5D7G: Human ATG5 E122D-ATG16L1 complex

Structure of human ATG5 E122D-ATG16L1 complex at 3.0 Angstroms. Determined by X-ray diffraction at 3.0 Å resolution. Released 3 Feb 2016.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 8
Atoms: 9,417
Mol. weight: 165.49 kDa
Released: 3 Feb 2016

Explore 5D7G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D7G contains 68 α-helices and 64 β-strands across 8 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: 14 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	15-22	8	1
β-strand	28	1	2
α-helix	33-34	2
β-strand	35-40	6	1
β-strand	44	1	3
α-helix	50-59	10
β-strand	60	1	2
β-strand	69-72	4	1
β-strand	75-76	2	1
α-helix	77	1
β-strand	82	1	3
α-helix	83-90	8
α-helix	95	1
β-strand	98-103	6	1
α-helix	118-137	20
α-helix	140-144	5
α-helix	147-158	12
α-helix	162-172	11
β-strand	187-190	4	4
β-strand	199	1	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
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

Chain B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	12-25	14
α-helix	26-30	5
α-helix	31-45	15

Chain C: 16 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	15-22	8	8
α-helix	23	1
α-helix	33-34	2
β-strand	35-40	6	8
β-strand	44	1	9
α-helix	50-57	8
β-strand	69-72	4	8
β-strand	75-76	2	8
α-helix	77-78	2
β-strand	82	1	9
α-helix	83-90	8
α-helix	95	1
β-strand	98-103	6	8
α-helix	118-137	20
α-helix	147-158	12
α-helix	162-172	11
α-helix	177-179	3
β-strand	187-190	4	10
α-helix	197-198	2
β-strand	199	1	10
β-strand	206	1	11
α-helix	211	1
β-strand	212	1	11
α-helix	213	1
β-strand	214	1	12
α-helix	215-222	8
β-strand	236-239	4	10
β-strand	240	1	13
β-strand	243	1	13
β-strand	250	1	12
α-helix	251-257	7
β-strand	265-271	7	10

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	12-25	14
α-helix	26-30	5
α-helix	31-47	17

Chain E: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	15-22	8	14
β-strand	35-40	6	14
α-helix	50-58	9
β-strand	69-72	4	14
β-strand	75-76	2	14
α-helix	83-90	8
α-helix	95	1
β-strand	98-103	6	14
α-helix	118-137	20
α-helix	140-144	5
α-helix	147-158	12
α-helix	162-172	11
β-strand	187-191	5	15
α-helix	197-198	2
β-strand	199	1	15
β-strand	206	1	16
α-helix	211	1
β-strand	212	1	16
α-helix	213	1
β-strand	214	1	17
α-helix	215-222	8
β-strand	236-239	4	15
β-strand	240	1	18
β-strand	243	1	18
β-strand	250	1	17
α-helix	251-257	7
β-strand	265-271	7	15
α-helix	272-273	2

Chain F: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	12-25	14
α-helix	26-30	5
α-helix	31-48	18

Chain G: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	5-13	9
β-strand	15-22	8	19
α-helix	23	1
α-helix	31-34	4
β-strand	35-40	6	19
α-helix	45-48	4
α-helix	50-59	10
β-strand	69-72	4	19
β-strand	75-76	2	19
α-helix	83-90	8
α-helix	95	1
β-strand	98-103	6	19
α-helix	118-137	20
α-helix	147-158	12
α-helix	162-172	11
β-strand	187-191	5	20
β-strand	199	1	20
β-strand	214	1	21
α-helix	215-222	8
β-strand	237-239	3	20
β-strand	240	1	22
β-strand	243	1	22
β-strand	250	1	21
α-helix	251-257	7
β-strand	265-270	6	20

Chain H: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	12-24	13
α-helix	25-30	6
α-helix	31-47	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Autophagy protein 5	A, C, E, G	protein	280	Homo sapiens	Q9H1Y0 (AlphaFold model)
Autophagy-related protein 16-1	B, D, F, H	protein	71	Homo sapiens	Q676U5 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>5D7G_1 Autophagy protein 5 (chains A, C, E, G)
GAMGSMTDDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKH
FQKVMRQEDISEIWFEYEGTPLKWHYPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHC
PSKDAIDAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQNDRFDQFWAINRKLMEY
PAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIDPEDGEKK
NQVMIHGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPTD

Sequence of entity 2 (B, D, F, H), FASTA

>5D7G_2 Autophagy-related protein 16-1 (chains B, D, F, H)
GSMSSGLRAADFPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKSDLHSVLAQKLQA
EKHDVPNRHEI

Primary citation

Mutation in ATG5 reduces autophagy and leads to ataxia with developmental delay. Kim, M., Sandford, E., Gatica, D. et al. Elife (2016) 5. DOI 10.7554/eLife.12245 · PubMed

Other PDB entries of the same protein (UniProt Q9H1Y0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4TQ1 1.8 Å, Crystal structure of human ATG5-TECAIR
4NAW 2.19 Å, Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3
4TQ0 2.7 Å, Crystal structure of human ATG5-ATG16N69
4GDK 2.7 Å, Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment…
4GDL 2.88 Å, Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment…
7W36 3.0 Å, Crystal structure of human Atg5 complexed with a stapled peptide
5NPV 3.1 Å, Structure of human ATG5-ATG16L1(ATG5BD) complex (I4)
5NPW 3.1 Å, Structure of human ATG5-ATG16L1(ATG5BD) complex (C2)

Browse structure collections

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