4NAW: Human ATG12~ATG5-ATG16N

Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3. Determined by X-ray diffraction at 2.19 Å resolution. Released 6 Nov 2013.

Method: X-ray diffraction
Resolution: 2.19 Å
Organism: Homo sapiens
Chains: 16
Atoms: 13,933
Mol. weight: 206.15 kDa
Released: 6 Nov 2013

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

Secondary structure: helices and β-sheets

4NAW contains 90 α-helices and 97 β-strands across 16 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	55-61	7	1
α-helix	66-68	3
β-strand	72-75	4	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: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
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	83-90	8
α-helix	95	1
β-strand	98-103	6	3
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
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	31-42	12

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	155-156	2	1
α-helix	157-163	7

Chain E: 4 helices, 8 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
α-helix	99-100	2
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	8
β-strand	128-134	7	8

Chain F: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	15-22	8	10
α-helix	31-34	4
β-strand	35-40	6	10
α-helix	45-48	4
α-helix	50-57	8
α-helix	62-64	3
β-strand	69-72	4	10
β-strand	75-76	2	10
α-helix	77-78	2
α-helix	83-90	8
α-helix	95	1
β-strand	98-103	6	10
α-helix	118-137	20
α-helix	140-143	4
α-helix	147-158	12
α-helix	162-172	11
β-strand	187-190	4	11
β-strand	199	1	11
β-strand	206	1	12
α-helix	211	1
β-strand	212	1	12
α-helix	213	1
β-strand	214	1	13
α-helix	215-222	8
β-strand	236-239	4	11
β-strand	240	1	14
β-strand	243	1	14
β-strand	250	1	13
α-helix	251-257	7
β-strand	265-271	7	11

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-28	17
α-helix	33-42	10

Chains H, L and P: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	155-156	2	8
α-helix	157-161	5

6 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like protein ATG12	A, E, I, M	protein	91	Homo sapiens	O94817 (AlphaFold model)
Autophagy protein 5	B, F, J, N	protein	275	Homo sapiens	Q9H1Y0 (AlphaFold model)
Autophagy-related protein 16-1	C, G, K, O	protein	36	Homo sapiens	Q676U5 (AlphaFold model)
Ubiquitin-like-conjugating enzyme ATG3	D, H, L, P	protein	34	Homo sapiens	Q9NT62 (AlphaFold model)

Sequence of entity 1 (A, E, I, M), FASTA

>4NAW_1 Ubiquitin-like protein ATG12 (chains A, E, I, M)
GSKKKIDILLKAVGDTPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFA
PSPDQEVGTLYECFGSDGKLVLHYCKSQAWG

Sequence of entity 2 (B, F, J, N), FASTA

>4NAW_2 Autophagy protein 5 (chains B, F, J, N)
MTDDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVM
RQEDISEIWFEYEGTPLKWHYPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDA
IEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQNDRFDQFWAINRKLMEYPAEEN
GFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIDPEDGEKKNQVMI
HGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPTD

Sequence of entity 3 (C, G, K, O), FASTA

>4NAW_3 Autophagy-related protein 16-1 (chains C, G, K, O)
SHMPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLL

Sequence of entity 4 (D, H, L, P), FASTA

>4NAW_4 Ubiquitin-like-conjugating enzyme ATG3 (chains D, H, L, P)
GHMSALCEEEEDEDEGEAADMEEYEESGLLETDE

Primary citation

Structural basis of ATG3 recognition by the autophagic ubiquitin-like protein ATG12. Metlagel, Z., Otomo, C., Takaesu, G. et al. Proc Natl Acad Sci U S A (2013) 110:18844-18849. DOI 10.1073/pnas.1314755110 · PubMed

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

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…

Browse structure collections

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