SAXSdb — 5aj2

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

NLR FAMILY CARD DOMAIN-CONTAINING PROTEIN 4

MUS MUSCULUS

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 1–355 Chain B； UniProt 356–580 Chain C； UniProt 580–1024	Fragment：RESIDUES 1-355 Fragment：RESIDUES 356-580 Fragment：RESIDUES 580-1024	No other associated polymer	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

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 5AJ2	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 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
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
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, 2, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–355； UniProt 1–355 Author chain B； PDBConstruct 1–225； UniProt 356–580 Author chain C； PDBConstruct 1–445； UniProt 580–1024

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5aj2
Deposition date deposition_date	2015-02-20
Structure title title	Cryo electron tomography of the Naip5-Nlrc4 inflammasome
Keywords keywords	APOPTOSIS; APOPTOSIS
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	37.43 Å
Radius of gyration Rg (electron density) rg_electron	37.53 Å
Forward intensity I(0) i0	151487000.00
Molecular weight molecular_weight	102880.0 kDa
Excluded volume excluded_volume	126790 Å³
Envelope volume envelope_volume	114480 Å³
Hydration-shell volume shell_volume	28243 Å³
Envelope diameter envelope_diameter	116.2 Å
Shell Rg shell_rg	39.06 Å
Envelope Rg envelope_rg	35.55 Å
Shape Rg shape_rg	37.63 Å
Total Rg total_rg	37.61 Å
Total atoms total_atoms	1
Residues n_residues	—
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	120.5 Å
Rg (real space) rg_real	37.72 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.5150e+08
I(0) uncertainty (real space) i0_real_error	2.7260e+06
Rg (reciprocal space) rg_reciprocal	37.55 Å
I(0) (reciprocal space) i0_reciprocal	151500000.0000
Solution quality estimate total_estimate	0.6239
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.4 Å
Skewness Skewness skewness	0.403
Kurtosis Kurtosis kurtosis	-0.714
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0003
Highest regularization parameter α highest_alpha	12220000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 0.080; Positv: 1.000; Valcen: 0.852; Smooth: 0.537

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	NLR FAMILY CARD DOMAIN-CONTAINING PROTEIN 4
Molecular weight formula_weight	40914.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	904

MNFIRNNRRALIQRMGLTVTKQICDDLFALNVLNNQEANVIYCEPLEQEAARKIIHMTMQKGSAACNLFLKSLENWDYFVYQDLTGQNLSYQVTEEDLNVLAQNLKDLYNSPAFLNFYPLGEDIDIIFNLEKTFTEPIMWKKDHRHHRVEQLTLGSLLEALKSPCLIEGESGKGKSTLLQRIAMLWASGGCRALKGFRLVFFIHLRSARGGLFETLYDQLLNIPDFISKPTFKALLLKLHKEVLFLLDGYNEFHPQNCPEIEALIKENHRFKNMVIVTTTTECLRHIRHVGALTAEVGDMTEDSAKDLIEAVLVPDQVERLWAQIQESRCLRNLMKTPLFVVITCAIQMGRQEFQ

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	HOUSE MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	HOMO SAPIENS

Entity 2 Entity 2 polymer

Description description	NLR FAMILY CARD DOMAIN-CONTAINING PROTEIN 4
Molecular weight formula_weight	25524.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AHTQTMLFQTFYDLLIQKNSHRYRGGASGDFARSLDYCGDLALEGVFAHKFDFEPEHGSSMNEDVLVTIGLLCKYTAQRLKPTYKFFHKSFQEYTAGRRLSSLLTSKEPEEVSKGNSYLNKMVSISDITSLYGNLLLYTCGSSTEATRAVMRHLAMVYQHGSLQGLSVTKRPLWRQESIQSLRNTTEQDVLKAINVNSFVECGINLFSESMSKSDLSQEFEAFFQ

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	HOUSE MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	HOMO SAPIENS

Entity 3 Entity 3 polymer

Description description	NLR FAMILY CARD DOMAIN-CONTAINING PROTEIN 4
Molecular weight formula_weight	50611.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QGKSLYINSENIPDYLFDFFEYLPNCASALDFVKLDFYERATESQDKAEENVPGVHTEGPSETYIPPRAVSLFFNWKQEFKTLEVTLRDINKLNKQDIKYLGKIFSSATNLRLHIKRCAAMAGRLSSVLRTCKNMHTLMVEASPLTTDDEQYITSVTGLQNLSIHRLHTQQLPGGLIDSLGNLKNLERLILDDIRMNEEDAKNLAEGLRSLKKMRLLHLTHLSDIGEGMDYIVKSLSEESCDLQEMKLVACCLTANSVKVLAQNLHNLIKLSILDISENYLEKDGNEALQELIGRLGVLGELTTLMLPWCWDVHTSLPKLLKQLEGTPGLAKLGLKNWRLRDEEIKSLGEFLEMNPLRDLQQLDLAGHCVSSDGWLYFMNVFENLKQLVFFDFSTEEFLPDAALVRKLSQVLSKLTLLQEVKLTGWEFDDYDISAIKGTFKLVTA

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	HOUSE MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	HOMO SAPIENS

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	40.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	40.00 Å
Resolution测定方法 resolution_method	CROSS-COMMON LINES
颗粒数 num_particles	50

fit	/app/data/saxs_computation/aj/5aj2/5aj2.fit
pddf	/app/data/pr_computation/aj/5aj2/5aj2.pr.out
profile	/app/data/saxs_computation/aj/5aj2/5aj2.dat

Cryo electron tomography of the Naip5-Nlrc4 inflammasome

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

NLR FAMILY CARD DOMAIN-CONTAINING PROTEIN 4

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)