Separin / Separase - 3D Mechanism Simulator

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References & Databases

START HERE — how to read RAD21 cleaved at one site A single anaphase-cut cartoon on the human separase–securin frame that exists: 7NJ1 (2.90 Å EM), chain A, with securin Phe118 in the pocket. That motif is a named occupancy, not RAD21 and not the cut product. The RAD21 peptide is [schematic]. N-fragment, C-fragment, thioester, and water are [schematic]. Cys2029 is the caspase-like nucleophile. Gold H⁺ leaves water; blue is the Cys-SG nucleophile, not a hydride. Overlay peptide distances are not geomClaims. Securin B is named occupancy, not animated. Yeast Esp1 is another gene. Cut, not walking. Not a pure A-page (E~acyl covalent).
Crystal structures PDB 7NJ1 — human separase–securin, 2.90 Å EM (Yu 2021). Coordinates are public. 7NJ0 is a lower-res companion — not this mesh. Yeast Esp1 structures are other genes.
Mechanism — Cys2029 nucleophile, thioester, water hydrolysis Yu et al., Nature 2021, PMID:34290405 — human separase–securin. UniProt Q14674 caspase-like nucleophile maps to Cys2029 on 7NJ1. His1635 is missing on this EM map. Product is cleaved RAD21 (anaphase). Physiological substrate teaching = cohesin kleisin — analog, not this mesh. Source: Yu 2021 · UniProt Q14674
0 — Setup: securin occupies the scissile cleft 7NJ1 holds separase and securin. Phe118 is the crystal occupant — not RAD21 and not the cut product. Opaque, no autoplay. Chemistry below uses schematic RAD21 peptide.Source: PDB 7NJ1
① — RAD21 analog presented A short RAD21 analog docks as a named stand-in for cohesin kleisin — [schematic], not RAD21 crystal and not securin. Carbonyl faces Cys2029. Overlay peptide Å are not geomClaims. No cohesin on this deposit.Source: compiled separase substrate identity · UniProt Q14674
② — Cys2029 attacks C → covalent E~acyl (hypothetical, lit.-based) Blue nucleophile rides from Cys2029 SG to analog C. Intact peptide fades in place to schematic N-fragment + C-fragment; the carbonyl C then slides to a real ~1.8 Å C–S covalent distance (thioester — the E~acyl bond length, no 3.2 Å gap). Overlay peptide Å are not geomClaims. Slow-motion on purpose. Not a pure A-page.Source: compiled caspase-like Cys · UniProt Q14674
③ — C-fragment leaves (hypothetical, lit.-based) Schematic C-fragment departs. E~acyl stays on Cys2029. Cut teaching = kleisin opened at one site.Source: EC 3.4.22.49 net accounting
④ — Water hydrolyses E~acyl (hypothetical, lit.-based) A schematic water moves in (glides) to the E~acyl face. Gold H⁺ leaves water H2 on the yellow arrow and vanishes right at the arrow tip at the leaving SG (thiol). Remaining O–H = OH⁻ attacks the carbonyl along the blue arrow; after the swap the water O is bound as the new carboxylate O on the N-fragment (red ball) and leaves with it. Thioester is hydrolysed — water-O mass is kept, not deleted. Overlay hydrolysis Å are not geomClaims.Source: compiled cysteine-protease hydrolysis · UniProt Q14674
⑤ — N-fragment leaves — cut [schematic] N-fragment departs carrying its new carboxylate O (from H₂O) — the red water O rides out bound to the product. Product is cleaved RAD21. Yeast Esp1 is another gene. Securin was occupancy, not this chemistry. Cut, not walking.Source: EC 3.4.22.49 net accounting

How to read this page — a first-pass primer First pass: Setup (Phe118 seated, Cys2029 ★) → ① RAD21 analog docks → ② blue SG → C, peptide becomes N + C fragments → ③ C-fragment leaves → ④ gold H⁺ then OH⁻ attacks E~acyl → ⑤ N-fragment leaves; cut. Second pass: 3.24 / 4.01 / 3.97 / 5.09 Å are crystal facts on 7NJ1; peptide, fragments, water, and H spheres are [schematic]. Third pass: open “Disagreements” for securin ≠ RAD21, His1635 missing, 7NJ0, and yeast Esp1.
Chemistry primer — cysteine protease, not a motor Separase cuts cohesin kleisin at one site via a cysteinyl thioester, then water hydrolyses E~acyl. Gold = H⁺. Blue = Cys-SG nucleophile (not hydride). Product is cleaved RAD21 — anaphase. This is not kinesin walking, and not APC/C ubiquitination.
Words used on screen — occupancy · analog · cut · Esp1 Occupancy — securin Phe118 is the crystal ligand; never relabeled as RAD21. Analog — the peptide is a short model occupancy for cohesin kleisin. Cut — one scissile site, not a walking motor. Yeast Esp1 — other gene. PDB numbering = UniProt Q14674; Cys2029 is the nucleophile on 7NJ1.

Legend & Fidelity

Mechanism fidelity — measured vs. inferred The measured layer: 7NJ1 (2.90 Å EM) with securin; Cys2029 SG ⋯ SEC O = 3.24 Å; Cys2029 SG ⋯ SEC C = 4.01 Å; Cys2029 SG ⋯ Val2064 CG2 = 3.97 Å; Cys2029 SG ⋯ Asp2063 OD1 = 5.09 Å. The inferred layer ([schematic]): RAD21 peptide, N/C fragments, E~acyl, water, transferring H⁺/nucleophile spheres, product leave, and capture/hydrolysis split. Binding order is compiled staging, not a kinetic fit. The protein mesh is static. Overlay peptide contacts are not geomClaims. His1635 is missing on this map.
Disagreements on record (a) Securin ≠ RAD21 ≠ cut product. Phe118 is occupancy. (b) Peptide ≠ cohesin. RAD21 analog is a model occupancy. (c) His1635 is modelled. 7NJ1 models chain-A His1635. (d) Capture vs hydrolysis split. Compiled cysteine protease writes two chemical events; this page plays five beats. (e) Yeast Esp1 is another gene. (f) 7NJ0 is not this mesh. (g) No protein-domain swing. (h) Not a pure A-page — E~acyl is covalent. (i) Cut, not walking.
Regulation — securin · CDK1-cyclin B1 · anaphase Securin occupies the cleft until APC/C (other path) removes it. CDK1-cyclin B1 also binds separase (Yu 2021) — named, not this occupancy. Anaphase teaching = one cut in kleisin.Source: UniProt Q14674 · Yu 2021 PMID:34290405
Kinetics scope (no measured timecourse on this page) One RAD21 cleavage event is drawn, not a steady-state run. Compiled BRENDA values for EC 3.4.22.49 are not re-asserted here — no measured k_cat/K_m on this page [schematic]. Pair with a kinetics chapter.Source: BRENDA EC 3.4.22.49 — no k_cat/K_m re-asserted
Sequence Human ESPL1 UniProt Q14674 · NCBI Gene 9700. Screen uses 7NJ1 PDB-author numbering. His1635 is missing on this map.
Simulation map — what you see is what is written Setup = 7NJ1 Phe118 seated (opaque, no autoplay). ① RAD21 analog moves in (schematic). ② slow-mo: blue nucleophile SG → C; peptide fades to N + C fragments. ③ C-fragment leaves. ④ gold H⁺ then OH⁻ attacks E~acyl. ⑤ N-fragment leaves; cut. Only these events move.
Sources — bibliography of this page S1 — PDB 7NJ1: human separase–securin, 2.90 Å EM — public coordinates; measured SG⋯O = 3.24 Å · SG⋯C = 4.01 Å · SG⋯CG2 = 3.97 Å · SG⋯OD1 = 5.09 Å S2 — Yu et al., Nature 2021, PMID:34290405 — structural basis of human separase regulation S3 — Sequence: UniProt Q14674 (human ESPL1) · NCBI Gene 9700 S4 — Kinetics: BRENDA EC 3.4.22.49 — 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., RAD21 peptide, N/C fragments, thioester, H⁺ flight, product release), the pose is drawn schematically and labeled as such in the narration.

separasesecurinONH⁺ (gold)nucleophile (blue)