9E8P: GABARAP-ATG3 conjugate

Crystal Structure of GABARAP-ATG3 conjugate. Determined by X-ray diffraction at 2.7 Å resolution. Released 6 Aug 2025.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,876
Mol. weight: 80.28 kDa
Released: 6 Aug 2025

Explore 9E8P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E8P contains 31 α-helices and 28 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: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	36-49	14
β-strand	54-56	3	1
α-helix	60-62	3
β-strand	73-81	9	1
β-strand	198-207	10	1
β-strand	212-220	9	1
α-helix	225	1
β-strand	226	1	1
α-helix	227-228	2
α-helix	229-232	4
α-helix	233-235	3
β-strand	245-248	4	1
α-helix	254	1
α-helix	257	1
β-strand	258-261	4	1
α-helix	263-265	3
α-helix	266-279	14
α-helix	289-297	9

Chain B: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	2
β-strand	33	1	2
α-helix	36-49	14
β-strand	54-56	3	3
α-helix	60-62	3
β-strand	73-81	9	3
β-strand	198-207	10	3
β-strand	212-220	9	3
α-helix	225	1
β-strand	226	1	3
α-helix	227-228	2
α-helix	229-232	4
α-helix	233-235	3
β-strand	245-248	4	3
α-helix	254	1
α-helix	257	1
β-strand	258-261	4	3
α-helix	266-279	14
α-helix	289-297	9

Chains C and D: 5 helices, 6 β-strands

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like-conjugating enzyme ATG3	A, B	protein	223	Homo sapiens	Q9NT62 (AlphaFold model)
Gamma-aminobutyric acid receptor-associated protein	C, D	protein	118	Homo sapiens	O95166 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9E8P_1 Ubiquitin-like-conjugating enzyme ATG3 (chains A, B)
GSKFKETGVITPEEFVAAGDHLVHHCPTWQWATGEELKVKAYLPTGKQFLVTKNVPCYKR
CKQMEYSDEDEGEAADMEEYEESGLLETDEATLDTRKIVEAAILQTRTYDLYITYDKYYQ
TPRLWLFGYDEQRQPLTVEHMYEDISQDHVKKTVTIENHPHLPPPPMCSVHPKRHAEVMK
KIIETVAEGGGELGVHMYLLIFLKFVQAVIPTIEYDYTRHFTM

Sequence of entity 2 (C, D), FASTA

>9E8P_2 Gamma-aminobutyric acid receptor-associated protein (chains C, D)
SHMKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVG
QFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYG

Primary citation

Structural Insights into the GABARAP-ATG3 Backside Interaction and Apo ATG3 Conformation. Ohashi, K., Kroon, G.J., Otomo, T. Biochemistry (2025) 64:3178-3189. DOI 10.1021/acs.biochem.4c00485 · PubMed

Other PDB entries of the same protein (UniProt Q9NT62 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4NAW 2.19 Å, Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3
8AFI 2.66 Å, GABARAP in complex with LIR motif of HsATG3
8FKM Human Atg3 with deletions of residues 1 to 25 and 90 to 190

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