6xkk

Cryo-EM structure of the NLRP1-CARD filament

Method: ELECTRON MICROSCOPY Dmax: 167.9 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

NACHT, LRR and PYD domains-containing protein 1

Homo sapiens

UniProt Q9C000

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 × 44 PDB declaration: 44-meric(44) Consistent with protein copy count Chain A; UniProt 1305–1399 Chain B; UniProt 1305–1399 Chain C; UniProt 1305–1399 Chain D; UniProt 1305–1399 Chain E; UniProt 1305–1399 Chain F; UniProt 1305–1399 Chain G; UniProt 1305–1399 Chain H; UniProt 1305–1399 Chain I; UniProt 1305–1399 Chain J; UniProt 1305–1399 Chain K; UniProt 1305–1399 Chain L; UniProt 1305–1399 Chain M; UniProt 1305–1399 Chain N; UniProt 1305–1399 Chain O; UniProt 1305–1399 Chain P; UniProt 1305–1399 Chain Q; UniProt 1305–1399 Chain R; UniProt 1305–1399 Chain S; UniProt 1305–1399 Chain T; UniProt 1305–1399 Chain U; UniProt 1305–1399 Chain V; UniProt 1305–1399 Chain a; UniProt 1305–1399 Chain b; UniProt 1305–1399 Chain c; UniProt 1305–1399 Chain d; UniProt 1305–1399 Chain e; UniProt 1305–1399 Chain f; UniProt 1305–1399 Chain g; UniProt 1305–1399 Chain h; UniProt 1305–1399 Chain i; UniProt 1305–1399 Chain j; UniProt 1305–1399 Chain k; UniProt 1305–1399 Chain l; UniProt 1305–1399 Chain m; UniProt 1305–1399 Chain n; UniProt 1305–1399 Chain o; UniProt 1305–1399 Chain p; UniProt 1305–1399 Chain q; UniProt 1305–1399 Chain r; UniProt 1305–1399 Chain s; UniProt 1305–1399 Chain t; UniProt 1305–1399 Chain u; UniProt 1305–1399 Chain v; UniProt 1305–1399 Fragment:CARD domain (UNP residues 1305-1399) No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.72 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.

11 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NLRP1_HUMAN
Isoform Q9C000-3
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–95; UniProt 1305–1399 Author chain B; PDBConstruct 1–95; UniProt 1305–1399 Author chain C; PDBConstruct 1–95; UniProt 1305–1399 Author chain D; PDBConstruct 1–95; UniProt 1305–1399 Author chain E; PDBConstruct 1–95; UniProt 1305–1399 Author chain F; PDBConstruct 1–95; UniProt 1305–1399 Author chain G; PDBConstruct 1–95; UniProt 1305–1399 Author chain H; PDBConstruct 1–95; UniProt 1305–1399 Author chain I; PDBConstruct 1–95; UniProt 1305–1399 Author chain J; PDBConstruct 1–95; UniProt 1305–1399 Author chain K; PDBConstruct 1–95; UniProt 1305–1399 Author chain L; PDBConstruct 1–95; UniProt 1305–1399 Author chain M; PDBConstruct 1–95; UniProt 1305–1399 Author chain N; PDBConstruct 1–95; UniProt 1305–1399 Author chain O; PDBConstruct 1–95; UniProt 1305–1399 Author chain P; PDBConstruct 1–95; UniProt 1305–1399 Author chain Q; PDBConstruct 1–95; UniProt 1305–1399 Author chain R; PDBConstruct 1–95; UniProt 1305–1399 Author chain S; PDBConstruct 1–95; UniProt 1305–1399 Author chain T; PDBConstruct 1–95; UniProt 1305–1399 Author chain U; PDBConstruct 1–95; UniProt 1305–1399 Author chain V; PDBConstruct 1–95; UniProt 1305–1399 Author chain a; PDBConstruct 1–95; UniProt 1305–1399 Author chain b; PDBConstruct 1–95; UniProt 1305–1399 Author chain c; PDBConstruct 1–95; UniProt 1305–1399 Author chain d; PDBConstruct 1–95; UniProt 1305–1399 Author chain e; PDBConstruct 1–95; UniProt 1305–1399 Author chain f; PDBConstruct 1–95; UniProt 1305–1399 Author chain g; PDBConstruct 1–95; UniProt 1305–1399 Author chain h; PDBConstruct 1–95; UniProt 1305–1399 Author chain i; PDBConstruct 1–95; UniProt 1305–1399 Author chain j; PDBConstruct 1–95; UniProt 1305–1399 Author chain k; PDBConstruct 1–95; UniProt 1305–1399 Author chain l; PDBConstruct 1–95; UniProt 1305–1399 Author chain m; PDBConstruct 1–95; UniProt 1305–1399 Author chain n; PDBConstruct 1–95; UniProt 1305–1399 Author chain o; PDBConstruct 1–95; UniProt 1305–1399 Author chain p; PDBConstruct 1–95; UniProt 1305–1399 Author chain q; PDBConstruct 1–95; UniProt 1305–1399 Author chain r; PDBConstruct 1–95; UniProt 1305–1399 Author chain s; PDBConstruct 1–95; UniProt 1305–1399 Author chain t; PDBConstruct 1–95; UniProt 1305–1399 Author chain u; PDBConstruct 1–95; UniProt 1305–1399 Author chain v; PDBConstruct 1–95; UniProt 1305–1399

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 6xkk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6xkk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6xkk
Deposition date deposition_date2020-06-26
Structure title titleCryo-EM structure of the NLRP1-CARD filament
Keywords keywordsFilament, inflammasome, signaling, UPA, CARD, FIIND, NLRP1, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier52.82
Radius of gyration Rg (electron density) rg_electron52.20
Forward intensity I(0) i02812270000.00
Molecular weight molecular_weight444070.0 kDa
Excluded volume excluded_volume556250 ų
Envelope volume envelope_volume826540 ų
Hydration-shell volume shell_volume125950 ų
Envelope diameter envelope_diameter172.8
Shell Rg shell_rg60.00
Envelope Rg envelope_rg51.18
Shape Rg shape_rg52.19
Total Rg total_rg52.44
Total atoms total_atoms31284
Residues n_residues3740
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax167.9
Rg (real space) rg_real52.58
Rg uncertainty (real space) rg_real_error0.92
I(0) (real space) i0_real2.8120e+09
I(0) uncertainty (real space) i0_real_error5.3210e+07
Rg (reciprocal space) rg_reciprocal53.02
I(0) (reciprocal space) i0_reciprocal2814000000.0000
Solution quality estimate total_estimate0.8705
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary67.2
Skewness Skewness skewness0.170
Kurtosis Kurtosis kurtosis-0.416
Angular range angular_range— – 0.1500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1550000000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.816

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

8. Citations (1)

9. Files and Curves (10)