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4kxf

Crystal structure of NLRC4 reveals its autoinhibition mechanism

Method: X-RAY DIFFRACTION Dmax: 262.8 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain K； UniProt 1–1024 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
10 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 1–1024 Chain F； UniProt 1–1024 Chain H； UniProt 1–1024 Chain L； UniProt 1–1024 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
11 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain D； UniProt 1–1024 Chain N； UniProt 1–1024 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–1024 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 1–1024 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
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain F； UniProt 1–1024 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
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain H； UniProt 1–1024 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
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain L； UniProt 1–1024 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
7 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain N； UniProt 1–1024 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
8 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain P； UniProt 1–1024 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
9 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain K； UniProt 1–1024 Chain P； UniProt 1–1024 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

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 4KXF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3JBL Cryo-EM Structure of the Activated NAIP2/NLRC4 Inflammasome Reveals Nucleated Polymerization Deposited 2015-09-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 11 PDB declaration: undecameric
Chain A 93–1024（932 aa） Fragment：UNP residues 93-1024, SEE REMARK 999
Chain B 93–1024（932 aa） Fragment：UNP residues 93-1024, SEE REMARK 999
Chain C 93–1024（932 aa） Fragment：UNP residues 93-1024, SEE REMARK 999
Chain D 93–1024（932 aa） Fragment：UNP residues 93-1024, SEE REMARK 999
Chain E 93–1024（932 aa） Fragment：UNP residues 93-1024, SEE REMARK 999
Chain F 93–1024（932 aa） Fragment：UNP residues 93-1024, SEE REMARK 999
Chain G 93–1024（932 aa） Fragment：UNP residues 93-1024, SEE REMARK 999
Chain H 93–1024（932 aa） Fragment：UNP residues 93-1024, SEE REMARK 999
Chain I 93–1024（932 aa） Fragment：UNP residues 93-1024, SEE REMARK 999
Chain J 93–1024（932 aa） Fragment：UNP residues 93-1024, SEE REMARK 999
Chain K 93–1024（932 aa） Fragment：UNP residues 93-1024, SEE REMARK 999
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) 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) 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) No recorded non-water small molecule 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
5AJ2 Cryo electron tomography of the Naip5-Nlrc4 inflammasome Deposited 2015-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 3 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 B； PDBConstruct 1–1024； UniProt 1–1024 Author chain D； PDBConstruct 1–1024； UniProt 1–1024 Author chain F； PDBConstruct 1–1024； UniProt 1–1024 Author chain H； PDBConstruct 1–1024； UniProt 1–1024 Author chain K； PDBConstruct 1–1024； UniProt 1–1024 Author chain L； PDBConstruct 1–1024； UniProt 1–1024 Author chain N； PDBConstruct 1–1024； UniProt 1–1024 Author chain P； PDBConstruct 1–1024； UniProt 1–1024

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 4kxf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4kxf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4kxf
Deposition date deposition_date2013-05-25
Structure title titleCrystal structure of NLRC4 reveals its autoinhibition mechanism
Keywords keywordsAuto-inhibition, Muti-domain, Innate Immunity, Phosphorylation, ADP BINDING, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier74.79 Å
Radius of gyration Rg (electron density) rg_electron74.62 Å
Forward intensity I(0) i08855030000.00
Molecular weight molecular_weight812180.0 kDa
Excluded volume excluded_volume1022000 ų
Envelope volume envelope_volume1554200 ų
Hydration-shell volume shell_volume175130 ų
Envelope diameter envelope_diameter270.2 Å
Shell Rg shell_rg72.63 Å
Envelope Rg envelope_rg72.53 Å
Shape Rg shape_rg74.60 Å
Total Rg total_rg74.67 Å
Total atoms total_atoms57081
Residues n_residues7138
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 dmax262.8 Å
Rg (real space) rg_real74.75 Å
Rg uncertainty (real space) rg_real_error2.62 Å
I(0) (real space) i0_real8.8550e+09
I(0) uncertainty (real space) i0_real_error2.1540e+08
Rg (reciprocal space) rg_reciprocal74.78 Å
I(0) (reciprocal space) i0_reciprocal8855000000.0000
Solution quality estimate total_estimate0.8593
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary87.6 Å
Skewness Skewness skewness0.302
Kurtosis Kurtosis kurtosis-0.342
Angular range angular_range— – 0.1050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha380000000.0000
Real-space data points n_real_points22
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.814; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.756
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id4kxfB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4kxfB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4kxfB04
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id4kxfD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4kxfD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4kxfD04
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id4kxfF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4kxfF02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4kxfF04
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id4kxfH01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4kxfH02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4kxfH04
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id4kxfK01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4kxfK02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4kxfK04
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id4kxfL01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4kxfL02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4kxfL04
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id4kxfN01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4kxfN02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4kxfN04
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id4kxfP01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4kxfP02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4kxfP04
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
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8. Citations (1)

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9. Files and Curves (10)