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7dac

Human RIPK3 amyloid fibril revealed by solid-state NMR

Method: SOLID-STATE NMR Dmax: 55.4 Å Quality: REASONABLE
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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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain A； UniProt 418–518 Chain B； UniProt 418–518 Chain C； UniProt 418–518 Chain D； UniProt 418–518 Chain E； UniProt 418–518 Not recorded No other associated polymer 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

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 7DAC 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 conditions 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions 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
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
8Z94 Cryo-EM structure of RIPK1 RHIM PFFs cross seeded RIPK3 RHIM amyloid fibril Deposited 2024-04-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 388–518（131 aa）
Chain B 388–518（131 aa）
Chain C 388–518（131 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.56 Å
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 8–108； UniProt 418–518 Author chain B； PDBConstruct 8–108； UniProt 418–518 Author chain C； PDBConstruct 8–108； UniProt 418–518 Author chain D； PDBConstruct 8–108； UniProt 418–518 Author chain E； PDBConstruct 8–108； UniProt 418–518

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 7dac

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7dac
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7dac
Deposition date deposition_date2020-10-16
Structure title titleHuman RIPK3 amyloid fibril revealed by solid-state NMR
Keywords keywordsprogrammed necrosis, amyloid, PROTEIN FIBRIL; PROTEIN FIBRIL
Experimental Method methodSOLID-STATE NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.17 Å
Radius of gyration Rg (electron density) rg_electron15.47 Å
Forward intensity I(0) i0560581000.00
Molecular weight molecular_weight191620.0 kDa
Excluded volume excluded_volume236660 ų
Envelope volume envelope_volume35619 ų
Hydration-shell volume shell_volume17271 ų
Envelope diameter envelope_diameter63.5 Å
Shell Rg shell_rg23.60 Å
Envelope Rg envelope_rg17.84 Å
Shape Rg shape_rg15.50 Å
Total Rg total_rg15.57 Å
Total atoms total_atoms26520
Residues n_residues1740
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 dmax55.4 Å
Rg (real space) rg_real15.12 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real5.6060e+08
I(0) uncertainty (real space) i0_real_error6.5690e+06
Rg (reciprocal space) rg_reciprocal15.13 Å
I(0) (reciprocal space) i0_reciprocal560600000.0000
Solution quality estimate total_estimate0.7408
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary20.3 Å
Skewness Skewness skewness0.297
Kurtosis Kurtosis kurtosis-0.092
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha667500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.566; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.934; Smooth: 0.000
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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)