4GSL: Atg7-Atg3 crosslinked complex

Crystal structure of an Atg7-Atg3 crosslinked complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 14 Nov 2012.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 12,543
Mol. weight: 211.47 kDa
Ligands: ZN
Released: 14 Nov 2012

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

Secondary structure: helices and β-sheets

4GSL contains 75 α-helices and 86 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, 31 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	19-27	9
β-strand	37-46	10	4
β-strand	57	1	5
β-strand	59-62	4	3
α-helix	64-67	4
α-helix	77	1
β-strand	78-87	10	4
α-helix	90-94	5
α-helix	98-113	16
α-helix	117-119	3
β-strand	123-130	8	4
β-strand	135-146	12	4
β-strand	151-157	7	1
α-helix	164-174	11
β-strand	180-183	4	1
β-strand	189-191	3	1
α-helix	194-200	7
β-strand	202-206	5	1
β-strand	209	1	5
β-strand	216	1	2
α-helix	218-229	12
β-strand	235-241	7	1
β-strand	248-256	9	1
α-helix	259-261	3
β-strand	269-273	5	4
α-helix	274-275	2
β-strand	284-287	4	4
α-helix	289-292	4
α-helix	294-312	19
α-helix	319-323	5
β-strand	326-330	5	6
α-helix	334-345	12
β-strand	350-354	5	6
β-strand	358	1	7
α-helix	363-365	3
α-helix	372-374	3
β-strand	378	1	7
α-helix	379-390	12
β-strand	395-399	5	6
α-helix	413-429	17
β-strand	432-435	4	6
α-helix	440-442	3
α-helix	444-452	9
β-strand	456-462	7	6
β-strand	466-471	6	6
α-helix	512-530	19
α-helix	532-534	3
β-strand	539-540	2	8
β-strand	543-544	2	8
β-strand	548-552	5	6
β-strand	557-561	5	6
α-helix	574-593	20
α-helix	595-602	8
α-helix	604-606	3

Chain B: 24 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	9
β-strand	10	1	10
β-strand	13-17	5	11
α-helix	19-30	12
β-strand	38-46	9	12
β-strand	57	1	13
β-strand	58-62	5	11
α-helix	64-67	4
β-strand	78-87	10	12
α-helix	90-95	6
α-helix	98-115	18
α-helix	117-119	3
β-strand	123-130	8	12
β-strand	135-146	12	12
β-strand	151-157	7	9
α-helix	164-174	11
β-strand	180-183	4	9
β-strand	189-190	2	9
α-helix	194-200	7
β-strand	202-206	5	9
β-strand	209	1	13
β-strand	216	1	10
α-helix	218-229	12
β-strand	235-241	7	9
β-strand	248-256	9	9
β-strand	269-273	5	12
α-helix	274-275	2
β-strand	281	1	14
β-strand	284-287	4	12
α-helix	289-292	4
α-helix	294-312	19
α-helix	319-323	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	413-429	17
β-strand	432-435	4	15
α-helix	444-453	10
β-strand	456-462	7	15
β-strand	466-471	6	15
β-strand	483	1	17
α-helix	484-485	2
α-helix	513-530	18
α-helix	532-534	3
β-strand	539-540	2	18
β-strand	543-544	2	18
β-strand	548-552	5	15
β-strand	557-561	5	15
β-strand	564	1	17
α-helix	565-566	2
α-helix	574-593	20
α-helix	595-602	8

Chain C: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
α-helix	30-43	14
β-strand	48-49	2	19
β-strand	56	1	20
α-helix	64-66	3
β-strand	69-76	8	19
α-helix	80-82	3
α-helix	133-139	7
β-strand	141	1	14
β-strand	167-175	9	19
β-strand	182-189	8	19
α-helix	194	1
β-strand	195	1	19
α-helix	196-197	2
α-helix	198-202	5
α-helix	207-213	7
β-strand	215-218	4	19
β-strand	222	1	20
β-strand	227-231	5	19
α-helix	239-243	5
α-helix	283-285	3
α-helix	286-297	12
β-strand	301	1	19

Chain D: 13 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
α-helix	30-43	14
β-strand	48-49	2	21
α-helix	50-51	2
β-strand	56	1	22
β-strand	68-76	9	21
α-helix	80-82	3
α-helix	133-138	6
β-strand	167-176	10	21
β-strand	181-189	9	21
α-helix	194	1
β-strand	195	1	21
α-helix	196-197	2
α-helix	198-201	4
α-helix	202-204	3
α-helix	207-210	4
β-strand	215-218	4	21
β-strand	222	1	22
β-strand	227-231	5	21
α-helix	239-244	6
α-helix	283-285	3
α-helix	286-297	12
β-strand	301	1	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like modifier-activating enzyme ATG7	A, B	protein	615	Saccharomyces cerevisiae	P38862 (AlphaFold model)
Autophagy-related protein 3	C, D	protein	312	Saccharomyces cerevisiae	P40344 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4GSL_1 Ubiquitin-like modifier-activating enzyme ATG7 (chains A, B)
GSMSSERVLSYAPAFKSFLDTSFFQELSRLKLDVLKLDSTCQPLTVNLDLHNIPKSADQV
PLFLTNRSFEKHNNKRTNEVPLQGSIFNFNVLDEFKNLDKQLFLHQRALECWEDGIKDIN
KCVSFVIISFADLKKYRFYYWLGVPCFQRPSSTVLHVRPEPSLKGLFSKCQKWFDVNYSK
WVCILDADDEIVNYDKCIIRKTKVLAIRDTSTMENVPSALTKNFLSVLQYDVPDLIDFKL
LIIRQNEGSFALNATFASIDPQSSSSNPDMKVSGWERNVQGKLAPRVVDLSSLLDPLKIA
DQSVDLNLKLMKWRILPDLNLDIIKNTKVLLLGAGTLGCYVSRALIAWGVRKITFVDNGT
VSYSNPVRQALYNFEDCGKPKAELAAASLKRIFPLMDATGVKLSIPMIGHKLVNEEAQHK
DFDRLRALIKEHDIIFLLVDSRESRWLPSLLSNIENKTVINAALGFDSYLVMRHGNRDEQ
SSKQLGCYFCHDVVAPTDSLTDRTLDQMCTVTRPGVAMMASSLAVELMTSLLQTKYSGSE
TTVLGDIPHQIRGFLHNFSILKLETPAYEHCPACSPKVIEAFTDLGWEFVKKALEHPLYL
EEISGLSVIKQEVER

Sequence of entity 2 (C, D), FASTA

>4GSL_2 Autophagy-related protein 3 (chains C, D)
GSMIRSTLSSWREYLTPITHKSTFLTTGQITPEEFVQAGDYLAHMFPTWKWNEESSDISY
RDFLPKNKQFLIIRKVPADKRAEQAVEVEGPDVIMKGFAEDGDEDDVLEYIGSETEHVQS
TPAGGTKDSSIDDIDELIQDMEIKEEDENDDTEEFNAKGGLAKDMAQERYYDLYIAYSTS
YRVPKMYIVGFNSNGSPLSPEQMFEDISADYRTKTATIEKLPFYKNSVLSVSIHPCKHAN
VMKILLDKVRVVRQRRRKELQEEQELDGVGDWEDLQDDIDDSLRVDQYLIVFLKFITSVT
PSIQHDYTMEGW

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
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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