4GSK: Atg7-Atg10 crosslinked complex

Crystal structure of an Atg7-Atg10 crosslinked complex. Determined by X-ray diffraction at 2.9 Å resolution. Released 14 Nov 2012.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 11,408
Mol. weight: 179.68 kDa
Ligands: ZN
Released: 14 Nov 2012

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

Secondary structure: helices and β-sheets

4GSK contains 62 α-helices and 78 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: 26 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
β-strand	10	1	2
β-strand	14-17	4	3
α-helix	19-29	11
β-strand	39-46	8	4
β-strand	57	1	5
β-strand	59-62	4	3
α-helix	64-66	3
β-strand	78-87	10	4
α-helix	90-95	6
α-helix	98-115	18
α-helix	117-119	3
β-strand	123-130	8	4
β-strand	135-146	12	4
β-strand	152-157	6	1
α-helix	159-164	6
α-helix	165-174	10
β-strand	180-183	4	1
β-strand	189-190	2	1
α-helix	194-200	7
β-strand	202-206	5	1
β-strand	209	1	5
β-strand	216	1	2
α-helix	219-229	11
β-strand	235-241	7	1
β-strand	248-255	8	1
β-strand	269-273	5	4
α-helix	274	1
β-strand	275	1	6
β-strand	281	1	6
β-strand	284-287	4	4
α-helix	294-308	15
α-helix	309-313	5
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	363-365	3
α-helix	372-374	3
β-strand	378	1	8
α-helix	379-390	12
β-strand	395-400	6	7
α-helix	404-405	2
α-helix	413-428	16
β-strand	432-435	4	7
α-helix	444-452	9
β-strand	456-462	7	7
β-strand	466-471	6	7
α-helix	486-488	3
α-helix	512-529	18
α-helix	532-534	3
β-strand	540	1	9
β-strand	543	1	9
β-strand	548-552	5	7
β-strand	557-561	5	7
α-helix	574-583	10
α-helix	585-593	9
α-helix	595-602	8

Chain B: 26 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	10
β-strand	10	1	11
β-strand	14-17	4	12
α-helix	19-29	11
β-strand	40-46	7	13
β-strand	57	1	14
β-strand	59-62	4	12
α-helix	64-67	4
β-strand	78-87	10	13
α-helix	90-95	6
α-helix	98-115	18
α-helix	117-119	3
β-strand	123-130	8	13
β-strand	135-146	12	13
β-strand	151-157	7	10
α-helix	159-164	6
α-helix	165-174	10
β-strand	180-183	4	10
β-strand	189-191	3	10
α-helix	194-200	7
β-strand	202-206	5	10
β-strand	209	1	14
β-strand	216	1	11
α-helix	219-229	11
β-strand	235-241	7	10
β-strand	248-256	9	10
β-strand	269-273	5	13
α-helix	274-275	2
β-strand	284-287	4	13
α-helix	289-292	4
α-helix	294-308	15
α-helix	309-313	5
α-helix	320-324	5
β-strand	326-330	5	15
α-helix	334-345	12
β-strand	350-354	5	15
β-strand	358	1	16
α-helix	363-366	4
α-helix	372-374	3
β-strand	378	1	16
α-helix	379-390	12
β-strand	395-399	5	15
α-helix	404-405	2
α-helix	413-429	17
β-strand	432-435	4	15
β-strand	439	1	17
α-helix	440-452	13
β-strand	456-462	7	15
β-strand	466-472	7	15
β-strand	505	1	17
α-helix	512-529	18
β-strand	539-540	2	18
β-strand	543-544	2	18
β-strand	548-552	5	15
β-strand	557-561	5	15
α-helix	564-566	3
α-helix	574-583	10
α-helix	585-593	9
α-helix	595-602	8

Chain Y: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-16	13
β-strand	26-31	6	13
β-strand	38-42	5	13
α-helix	43-45	3
α-helix	46-54	9
β-strand	59-70	12	13
β-strand	75-87	13	13
β-strand	92-97	6	13
β-strand	128-129	2	13
α-helix	149-157	9

Chain Z: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-16	13
β-strand	26-31	6	4
β-strand	38-42	5	4
α-helix	43-45	3
α-helix	46-55	10
β-strand	59-70	12	4
β-strand	75-87	13	4
β-strand	92-97	6	4
β-strand	128-129	2	4
α-helix	149-154	6
α-helix	155-159	5
α-helix	160-162	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like modifier-activating enzyme ATG7	A, B	protein	615	Saccharomyces cerevisiae	P38862 (AlphaFold model)
Ubiquitin-like-conjugating enzyme ATG10	Y, Z	protein	173	Saccharomyces cerevisiae	Q07879 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4GSK_1 Ubiquitin-like modifier-activating enzyme ATG7 (chains A, B)
GSMSSERVLSYAPAFKSFLDTSFFQELSRLKLDVLKLDSTSQPLTVNLDLHNIPKSADQV
PLFLTNRSFEKHNNKRTNEVPLQGSIFNFNVLDEFKNLDKQLFLHQRALECWEDGIKDIN
KCVSFVIISFADLKKYRFYYWLGVPCFQRPSSTVLHVRPEPSLKGLFSKCQKWFDVNYSK
WVCILDADDEIVNYDKSIIRKTKVLAIRDTSTMENVPSALTKNFLSVLQYDVPDLIDFKL
LIIRQNEGSFALNATFASIDPQSSSSNPDMKVSGWERNVQGKLAPRVVDLSSLLDPLKIA
DQSVDLNLKLMKWRILPDLNLDIIKNTKVLLLGAGTLGCYVSRALIAWGVRKITFVDNGT
VSYSNPVRQALYNFEDAGKPKAELAAASLKRIFPLMDATGVKLSIPMIGHKLVNEEAQHK
DFDRLRALIKEHDIIFLLVDSRESRWLPSLLSNIENKTVINAALGFDSYLVMRHGNRDEQ
SSKQLGCYFCHDVVAPTDSLTDRTLDQMCTVTRPGVAMMASSLAVELMTSLLQTKYSGSE
TTVLGDIPHQIRGFLHNFSILKLETPAYEHCPACSPKVIEAFTDLGWEFVKKALEHPLYL
EEISGLSVIKQEVER

Sequence of entity 2 (Y, Z), FASTA

>4GSK_2 Ubiquitin-like-conjugating enzyme ATG10 (chains Y, Z)
GSGGSGMIPYQEWHSQLQSLYDSQIFHNWALSQDVHLNDEKDGLLLRLIPTRQLQKNTER
IENKLLNHIELYLTYSKVYNEPLLLLRIWEEKSIDGIPMTKLMLPTDIESLLDVQGKFQL
GLDTIINLEGSVWYSFHPCDTSSIVGDQAEFMSTYLRRWVSIFIFSWLGYEDS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7-Atg3 and Atg7-Atg10 structures. Kaiser, S.E., Mao, K., Taherbhoy, A.M. et al. Nat Struct Mol Biol (2012) 19:1242-1249. DOI 10.1038/nsmb.2415 · 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
5YEC 2.15 Å, Crystal structure of Atg7CTD-Atg8-MgATP complex in form II
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
3VH1 3.0 Å, Crystal structure of Saccharomyces cerevisiae Atg7 (1-595)

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