5NPW: Human ATG5-ATG16L1(ATG5BD) complex

Structure of human ATG5-ATG16L1(ATG5BD) complex (C2). Determined by X-ray diffraction at 3.1 Å resolution. Released 11 Oct 2017.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 8
Atoms: 9,952
Mol. weight: 271.91 kDa
Released: 11 Oct 2017

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

Secondary structure: helices and β-sheets

5NPW contains 84 α-helices and 61 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: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	15-22	8	1
β-strand	35-40	6	1
α-helix	45-48	4
α-helix	50-57	8
α-helix	62-64	3
β-strand	69-72	4	1
β-strand	75-76	2	1
α-helix	77-78	2
α-helix	83-86	4
α-helix	87-91	5
α-helix	95	1
β-strand	98-103	6	1
α-helix	118-136	19
α-helix	140-143	4
α-helix	147-159	13
α-helix	162-169	8
α-helix	170-173	4
β-strand	187-191	5	2
β-strand	199	1	2
β-strand	206	1	3
α-helix	211	1
β-strand	212	1	3
α-helix	213	1
β-strand	214	1	4
α-helix	215-222	8
α-helix	224-226	3
β-strand	236-239	4	2
β-strand	240	1	5
β-strand	243	1	5
β-strand	250	1	4
α-helix	251-257	7
β-strand	265-271	7	2
α-helix	272-273	2

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-27	16
α-helix	29-47	19

Chain C: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	15-22	8	6
β-strand	35-40	6	6
α-helix	45-48	4
α-helix	50-57	8
β-strand	69-72	4	6
β-strand	75-76	2	6
α-helix	77-78	2
α-helix	83-86	4
α-helix	87-91	5
α-helix	95	1
β-strand	98-103	6	6
α-helix	118-136	19
α-helix	140-143	4
α-helix	147-158	12
α-helix	162-172	11
β-strand	187-191	5	7
β-strand	198-199	2	7
β-strand	206	1	8
α-helix	211	1
β-strand	212	1	8
α-helix	213	1
β-strand	214	1	9
α-helix	215-222	8
α-helix	224-226	3
β-strand	236-239	4	7
β-strand	240	1	10
β-strand	243	1	10
β-strand	250	1	9
α-helix	251-257	7
β-strand	265-271	7	7
α-helix	272-273	2

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-11	3
α-helix	12-27	16
α-helix	29-46	18

Chain E: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	15-22	8	11
β-strand	35-40	6	11
β-strand	44	1	12
α-helix	45-48	4
α-helix	50-57	8
α-helix	62-64	3
β-strand	69-72	4	11
β-strand	75-76	2	11
α-helix	77-78	2
β-strand	82	1	12
α-helix	83-86	4
α-helix	87-91	5
α-helix	95	1
β-strand	98-103	6	11
α-helix	113-117	5
α-helix	118-136	19
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	13
α-helix	197-198	2
β-strand	199	1	13
β-strand	206	1	14
α-helix	211	1
β-strand	212	1	14
α-helix	213	1
β-strand	214	1	15
α-helix	215-222	8
α-helix	224-226	3
β-strand	236-239	4	13
β-strand	240	1	16
β-strand	243	1	16
β-strand	250	1	15
α-helix	251-257	7
β-strand	265-271	7	13

Chain F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-27	16
α-helix	29-46	18

Chain G: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	15-22	8	17
β-strand	35-40	6	17
α-helix	45-48	4
α-helix	50-57	8
β-strand	69-72	4	17
β-strand	75-76	2	17
α-helix	77-78	2
α-helix	83-86	4
α-helix	87-91	5
α-helix	95	1
β-strand	98-103	6	17
α-helix	118-136	19
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	18
β-strand	206	1	19
α-helix	211	1
β-strand	212	1	19
α-helix	213	1
β-strand	214	1	20
α-helix	215-222	8
α-helix	224-226	3
β-strand	236-239	4	18
β-strand	240	1	21
β-strand	243	1	21
β-strand	250	1	20
α-helix	251-257	7
β-strand	265-271	7	18
α-helix	272-273	2

Chain H: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	12-24	13
α-helix	25-29	5
α-helix	30-47	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Autophagy protein 5	A, C, E, G	protein	282	Homo sapiens	Q9H1Y0 (AlphaFold model)
Autophagy-related protein 16-1	B, D, F, H	protein	301	Homo sapiens	Q676U5 (AlphaFold model)

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

>5NPW_1 Autophagy protein 5 (chains A, C, E, G)
GAHMSGRMTDDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVK
KHFQKVMRQEDISEIWFEYEGTPLKWHYPIGLLFDLLASSSALPWNITVHFKSFPEKDLL
HCPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQNDRFDQFWAINRKLM
EYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIDPEDGE
KKNQVMIHGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPTD

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

>5NPW_2 Autophagy-related protein 16-1 (chains B, D, F, H)
GGGRPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKSDLHSVLAQKLQAEKHDVPNR
HEISPGHDGTWNDNQLQEMAQLRIKHQEELTELHKKRGELAQLVIDLNNQMQRKDREMQM
NEAKIAECLQTISDLETECLDLRTKLCDLERANQTLKDEYDALQITFTALEGKLRKTTEE
NQELVTRWMAEKAQEANRLNAENEKDSRRRQARLQKELAEAAKEPLPVEQDDDIEVIVDE
TSDHTEETSPVRAISRAATKRLSQPAGGLLDSITNIFGRRSVSSFPVPQDNVDTHPGSGK
E

Primary citation

Identification, biochemical characterization and crystallization of the central region of human ATG16L1. Archna, A., Scrima, A. Acta Crystallogr F Struct Biol Commun (2017) 73:560-567. DOI 10.1107/S2053230X17013280 · 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…
5D7G 3.0 Å, Structure of human ATG5 E122D-ATG16L1 complex at 3.0 Angstroms
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)

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