SAXSdb — 4n1k

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

NACHT, LRR and PYD domains-containing protein 14

Homo sapiens

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–100 Chain B； UniProt 1–100	Fragment：UNP residues 1-100 Mutation：D86V	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2 M Cesium chloride and 2.2 M Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.00 Å R-free 0.268
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–100 Chain D； UniProt 1–100	Fragment：UNP residues 1-100 Mutation：D86V	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2 M Cesium chloride and 2.2 M Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.00 Å R-free 0.268
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–100 Chain B； UniProt 1–100 Chain C； UniProt 1–100 Chain D； UniProt 1–100	Fragment：UNP residues 1-100 Mutation：D86V	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2 M Cesium chloride and 2.2 M Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.00 Å R-free 0.268

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 4N1K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4N1J Crystal structures of NLRP14 pyrin domain reveal a conformational switch mechanism, regulating its molecular interactions Deposited 2013-10-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–100（100 aa） Fragment：UNP residues 1-100 Chain B 1–100（100 aa） Fragment：UNP residues 1-100	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 2.6 M Ammonium sulfate and 2% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.255
4N1J Crystal structures of NLRP14 pyrin domain reveal a conformational switch mechanism, regulating its molecular interactions Deposited 2013-10-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–100（100 aa） Fragment：UNP residues 1-100 Chain D 1–100（100 aa） Fragment：UNP residues 1-100	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 2.6 M Ammonium sulfate and 2% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.255
4N1J Crystal structures of NLRP14 pyrin domain reveal a conformational switch mechanism, regulating its molecular interactions Deposited 2013-10-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–100（100 aa） Fragment：UNP residues 1-100 Chain B 1–100（100 aa） Fragment：UNP residues 1-100 Chain C 1–100（100 aa） Fragment：UNP residues 1-100 Chain D 1–100（100 aa） Fragment：UNP residues 1-100	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)	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 2.6 M Ammonium sulfate and 2% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.255
4N1L Crystal structures of NLRP14 pyrin domain reveal a conformational switch mechanism, regulating its molecular interactions Deposited 2013-10-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–100（100 aa） Fragment：UNP residues 1-100	Mutation：L84R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2 M Ammonium acetate and 2.2 M Ammonium sulfate , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.99 Å R-free 0.222
9LN6 Structure of human NLRP14-UHRF1 complex Deposited 2025-01-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1093（1093 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.49 Å

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NAL14_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–103； UniProt 1–100 Author chain B； PDBConstruct 4–103； UniProt 1–100 Author chain C； PDBConstruct 4–103； UniProt 1–100 Author chain D； PDBConstruct 4–103； UniProt 1–100

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	4n1k
Deposition date deposition_date	2013-10-04
Structure title title	Crystal structures of NLRP14 pyrin domain reveal a conformational switch mechanism, regulating its molecular interactions
Keywords keywords	death domain fold, pyrin domain, NOD-like receptor, signaling protein, protein binding, spermatogenesis, innate immunity; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	24.61 Å
Radius of gyration Rg (electron density) rg_electron	23.60 Å
Forward intensity I(0) i0	27402700.00
Molecular weight molecular_weight	42540.0 kDa
Excluded volume excluded_volume	54359 Å³
Envelope volume envelope_volume	67592 Å³
Hydration-shell volume shell_volume	24531 Å³
Envelope diameter envelope_diameter	87.9 Å
Shell Rg shell_rg	30.03 Å
Envelope Rg envelope_rg	23.86 Å
Shape Rg shape_rg	23.60 Å
Total Rg total_rg	24.44 Å
Total atoms total_atoms	3000
Residues n_residues	360
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	82.5 Å
Rg (real space) rg_real	24.63 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	2.7400e+07
I(0) uncertainty (real space) i0_real_error	4.2100e+05
Rg (reciprocal space) rg_reciprocal	24.63 Å
I(0) (reciprocal space) i0_reciprocal	27400000.0000
Solution quality estimate total_estimate	0.8007
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.394
Kurtosis Kurtosis kurtosis	-0.196
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7210000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4n1kA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	4n1kB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	4n1kC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	4n1kD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

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8. Citations (1)

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Unit-cell length a length_a	89.210 Å
Unit-cell length b length_b	89.210 Å
Unit-cell length c length_c	106.571 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	32.000 Å
R factor r_factor	0.2162
R_work r_work	0.2138
R_free r_free	0.2680

Description description	NACHT, LRR and PYD domains-containing protein 14
Molecular weight formula_weight	12249.0 kDa
Mutation mutation	D86V
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3013

Crystal structures of NLRP14 pyrin domain reveal a conformational switch mechanism, regulating its molecular interactions

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

NACHT, LRR and PYD domains-containing protein 14

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

fit	/app/data/saxs_computation/n1/4n1k/4n1k.fit
pddf	/app/data/pr_computation/n1/4n1k/4n1k.pr.out
profile	/app/data/saxs_computation/n1/4n1k/4n1k.dat