SAXSdb — 6npy

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

Interferon-induced, double-stranded RNA-activated protein kinase,Serine/threonine-protein kinase Nek7

Homo sapiens

UniProt P19525

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Isoform 2 of NACHT, LRR and PYD domains-containing protein 3 × 1 （Q96P20） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	E2AK2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 4–10； UniProt 260–266

Interferon-induced, double-stranded RNA-activated protein kinase,Serine/threonine-protein kinase Nek7

Homo sapiens

UniProt Q8TDX7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Isoform 2 of NACHT, LRR and PYD domains-containing protein 3 × 1 （Q96P20） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NEK7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 11–279； UniProt 34–302

Isoform 2 of NACHT, LRR and PYD domains-containing protein 3

Homo sapiens

UniProt Q96P20

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Interferon-induced, double-stranded RNA-activated protein kinase,Serine/threonine-protein kinase Nek7 × 1 （P19525,Q8TDX7） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NLRP3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–1034； UniProt 3–1036

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	6npy
Deposition date deposition_date	2019-01-18
Structure title title	Cryo-EM structure of NLRP3 bound to NEK7
Keywords keywords	;Inflammasome, Activator, Biological process Immunity, Inflammatory response, Innate immunity, Transcription, Transcription regulation Ligand, ATP binding, Nucleotide binding, IMMUNE SYSTEM ;; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6npy__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6npy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6npy__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.17 Å
Rg (electron density)	33.50 Å
Total Rg	34.13 Å
Atom count	8017
Residues	1001
Excluded volume	143780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6npy__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Interferon-induced, double-stranded RNA-activated protein kinase,Serine/threonine-protein kinase Nek7
Molecular weight formula_weight	32015.2 kDa
EC 编号 ec_number	2.7.11.1,2.7.10.2,2.7.11.34
Mutation mutation	L54R,V58K,P59T,K87A,A99V,S100C,E103T,D104G
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	8017

GSTDKRFGMDFRIEKKIGRGQFSEVYRAACRLDGKTVALKKVQIFDLMDAKARADCIKEIDLLAQLNHPNVIKYYVCFITGNELNIVLELADAGDLSRMIKHFKKQKRLIPERTVWKYFVQLCSALEHMHSRRVMHRDIKPANVFITATGVVKLGDLGLGRFFSSKTTAAHSLVGTPYYMSPERIHENGYNFKSDIWSLGCLLYEMAALQSPFYGDKMNLYSLCKKIEQCDYPPLPSDHYSEELRQLVNMCINPDPEKRPDVTYVYDVAKRMHACTASS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Isoform 2 of NACHT, LRR and PYD domains-containing protein 3
Molecular weight formula_weight	117891.0 kDa
EC 编号 ec_number	3.6.4.-
Mutation mutation	D133I, R135C, K136A, K140A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MASTRCKLARYLEDLEDVDLKKFKMHLEDYPPQKGCIPLPRGQTEKADHVDLATLMIDFNGEEKAWAMAVWIFAAINRRDLYEKAKRDEPKWGSDNARVSNPTVICQEDSIEEEWMGLLEYLSRISICKMKKIYCAKYRAYVRSRFQCIEDRNARLGESVSLNKRYTRLRLIKEHRSQQEREQELLAIGKTKTCESPVSPIKMELLFDPDDEHSEPVHTVVFQGAAGIGKTILARKMMLDWASGTLYQDRFDYLFYIHCREVSLVTQRSLGDLIMSCCPDPNPPIHKIVRKPSRILFLMDGFDELQGAFDEHIGPLCTDWQKAERGDILLSSLIRKKLLPEASLLITTRPVALEKLQHLLDHPRHVEILGFSEAKRKEYFFKYFSDEAQARAAFSLIQENEVLFTMCFIPLVCWIVCTGLKQQMESGKSLAQTSKTTTAVYVFFLSSLLQPRGGSQEHGLCAHLWGLCSLAADGIWNQKILFEESDLRNHGLQKADVSAFLRMNLFQKEVDCEKFYSFIHMTFQEFFAAMYYLLEEEKEGRTNVPGSRLKLPSRDVTVLLENYGKFEKGYLIFVVRFLFGLVNQERTSYLEKKLSCKISQQIRLELLKWIEVKAKAKKLQIQPSQLELFYCLYEMQEEDFVQRAMDYFPKIEINLSTRMDHMVSSFCIENCHRVESLSLGFLHNMPKEEEEEEKEGRHLDMVQCVLPSSSHAACSHGLVNSHLTSSFCRGLFSVLSTSQSLTELDLSDNSLGDPGMRVLCETLQHPGCNIRRLWLGRCGLSHECCFDISLVLSSNQKLVELDLSDNALGDFGIRLLCVGLKHLLCNLKKLWLVSCCLTSACCQDLASVLSTSHSLTRLYVGENALGDSGVAILCEKAKNPQCNLQKLGLVNSGLTSVCCSALSSVLSTNQNLTHLYLRGNTLGDKGIKLLCEGLLHPDCKLQVLELDNCNLTSHCCWDLSTLLTSSQSLRKLSLGNNDLGDLGVMMFCEVLKQQSCLLQNLGLSEMYFNYETKSALETLQEEKPELTVVFEPSW

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6npyB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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Resolution resolution	3.800 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	108771

Cryo-EM structure of NLRP3 bound to NEK7

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

Interferon-induced, double-stranded RNA-activated protein kinase,Serine/threonine-protein kinase Nek7

State in the Current Structure

Other States of the Same Protein in the Database

Interferon-induced, double-stranded RNA-activated protein kinase,Serine/threonine-protein kinase Nek7

State in the Current Structure

Other States of the Same Protein in the Database

Isoform 2 of NACHT, LRR and PYD domains-containing protein 3

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6npy__assembly_1__model_1

6npy__assembly_1__model_1 | I(q)

6npy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Cryo-EM structure of NLRP3 bound to NEK7

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

Interferon-induced, double-stranded RNA-activated protein kinase,Serine/threonine-protein kinase Nek7

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Interferon-induced, double-stranded RNA-activated protein kinase,Serine/threonine-protein kinase Nek7

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Isoform 2 of NACHT, LRR and PYD domains-containing protein 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6npy__assembly_1__model_1

6npy__assembly_1__model_1 | I(q)

6npy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)