[English] 日本語
Yorodumi
- EMDB-0476: Cryo-EM structure of NLRP3 bound to NEK7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0476
TitleCryo-EM structure of NLRP3 bound to NEK7
Map data
Sample
  • Complex: NL3-NEK7
    • Complex: NLRP3
      • Protein or peptide: Isoform 2 of NACHT, LRR and PYD domains-containing protein 3
    • Complex: NEK7
      • Protein or peptide: Interferon-induced, double-stranded RNA-activated protein kinase,Serine/threonine-protein kinase Nek7
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsInflammasome / Activator / Biological process Immunity / Inflammatory response / Innate immunity / Transcription / Transcription regulation Ligand / ATP binding / Nucleotide binding / IMMUNE SYSTEM
Function / homology
Function and homology information


NEK6-subfamily protein kinase / Inhibition of PKR / regulation of NLRP3 inflammasome complex assembly / detection of biotic stimulus / molecular sensor activity / eukaryotic translation initiation factor 2alpha kinase activity / response to interferon-alpha / phosphatidylinositol phosphate binding / negative regulation of osteoblast proliferation / positive regulation of T-helper 2 cell differentiation ...NEK6-subfamily protein kinase / Inhibition of PKR / regulation of NLRP3 inflammasome complex assembly / detection of biotic stimulus / molecular sensor activity / eukaryotic translation initiation factor 2alpha kinase activity / response to interferon-alpha / phosphatidylinositol phosphate binding / negative regulation of osteoblast proliferation / positive regulation of T-helper 2 cell differentiation / Activation of NIMA Kinases NEK9, NEK6, NEK7 / positive regulation of T-helper 2 cell cytokine production / regulation of hematopoietic progenitor cell differentiation / interphase microtubule organizing center / positive regulation of stress-activated MAPK cascade / positive regulation of type 2 immune response / NLRP3 inflammasome complex assembly / NLRP3 inflammasome complex / Nuclear Pore Complex (NPC) Disassembly / protein phosphatase regulator activity / peptidoglycan binding / cysteine-type endopeptidase activator activity / SUMOylation of immune response proteins / osmosensory signaling pathway / regulation of hematopoietic stem cell proliferation / phosphatidylinositol-4-phosphate binding / cellular response to potassium ion / negative regulation of non-canonical NF-kappaB signal transduction / regulation of hematopoietic stem cell differentiation / pattern recognition receptor signaling pathway / regulation of translational initiation / negative regulation of interleukin-1 beta production / negative regulation of viral genome replication / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of interleukin-4 production / pyroptotic inflammatory response / negative regulation of acute inflammatory response / positive regulation of telomere maintenance / microtubule organizing center / The NLRP3 inflammasome / endoplasmic reticulum unfolded protein response / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / spindle assembly / signaling adaptor activity / antiviral innate immune response / EML4 and NUDC in mitotic spindle formation / regulation of mitotic cell cycle / molecular function activator activity / cellular response to amino acid starvation / positive regulation of cytokine production / protein maturation / positive regulation of interleukin-1 beta production / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / molecular condensate scaffold activity / defense response / positive regulation of non-canonical NF-kappaB signal transduction / : / Cytoprotection by HMOX1 / ADP binding / protein homooligomerization / PKR-mediated signaling / cellular response to virus / Evasion by RSV of host interferon responses / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / negative regulation of inflammatory response / ISG15 antiviral mechanism / response to virus / Metalloprotease DUBs / spindle pole / positive regulation of inflammatory response / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / kinase activity / double-stranded RNA binding / protein autophosphorylation / cellular response to lipopolysaccharide / regulation of inflammatory response / protein-macromolecule adaptor activity / defense response to virus / sequence-specific DNA binding / DNA-binding transcription factor binding / molecular adaptor activity / microtubule / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of MAPK cascade / negative regulation of translation / ribosome / translation / inflammatory response / Golgi membrane / negative regulation of cell population proliferation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / centrosome
Similarity search - Function
EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / NACHT-associated domain / Fish-specific NACHT associated domain / Fish-specific NACHT associated domain / : / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain ...EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / NACHT-associated domain / Fish-specific NACHT associated domain / Fish-specific NACHT associated domain / : / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Interferon-induced, double-stranded RNA-activated protein kinase / Serine/threonine-protein kinase Nek7 / NACHT, LRR and PYD domains-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSharif H / Wang L / Wu H
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R01 Al124491 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1DP1 HD087988 United States
CitationJournal: Nature / Year: 2019
Title: Structural mechanism for NEK7-licensed activation of NLRP3 inflammasome.
Authors: Humayun Sharif / Li Wang / Wei Li Wang / Venkat Giri Magupalli / Liudmila Andreeva / Qi Qiao / Arthur V Hauenstein / Zhaolong Wu / Gabriel Núñez / Youdong Mao / Hao Wu /
Abstract: The NLRP3 inflammasome can be activated by stimuli that include nigericin, uric acid crystals, amyloid-β fibrils and extracellular ATP. The mitotic kinase NEK7 licenses the assembly and activation ...The NLRP3 inflammasome can be activated by stimuli that include nigericin, uric acid crystals, amyloid-β fibrils and extracellular ATP. The mitotic kinase NEK7 licenses the assembly and activation of the NLRP3 inflammasome in interphase. Here we report a cryo-electron microscopy structure of inactive human NLRP3 in complex with NEK7, at a resolution of 3.8 Å. The earring-shaped NLRP3 consists of curved leucine-rich-repeat and globular NACHT domains, and the C-terminal lobe of NEK7 nestles against both NLRP3 domains. Structural recognition between NLRP3 and NEK7 is confirmed by mutagenesis both in vitro and in cells. Modelling of an active NLRP3-NEK7 conformation based on the NLRC4 inflammasome predicts an additional contact between an NLRP3-bound NEK7 and a neighbouring NLRP3. Mutations to this interface abolish the ability of NEK7 or NLRP3 to rescue NLRP3 activation in NEK7-knockout or NLRP3-knockout cells. These data suggest that NEK7 bridges adjacent NLRP3 subunits with bipartite interactions to mediate the activation of the NLRP3 inflammasome.
History
DepositionJan 18, 2019-
Header (metadata) releaseJun 19, 2019-
Map releaseJun 19, 2019-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00926
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.00926
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6npy
  • Surface level: 0.00926
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0476.png

Downloads & links

-
Map

FileDownload / File: emd_0476.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 240 pix.
= 201.6 Å		0.84 Å/pix.
x 240 pix.
= 201.6 Å		0.84 Å/pix.
x 240 pix.
= 201.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00926 / Movie #1: 0.00926
Minimum - Maximum-0.022114016 - 0.04407179
Average (Standard dev.)0.00021862681 (±0.001666536)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 201.59999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z201.600201.600201.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0220.0440.000

-
Supplemental data

-
Sample components

-
Entire : NL3-NEK7

EntireName: NL3-NEK7
Components
  • Complex: NL3-NEK7
    • Complex: NLRP3
      • Protein or peptide: Isoform 2 of NACHT, LRR and PYD domains-containing protein 3
    • Complex: NEK7
      • Protein or peptide: Interferon-induced, double-stranded RNA-activated protein kinase,Serine/threonine-protein kinase Nek7
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

-
Supramolecule #1: NL3-NEK7

SupramoleculeName: NL3-NEK7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1

-
Supramolecule #2: NLRP3

SupramoleculeName: NLRP3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Details: The sequence is according to NP_001230062.1 isoform which lacks 2 residues from N-terminus. Total residues are 1034aa as compared to 1036 in UNP Q96P20. There are mutations in YRKKYRKY ...Details: The sequence is according to NP_001230062.1 isoform which lacks 2 residues from N-terminus. Total residues are 1034aa as compared to 1036 in UNP Q96P20. There are mutations in YRKKYRKY instead its IYCAKYRAY mutations were intended to introduce so that the class of MBP and NLRP3 is avoided
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: NEK7

SupramoleculeName: NEK7 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Interferon-induced, double-stranded RNA-activated protein kinase,...

MacromoleculeName: Interferon-induced, double-stranded RNA-activated protein kinase,Serine/threonine-protein kinase Nek7
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.01515 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSTDKRFGMD FRIEKKIGRG QFSEVYRAAC RLDGKTVALK KVQIFDLMDA KARADCIKEI DLLAQLNHPN VIKYYVCFIT GNELNIVLE LADAGDLSRM IKHFKKQKRL IPERTVWKYF VQLCSALEHM HSRRVMHRDI KPANVFITAT GVVKLGDLGL G RFFSSKTT ...String:
GSTDKRFGMD FRIEKKIGRG QFSEVYRAAC RLDGKTVALK KVQIFDLMDA KARADCIKEI DLLAQLNHPN VIKYYVCFIT GNELNIVLE LADAGDLSRM IKHFKKQKRL IPERTVWKYF VQLCSALEHM HSRRVMHRDI KPANVFITAT GVVKLGDLGL G RFFSSKTT AAHSLVGTPY YMSPERIHEN GYNFKSDIWS LGCLLYEMAA LQSPFYGDKM NLYSLCKKIE QCDYPPLPSD HY SEELRQL VNMCINPDPE KRPDVTYVYD VAKRMHACTA SS

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

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

MacromoleculeName: Isoform 2 of NACHT, LRR and PYD domains-containing protein 3
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 117.890984 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASTRCKLAR YLEDLEDVDL KKFKMHLEDY PPQKGCIPLP RGQTEKADHV DLATLMIDFN GEEKAWAMAV WIFAAINRRD LYEKAKRDE PKWGSDNARV SNPTVICQED SIEEEWMGLL EYLSRISICK MKKIYCAKYR AYVRSRFQCI EDRNARLGES V SLNKRYTR ...String:
MASTRCKLAR YLEDLEDVDL KKFKMHLEDY PPQKGCIPLP RGQTEKADHV DLATLMIDFN GEEKAWAMAV WIFAAINRRD LYEKAKRDE PKWGSDNARV SNPTVICQED SIEEEWMGLL EYLSRISICK MKKIYCAKYR AYVRSRFQCI EDRNARLGES V SLNKRYTR LRLIKEHRSQ QEREQELLAI GKTKTCESPV SPIKMELLFD PDDEHSEPVH TVVFQGAAGI GKTILARKMM LD WASGTLY QDRFDYLFYI HCREVSLVTQ RSLGDLIMSC CPDPNPPIHK IVRKPSRILF LMDGFDELQG AFDEHIGPLC TDW QKAERG DILLSSLIRK KLLPEASLLI TTRPVALEKL QHLLDHPRHV EILGFSEAKR KEYFFKYFSD EAQARAAFSL IQEN EVLFT MCFIPLVCWI VCTGLKQQME SGKSLAQTSK TTTAVYVFFL SSLLQPRGGS QEHGLCAHLW GLCSLAADGI WNQKI LFEE SDLRNHGLQK ADVSAFLRMN LFQKEVDCEK FYSFIHMTFQ EFFAAMYYLL EEEKEGRTNV PGSRLKLPSR DVTVLL ENY GKFEKGYLIF VVRFLFGLVN QERTSYLEKK LSCKISQQIR LELLKWIEVK AKAKKLQIQP SQLELFYCLY EMQEEDF VQ RAMDYFPKIE INLSTRMDHM VSSFCIENCH RVESLSLGFL HNMPKEEEEE EKEGRHLDMV QCVLPSSSHA ACSHGLVN S HLTSSFCRGL FSVLSTSQSL TELDLSDNSL GDPGMRVLCE TLQHPGCNIR RLWLGRCGLS HECCFDISLV LSSNQKLVE LDLSDNALGD FGIRLLCVGL KHLLCNLKKL WLVSCCLTSA CCQDLASVLS TSHSLTRLYV GENALGDSGV AILCEKAKNP QCNLQKLGL VNSGLTSVCC SALSSVLSTN QNLTHLYLRG NTLGDKGIKL LCEGLLHPDC KLQVLELDNC NLTSHCCWDL S TLLTSSQS LRKLSLGNND LGDLGVMMFC EVLKQQSCLL QNLGLSEMYF NYETKSALET LQEEKPELTV VFEPSW

UniProtKB: NACHT, LRR and PYD domains-containing protein 3

-
Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.1 K / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeTFS TITAN THEMIS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 108771
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6npy:
Cryo-EM structure of NLRP3 bound to NEK7

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more