ATG12~ATG5 conjugate - 3D Mechanism Simulator

Loading structural data… (4GDL)

References & Databases

START HERE — how to read ATG12~ATG5 presents LC3 An occupancy cartoon on the human ATG12~ATG5 frame that actually exists: 4GDL (2.88 Å) with an N-terminal fragment of ATG16L1. Occupancy is the ATG12 Gly140 C—ATG5 Lys130 NZ isopeptide (LINK 1.33 Å), not free ATG12 and not a catalyst. ATG12 is not an enzyme — this page is the conjugate (atg5), not atg12. Gly140 is the C-term ligand, not on the ATG12 tube. Lys130 ★ is the deposited isopeptide lysine, not a catalytic nucleophile. ATG16N stays. Schematic LC3 cargo is [schematic]. No nucleophile arrow. Measured Å are deposited 4GDL pairs only. Schematic cargo Å are not geomClaims. 4NAW is ATG12~ATG5–ATG16N + ATG3 peptide, not this mesh. PE / LC3-II is not this cartoon. Why no PE: 4GDL is a conjugate crystal and PE is a membrane lipid, not a ligand of this soluble complex — no PE coordinates exist on this frame; LC3→PE lipidation (ATG7/ATG3) is a separate reaction, so this page names PE but cannot draw it. Na ion not extracted.
Crystal structures PDB 4GDL — human ATG12~ATG5 conjugate + ATG16L1 N-term, 2.88 Å (Otomo 2013). Coordinates are public. ATG12 UniProt O94817. ATG5 UniProt Q9H1Y0. ATG16L1 UniProt Q676U5. 4NAW adds an ATG3 peptide — not this mesh.
Mechanism — E3-like scaffold, not catalysis ATG12~ATG5·ATG16L1 is the autophagy E3-like scaffold that presents LC3/ATG8 toward PE. No EC number. No ACT_SITE. The Gly140–Lys130 isopeptide is already formed on this deposit — this page does not draw that ligation. Gold H⁺ and blue nucleophile are not drawn. PE lipidation is compiled, not a crystal movie. Source: Otomo et al., Nat. Struct. Mol. Biol. 2013, PMID:23202584 · UniProt Q9H1Y0
0 — Setup: ATG12~ATG5 isopeptide 4GDL holds the Gly140–Lys130 isopeptide. The conjugate is shown so the occupancy can be named. Lys130 NZ ⋯ Gly140 C = 1.33 Å. ATG16N stays. ATG12 is not an enzyme. Opaque, run:null (no autoplay). No catalytic arrows.Source: PDB 4GDL (2.88 Å)
① — Schematic LC3 docks [schematic] LC3 cargo docks onto the conjugate. The crystal holds ATG12~ATG5 + ATG16N, not LC3 and not PE. Gly140 stays as the isopeptide ligand. Schematic cargo Å are not geomClaims.Source: schematic LC3 on 4GDL conjugate
② — Conjugate presents LC3 to PE (hypothetical, lit.-based) The ATG12~ATG5·ATG16L1 conjugate presents LC3 toward PE [schematic]. The protein mesh is static — 4GDL is isopeptide occupancy, not a lipidation movie. No nucleophile arrow. Slow-motion on purpose.Source: compiled E3-like scaffold · Otomo 2013 PMID:23202584
③ — LC3 stays — PE is not this cartoon Schematic LC3 stays. Crystal Gly140 stays as the deposited isopeptide. Lys130 NZ ⋯ Gly140 C = 1.33 Å. Lys130 NZ ⋯ Gly140 O = 2.25 Å. This is occupancy, not catalysis. PE / LC3-II is not this cartoon. 4NAW is not this mesh.Source: 4GDL Lys130 NZ ⋯ Gly140 C

How to read this page — a first-pass primer First pass: Setup (isopeptide occupancy, Lys130 ★, ATG16N stays) → ① schematic LC3 docks → ② conjugate presents LC3 to PE, no nucleophile → ③ LC3 stays; PE is not this cartoon. Second pass: 1.33 / 2.25 / 2.47 / 3.38 Å are crystal facts on 4GDL; LC3 cargo and “presents” are [schematic]. Third pass: open “Disagreements” for ATG12 ≠ enzyme, isopeptide ≠ catalysis, 4NAW peptide, and PE not this cartoon.
Chemistry primer — occupancy, not catalysis ATG5 is not a hydrolase and not an E1/E2. The Gly140–Lys130 isopeptide is already formed. This page names that occupancy and parks schematic LC3. Gold H⁺ and blue nucleophile are not drawn — there is no catalytic event on this page. ATG12 alone is not a page. ATG7 / ATG3 / ATG4 are other ids.
Words used on screen — isopeptide · ATG16N · presents Isopeptide — covalent Gly140 C—Lys130 NZ on this deposit (LINK 1.33 Å). ATG16N — the N-terminal fragment of ATG16L1 on chain C; it stays. Presents — compiled E3-like staging drawn as a label on a static protein, not a morph. Lys130 ★ — PDB id on this ATG5 frame; not a catalytic nucleophile.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 4GDL (2.88 Å) human ATG12~ATG5 + ATG16N; Lys130 NZ ⋯ Gly140 C = 1.33 Å; Lys130 NZ ⋯ Gly140 O = 2.25 Å; Lys130 CE ⋯ Gly140 C = 2.47 Å; Lys130 CD ⋯ Gly140 C = 3.38 Å. The inferred layer ([schematic]): LC3 cargo, “presents LC3 to PE” label. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. Schematic cargo Å are not geomClaims. His150 ND1 ⋯ Gly140 C is spoken in extract notes, not a geomClaim.
Disagreements on record (a) ATG12 is not an enzyme. This page is the conjugate (atg5), not atg12. (b) Isopeptide occupancy ≠ catalysis. Gly140–Lys130 is already formed; this page does not draw that ligation. (c) Not a hydrolase. No nucleophile arrow. Same honesty class as a carrier occupancy page. (d) 4NAW is ATG12~ATG5–ATG16N + ATG3 peptide, not this mesh. (e) PE / LC3-II is not this cartoon. (f) Na ion in 4GDL is not extracted. (g) gap 228–234 named, not drawn. (h) no protein-domain swing.
Regulation — conjugate · ATG16L1 · starvation This mesh is ATG12~ATG5 holding ATG16N. The conjugate is required for LC3 lipidation — named, not a phagophore movie. ATG16L1 beyond the N-term fragment is not this cartoon. Starvation / ULK1 / BECN1 gating is drawer, not motion. Flexible loop 228–234 is missing on 4GDL.Source: UniProt Q9H1Y0 · Otomo 2013
Kinetics scope (no measured timecourse on this page) One occupancy / present event is drawn, not a steady-state run. No measured k_cat/K_m is re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with an autophagy chapter.Source: Otomo 2013 — no k_cat/K_m re-asserted
Sequence Human ATG5 UniProt Q9H1Y0 · NCBI Gene 9474. ATG12 O94817 · Gene 9140. ATG16L1 Q676U5 · Gene 55054. This screen uses PDB numbering (Lys130 on 4GDL = UniProt Lys130). ATG5 chain B Cα 3–274, gap 228–234. ATG12 chain A Cα 53–139 offset +1000; Gly140 is the ligand, not on the tube. ATG16N chain C Cα 10–43 offset +2000.
Simulation map — what you see is what is written Setup = 4GDL isopeptide occupancy (opaque, no autoplay). ① schematic LC3 moves in. ② slow-mo present label on a static protein; no nucleophile. ③ LC3 stays; PE is not this cartoon. Only these events move.
Sources — bibliography of this page S1 — PDB 4GDL: human ATG12~ATG5 + ATG16N, 2.88 Å — public coordinates; measured NZ⋯C = 1.33 Å · NZ⋯O = 2.25 Å · CE⋯C = 2.47 Å · CD⋯C = 3.38 Å S2 — Otomo et al., Nat. Struct. Mol. Biol. 2013, PMID:23202584 — ATG12~ATG5 conjugate required for LC3 lipidation S3 — Sequence: UniProt Q9H1Y0 (ATG5) · O94817 (ATG12) · Q676U5 (ATG16L1) · NCBI Gene 9474 S4 — Kinetics: no k_cat/K_m re-asserted on this page

› Backbones and ligand poses are taken directly from the listed PDB entries, superposed into one common frame. Where no crystalline state exists for a step (e.g., LC3 cargo, presenting LC3 to PE), the pose is drawn schematically and labeled as such in the narration. PE itself is a membrane lipid absent from 4GDL, so it is named, never drawn — LC3→PE lipidation is compiled on the ATG7/ATG3/ATG4 pages. The Gly140–Lys130 isopeptide is occupancy, not a catalytic event.

ATG5ATG12ATG16NON