 2.19 Å, Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3
4GDL 2.88 Å, Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment…

Browse structure collections

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