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3jbl

Cryo-EM Structure of the Activated NAIP2/NLRC4 Inflammasome Reveals Nucleated Polymerization

Method: ELECTRON MICROSCOPY Dmax: 332.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NLR family CARD domain-containing protein 4

Mus musculus

UniProt Q3UP24

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 × 11 PDB declaration: undecameric（11） Consistent with protein copy count Chain A； UniProt 93–1024 Chain B； UniProt 93–1024 Chain C； UniProt 93–1024 Chain D； UniProt 93–1024 Chain E； UniProt 93–1024 Chain F； UniProt 93–1024 Chain G； UniProt 93–1024 Chain H； UniProt 93–1024 Chain I； UniProt 93–1024 Chain J； UniProt 93–1024 Chain K； UniProt 93–1024 Fragment：UNP residues 93-1024, SEE REMARK 999 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：25 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM DTT；pH 8；25 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM DTT cryo-EM vitrification conditions：Blot for one second before plunging；103 K；Cryogen ETHANE；Blotted for one second before plunging into liquid ethane (FEI VITROBOT MARK IV). Resolution 4.70 Å R-free 0.383

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 3JBL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4KXF Crystal structure of NLRC4 reveals its autoinhibition mechanism Deposited 2013-05-25 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 K 1–1024（1024 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；1.65M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, 1% n-propyl formate., pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.266
4KXF Crystal structure of NLRC4 reveals its autoinhibition mechanism Deposited 2013-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 10 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1024（1024 aa）
Chain F 1–1024（1024 aa）
Chain H 1–1024（1024 aa）
Chain L 1–1024（1024 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 4 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；1.65M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, 1% n-propyl formate., pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.266
4KXF Crystal structure of NLRC4 reveals its autoinhibition mechanism Deposited 2013-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 11 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain D 1–1024（1024 aa）
Chain N 1–1024（1024 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 4 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；1.65M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, 1% n-propyl formate., pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.266
4KXF Crystal structure of NLRC4 reveals its autoinhibition mechanism Deposited 2013-05-25 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 1–1024（1024 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；1.65M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, 1% n-propyl formate., pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.266
4KXF Crystal structure of NLRC4 reveals its autoinhibition mechanism Deposited 2013-05-25 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 D 1–1024（1024 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；1.65M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, 1% n-propyl formate., pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.266
4KXF Crystal structure of NLRC4 reveals its autoinhibition mechanism Deposited 2013-05-25 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 F 1–1024（1024 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；1.65M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, 1% n-propyl formate., pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.266
4KXF Crystal structure of NLRC4 reveals its autoinhibition mechanism Deposited 2013-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 1–1024（1024 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；1.65M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, 1% n-propyl formate., pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.266
4KXF Crystal structure of NLRC4 reveals its autoinhibition mechanism Deposited 2013-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain L 1–1024（1024 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；1.65M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, 1% n-propyl formate., pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.266
4KXF Crystal structure of NLRC4 reveals its autoinhibition mechanism Deposited 2013-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain N 1–1024（1024 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；1.65M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, 1% n-propyl formate., pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.266
4KXF Crystal structure of NLRC4 reveals its autoinhibition mechanism Deposited 2013-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain P 1–1024（1024 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；1.65M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, 1% n-propyl formate., pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.266
4KXF Crystal structure of NLRC4 reveals its autoinhibition mechanism Deposited 2013-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 9 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain K 1–1024（1024 aa）
Chain P 1–1024（1024 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；291 K；1.65M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, 1% n-propyl formate., pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.266
5AJ2 Cryo electron tomography of the Naip5-Nlrc4 inflammasome Deposited 2015-02-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–355（355 aa） Fragment：RESIDUES 1-355
Chain B 356–580（225 aa） Fragment：RESIDUES 356-580
Chain C 580–1024（445 aa） Fragment：RESIDUES 580-1024
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 100 MM NACL, 20 MM HEPES, 2MM BENZAMIDIN, 2MM DTT；pH 7.5；100 MM NACL, 20 MM HEPES, 2MM BENZAMIDIN, 2MM DTT
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, HUMIDITY- 95, INSTRUMENT- LEICA EM GP, METHOD- 3 SECONDS BLOTTING,
Resolution 40.00 Å
6B5B Cryo-EM structure of the NAIP5-NLRC4-flagellin inflammasome Deposited 2017-09-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1024（1024 aa）
Chain C 1–1024（1024 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.20 Å

3 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NLRC4_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–932； UniProt 93–1024 Author chain B； PDBConstruct 1–932； UniProt 93–1024 Author chain C； PDBConstruct 1–932； UniProt 93–1024 Author chain D； PDBConstruct 1–932； UniProt 93–1024 Author chain E； PDBConstruct 1–932； UniProt 93–1024 Author chain F； PDBConstruct 1–932； UniProt 93–1024 Author chain G； PDBConstruct 1–932； UniProt 93–1024 Author chain H； PDBConstruct 1–932； UniProt 93–1024 Author chain I； PDBConstruct 1–932； UniProt 93–1024 Author chain J； PDBConstruct 1–932； UniProt 93–1024 Author chain K； PDBConstruct 1–932； UniProt 93–1024

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 3jbl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3jbl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3jbl
Deposition date deposition_date2015-09-05
Structure title titleCryo-EM Structure of the Activated NAIP2/NLRC4 Inflammasome Reveals Nucleated Polymerization
Keywords keywordsInflammasome, NLRC4, NAIP2, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier— Å
Radius of gyration Rg (electron density) rg_electron107.80 Å
Forward intensity I(0) i016983100000.00
Molecular weight molecular_weight1139600.0 kDa
Excluded volume excluded_volume1436500 ų
Envelope volume envelope_volume2750300 ų
Hydration-shell volume shell_volume216720 ų
Envelope diameter envelope_diameter310.5 Å
Shell Rg shell_rg107.70 Å
Envelope Rg envelope_rg99.26 Å
Shape Rg shape_rg107.70 Å
Total Rg total_rg108.10 Å
Total atoms total_atoms80124
Residues n_residues9988
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 dmax332.0 Å
Rg (real space) rg_real110.80 Å
Rg uncertainty (real space) rg_real_error1.65 Å
I(0) (real space) i0_real1.6820e+10
I(0) uncertainty (real space) i0_real_error4.0750e+08
Rg (reciprocal space) rg_reciprocal107.20 Å
I(0) (reciprocal space) i0_reciprocal16900000000.0000
Solution quality estimate total_estimate0.8955
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary166.0 Å
Skewness Skewness skewness0.161
Kurtosis Kurtosis kurtosis-0.684
Angular range angular_range— – 0.0700 Å−1
Current regularization parameter α current_alpha1.6610
Highest regularization parameter α highest_alpha502300000.0000
Real-space data points n_real_points15
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.998; Stabil: 0.898; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; 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)