5YEC: Atg7CTD-Atg8-MgATP complex in form II

Crystal structure of Atg7CTD-Atg8-MgATP complex in form II. Determined by X-ray diffraction at 2.15 Å resolution. Released 28 Mar 2018.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 4
Atoms: 6,403
Mol. weight: 105 kDa
Ligands: ZN, ATP, MG
Released: 28 Mar 2018

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

Secondary structure: helices and β-sheets

5YEC contains 47 α-helices and 39 β-strands across 4 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: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	297-313	17
α-helix	319-323	5
β-strand	326-330	5	1
α-helix	334-345	12
β-strand	350-355	6	1
β-strand	358	1	2
α-helix	372-374	3
β-strand	378	1	2
α-helix	379-390	12
β-strand	395-400	6	1
α-helix	402-404	3
α-helix	413-429	17
β-strand	432-435	4	1
α-helix	440-442	3
α-helix	444-452	9
β-strand	456-462	7	1
β-strand	466-471	6	1
α-helix	472-473	2
β-strand	483	1	3
α-helix	488-492	5
α-helix	513-530	18
α-helix	532-534	3
β-strand	539-540	2	4
β-strand	543-544	2	4
β-strand	548-552	5	1
β-strand	557-561	5	1
β-strand	564	1	3
α-helix	565-566	2
α-helix	574-583	10
α-helix	585-593	9
α-helix	595-602	8
α-helix	604-615	12

Chain B: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	11-24	14
β-strand	28-35	8	5
α-helix	42-44	3
β-strand	48-52	5	5
β-strand	56	1	6
α-helix	57-67	11
β-strand	77-79	3	5
β-strand	90	1	6
α-helix	91-98	8
α-helix	104	1
β-strand	105-110	6	5

Chain C: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	303-313	11
α-helix	320-323	4
β-strand	326-330	5	7
α-helix	334-345	12
β-strand	350-355	6	7
β-strand	358	1	8
α-helix	372-374	3
β-strand	378	1	8
α-helix	379-390	12
β-strand	395-400	6	7
α-helix	402-404	3
α-helix	413-429	17
β-strand	432-435	4	7
α-helix	440-442	3
α-helix	444-452	9
β-strand	456-462	7	7
β-strand	466-471	6	7
α-helix	472-473	2
β-strand	483	1	9
α-helix	486-492	7
α-helix	508-511	4
α-helix	512-529	18
α-helix	532-534	3
β-strand	539-540	2	10
β-strand	543-544	2	10
β-strand	548-552	5	7
β-strand	557-561	5	7
β-strand	564	1	9
α-helix	565-566	2
α-helix	574-583	10
α-helix	585-593	9
α-helix	595-602	8
α-helix	604-614	11

Chain D: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	11-24	14
β-strand	28-34	7	11
β-strand	48-52	5	11
β-strand	56	1	12
α-helix	57-68	12
β-strand	90	1	12
α-helix	91-98	8
β-strand	105-108	4	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like modifier-activating enzyme ATG7	A, C	protein	340	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P38862 (AlphaFold model)
Autophagy-related protein 8	B, D	protein	119	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P38182 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5YEC_1 Ubiquitin-like modifier-activating enzyme ATG7 (chains A, C)
GPHMLKIADQSVDLNLKLMKWRILPDLNLDIIKNTKVLLLGAGTLGCYVSRALIAWGVRK
ITFVDNGTVSYSNPVRQALYNFEDCGKPKAELAAASLKRIFPLMDATGVKLSIPMIGHKL
VNEEAQHKDFDRLRALIKEHDIIFLLVDSRESRWLPSLLSNIENKTVINAALGFDSYLVM
RHGNRDEQSSKQLGCYFCHDVVAPTDSLTDRTLDQMCTVTRPGVAMMASSLAVELMTSLL
QTKYSGSETTVLGDIPHQIRGFLHNFSILKLETPAYEHCPACSPKVIEAFTDLGWEFVKK
ALEHPLYLEEISGLSVIKQEVERLGNDVFEWEDDESDEIA

Sequence of entity 2 (B, D), FASTA

>5YEC_2 Autophagy-related protein 8 (chains B, D)
GPHMKSTFKSEYPFEKRKAESERIADRFPNRIPVICEKAEKSDIPEIDKRKYLVPADLTV
GQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKDKDGFLYVTYSGENTFG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
MG	Magnesium ion	Mg	2

Primary citation

Atg7 Activates an Autophagy-Essential Ubiquitin-like Protein Atg8 through Multi-Step Recognition. Yamaguchi, M., Satoo, K., Suzuki, H. et al. J Mol Biol (2018) 430:249-257. DOI 10.1016/j.jmb.2017.12.002 · PubMed

Other PDB entries of the same protein (UniProt P38862 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3T7H 1.6 Å, Atg8 transfer from Atg7 to Atg3: a distinctive E1-E2 architecture and mechanism in the…
4GSJ 1.7 Å, Crystal structure of Atg7 NTD K14A F16A D18A mutant
3T7F 1.89 Å, Atg8 transfer from Atg7 to Atg3: a distinctive E1-E2 architecture and mechanism in the…
3RUI 1.91 Å, Crystal structure of Atg7C-Atg8 complex
3VH3 2.0 Å, Crystal structure of Atg7CTD-Atg8 complex
3T7G 2.08 Å, Atg8 transfer from Atg7 to Atg3: a distinctive E1-E2 architecture and mechanism in the…
3RUJ 2.1 Å, Crystal Structure of N-terminal region of yeast Atg7
3T7E 2.25 Å, Atg8 transfer from Atg7 to Atg3: a distinctive E1-E2 architecture and mechanism in the…
3VH4 2.65 Å, Crystal structure of Atg7CTD-Atg8-MgATP complex
4GSL 2.7 Å, Crystal structure of an Atg7-Atg3 crosslinked complex
4GSK 2.9 Å, Crystal structure of an Atg7-Atg10 crosslinked complex
3VH1 3.0 Å, Crystal structure of Saccharomyces cerevisiae Atg7 (1-595)

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