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8z94

Cryo-EM structure of RIPK1 RHIM PFFs cross seeded RIPK3 RHIM amyloid fibril

Method: ELECTRON MICROSCOPY Dmax: 39.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Receptor-interacting serine/threonine-protein kinase 3

Homo sapiens

UniProt Q9Y572

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 388–518 Chain B； UniProt 388–518 Chain C； UniProt 388–518 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.56 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8Z94 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
12KL SSNMR Structure of Anti-necroptosis Viral:Human Functional Hetero-amyloid M45:RIPK3 Deposited 2026-04-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 388–518（131 aa）
Chain C 388–518（131 aa）
Chain E 388–518（131 aa）
Chain G 388–518（131 aa）
Not recorded No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions pH 7.4；285 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition 5 mM U-13C,15N M45, 5 mM RIPK3, water | water
NMR sample composition 5 mM 2-13C-glycerol,15N M45, 5 mM 1,3-13C-glycerol,15N RIPK3, water | water
NMR sample composition 5 mM U-13C,15N RIPK3, 5 mM M45, water | water
NMR sample composition 5 mM U-13C,15N RIPK3, water | water
NMR sample composition 5 mM U-13C,15N M45, water | water
NMR sample composition 5 mM 1,3-13C-glycerol, 15N M45, 5 mM RIPK3, water | water
NMR sample composition 5 mM 2-13C-glycerol,15N M45, 5 mM RIPK3, water | water
NMR sample composition 5 mM 1,3-13C-glycerol,15N RIPK3, 5 mM M45, water | water
NMR sample composition 5 mM 2-13C-glycerol,15N RIPK3, 5 mM M45, water | water
NMR sample composition 5 mM 2-13C-glycerol,15N RIPK3, 5 mM 1,3-13C-glycerol,15N M45, water | water
Resolution not provided
5ZCK Structure of the RIP3 core region Deposited 2018-02-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 458–461（4 aa）
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M magnesium chloride, 0.1 M sodium cacodylate, 20% (v/v) PEG 200
Resolution 1.27 Å R-free 0.152
7DA4 Cryo-EM structure of amyloid fibril formed by human RIPK3 Deposited 2020-10-14 Different construct Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 388–518（131 aa） Fragment：C-terminal domain
Chain B 388–518（131 aa） Fragment：C-terminal domain
Chain C 388–518（131 aa） Fragment：C-terminal domain
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.24 Å
7DAC Human RIPK3 amyloid fibril revealed by solid-state NMR Deposited 2020-10-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 418–518（101 aa）
Chain B 418–518（101 aa）
Chain C 418–518（101 aa）
Chain D 418–518（101 aa）
Chain E 418–518（101 aa）
Not recorded No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 5 mg/mL [U-100% 13C; U-100% 15N] human RIPK3 fibrils, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 5 mg/mL [U-100% 2-13C Glycerol; U-100% 15N] human RIPK3 fibrils, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 5 mg/mL [U-100% 1, 3-13C Glycerol; U-100% 15N] human RIPK3 fibrils, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 5 mg/mL [U-50% 13C; natural abundance N][natural abandance 13C; U-50% 15N] human RIPK3 fibrils, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
7MON Structure of human RIPK3-MLKL complex Deposited 2021-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–316（316 aa）
Mutation：C3S, C110A Non-standard monomer：Yes (specific site not provided by mmCIF) ZL1 N-[4-({2-[(cyclopropanecarbonyl)amino]pyridin-4-yl}oxy)-3-fluorophenyl]-1-(4-fluorophenyl)-2-oxo-1,2-dihydropyridine-3-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；281.15 K；0.2 M ammonium acetate 30%w/v PEG 4000 0.1 M trisodium citrate-citric acid pH 5.5
Resolution 2.23 Å R-free 0.260
7MX3 Crystal structure of human RIPK3 complexed with GSK'843 Deposited 2021-05-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–315（314 aa）
Mutation：C3S, C110A ZOV 3-(1,3-benzothiazol-5-yl)-7-(1,3-dimethyl-1H-pyrazol-5-yl)thieno[3,2-c]pyridin-4-amine × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；281.15 K；0.2 M magnesium chloride, 25% (w/v) polyethylene glycol 3350, 0.1 M Tris pH 8.5
Resolution 3.23 Å R-free 0.285
7MX3 Crystal structure of human RIPK3 complexed with GSK'843 Deposited 2021-05-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–315（314 aa）
Mutation：C3S, C110A ZOV 3-(1,3-benzothiazol-5-yl)-7-(1,3-dimethyl-1H-pyrazol-5-yl)thieno[3,2-c]pyridin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；281.15 K；0.2 M magnesium chloride, 25% (w/v) polyethylene glycol 3350, 0.1 M Tris pH 8.5
Resolution 3.23 Å R-free 0.285
7MX3 Crystal structure of human RIPK3 complexed with GSK'843 Deposited 2021-05-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 2–315（314 aa）
Mutation：C3S, C110A ZOV 3-(1,3-benzothiazol-5-yl)-7-(1,3-dimethyl-1H-pyrazol-5-yl)thieno[3,2-c]pyridin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；281.15 K；0.2 M magnesium chloride, 25% (w/v) polyethylene glycol 3350, 0.1 M Tris pH 8.5
Resolution 3.23 Å R-free 0.285
7MX3 Crystal structure of human RIPK3 complexed with GSK'843 Deposited 2021-05-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 2–315（314 aa）
Mutation：C3S, C110A ZOV 3-(1,3-benzothiazol-5-yl)-7-(1,3-dimethyl-1H-pyrazol-5-yl)thieno[3,2-c]pyridin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；281.15 K；0.2 M magnesium chloride, 25% (w/v) polyethylene glycol 3350, 0.1 M Tris pH 8.5
Resolution 3.23 Å R-free 0.285
9LFU Crystal structure of human RIP3 kinase domain complexed with LK01003 Deposited 2025-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–315（314 aa）
Mutation：C3S, C110A A1D97 2-cyclopentyl-~{N}-(6-propan-2-ylsulfonylquinolin-4-yl)-1,3-benzothiazol-5-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M magnesium chloride, 22.5% (w/v) polyethylene glycol 3350, 0.1 M Tris, pH 7.5
Resolution 2.93 Å R-free 0.319
9LFU Crystal structure of human RIP3 kinase domain complexed with LK01003 Deposited 2025-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–315（314 aa）
Mutation：C3S, C110A A1D97 2-cyclopentyl-~{N}-(6-propan-2-ylsulfonylquinolin-4-yl)-1,3-benzothiazol-5-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M magnesium chloride, 22.5% (w/v) polyethylene glycol 3350, 0.1 M Tris, pH 7.5
Resolution 2.93 Å R-free 0.319

7 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RIPK3_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–133； UniProt 388–518 Author chain B； PDBConstruct 3–133； UniProt 388–518 Author chain C； PDBConstruct 3–133； UniProt 388–518

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8z94

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8z94
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8z94
Deposition date deposition_date2024-04-22
Structure title titleCryo-EM structure of RIPK1 RHIM PFFs cross seeded RIPK3 RHIM amyloid fibril
Keywords keywordsamyloid fibril, PROTEIN FIBRIL; PROTEIN FIBRIL
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.38 Å
Radius of gyration Rg (electron density) rg_electron11.38 Å
Forward intensity I(0) i01282110.00
Molecular weight molecular_weight7274.0 kDa
Excluded volume excluded_volume8952 ų
Envelope volume envelope_volume9606 ų
Hydration-shell volume shell_volume7614 ų
Envelope diameter envelope_diameter37.1 Å
Shell Rg shell_rg16.34 Å
Envelope Rg envelope_rg11.69 Å
Shape Rg shape_rg11.37 Å
Total Rg total_rg12.64 Å
Total atoms total_atoms507
Residues n_residues66
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax39.6 Å
Rg (real space) rg_real12.33 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real1.2820e+06
I(0) uncertainty (real space) i0_real_error1.3990e+04
Rg (reciprocal space) rg_reciprocal12.33 Å
I(0) (reciprocal space) i0_reciprocal1282000.0000
Solution quality estimate total_estimate0.9009
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.0 Å
Skewness Skewness skewness0.155
Kurtosis Kurtosis kurtosis-0.443
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha135800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.953
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)