[English] 日本語
Yorodumi
- EMDB-14713: Human NLRP3-deltaPYD hexamer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14713
TitleHuman NLRP3-deltaPYD hexamer
Map dataMap sharpened by DeepEMhancer from two halfmaps
Sample
  • Complex: NLRP3 hexamer
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 3
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Function / homology
Function and homology information


small molecule sensor activity / detection of biotic stimulus / phosphatidylinositol phosphate binding / cysteine-type endopeptidase activator activity / positive regulation of T-helper 2 cell differentiation / NLRP3 inflammasome complex assembly / interphase microtubule organizing center / positive regulation of T-helper 2 cell cytokine production / positive regulation of type 2 immune response / NLRP3 inflammasome complex ...small molecule sensor activity / detection of biotic stimulus / phosphatidylinositol phosphate binding / cysteine-type endopeptidase activator activity / positive regulation of T-helper 2 cell differentiation / NLRP3 inflammasome complex assembly / interphase microtubule organizing center / positive regulation of T-helper 2 cell cytokine production / positive regulation of type 2 immune response / NLRP3 inflammasome complex / peptidoglycan binding / osmosensory signaling pathway / phosphatidylinositol-4-phosphate binding / negative regulation of non-canonical NF-kappaB signal transduction / pattern recognition receptor signaling pathway / negative regulation of interleukin-1 beta production / microtubule organizing center / negative regulation of NF-kappaB transcription factor activity / positive regulation of interleukin-4 production / pyroptotic inflammatory response / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of acute inflammatory response / The NLRP3 inflammasome / protein maturation / Purinergic signaling in leishmaniasis infection / signaling adaptor activity / molecular condensate scaffold activity / positive regulation of interleukin-1 beta production / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein homooligomerization / Cytoprotection by HMOX1 / Metalloprotease DUBs / ADP binding / cellular response to virus / defense response / negative regulation of inflammatory response / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / SARS-CoV-1 activates/modulates innate immune responses / protein-macromolecule adaptor activity / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / DNA-binding transcription factor binding / sequence-specific DNA binding / molecular adaptor activity / inflammatory response / Golgi membrane / innate immune response / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / signal transduction / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / ATP binding / membrane / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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 / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin 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 / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NACHT, LRR and PYD domains-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsRaisch T / Machtens DA / Bresch IB / Eberhage J / Prumbaum D / Reubold TF / Raunser S / Eschenburg S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of the NEK7-independent NLRP3 inflammasome
Authors: Raisch T / Machtens DA / Bresch IB / Eberhage J / Prumbaum D / Reubold TF / Raunser S / Eschenburg S
History
DepositionApr 4, 2022-
Header (metadata) releaseMay 18, 2022-
Map releaseMay 18, 2022-
UpdateMay 18, 2022-
Current statusMay 18, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14713.png

Downloads & links

-
Map

FileDownload / File: emd_14713.map.gz / Format: CCP4 / Size: 391 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap sharpened by DeepEMhancer from two halfmaps
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 468 pix.
= 318.24 Å		0.68 Å/pix.
x 468 pix.
= 318.24 Å		0.68 Å/pix.
x 468 pix.
= 318.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.01944729 - 1.6393752
Average (Standard dev.)0.0019758798 (±0.026529612)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions468468468
Spacing468468468
CellA=B=C: 318.24 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Additional map sharpened by Phenix

Fileemd_14713_additional_1.map
AnnotationAdditional map sharpened by Phenix
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1 from Sphire

Fileemd_14713_half_map_1.map
AnnotationHalf map 1 from Sphire
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 from Sphire

Fileemd_14713_half_map_2.map
AnnotationHalf map 2 from Sphire
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : NLRP3 hexamer

EntireName: NLRP3 hexamer
Components
  • Complex: NLRP3 hexamer
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 3
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

-
Supramolecule #1: NLRP3 hexamer

SupramoleculeName: NLRP3 hexamer / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

-
Macromolecule #1: NACHT, LRR and PYD domains-containing protein 3

MacromoleculeName: NACHT, LRR and PYD domains-containing protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 105.169375 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRISICKMKK DYRKKYRKYV RSRFQCIEDR NARLGESVSL NKRYTRLRLI KEHRSQQERE QELLAIGKTK TCESPVSPIK MELLFDPDD EHSEPVHTVV FQGAAGIGKT ILARKMMLDW ASGTLYQDRF DYLFYIHCRE VSLVTQRSLG DLIMSCCPDP N PPIHKIVR ...String:
MRISICKMKK DYRKKYRKYV RSRFQCIEDR NARLGESVSL NKRYTRLRLI KEHRSQQERE QELLAIGKTK TCESPVSPIK MELLFDPDD EHSEPVHTVV FQGAAGIGKT ILARKMMLDW ASGTLYQDRF DYLFYIHCRE VSLVTQRSLG DLIMSCCPDP N PPIHKIVR KPSRILFLMD GFDELQGAFD EHIGPLCTDW QKAERGDILL SSLIRKKLLP EASLLITTRP VALEKLQHLL DH PRHVEIL GFSEAKRKEY FFKYFSDEAQ ARAAFSLIQE NEVLFTMCFI PLVCWIVCTG LKQQMESGKS LAQTSKTTTA VYV FFLSSL LQPRGGSQEH GLCAHLWGLC SLAADGIWNQ KILFEESDLR NHGLQKADVS AFLRMNLFQK EVDCEKFYSF IHMT FQEFF AAMYYLLEEE KEGRTNVPGS RLKLPSRDVT VLLENYGKFE KGYLIFVVRF LFGLVNQERT SYLEKKLSCK ISQQI RLEL LKWIEVKAKA KKLQIQPSQL ELFYCLYEMQ EEDFVQRAMD YFPKIEINLS TRMDHMVSSF CIENCHRVES LSLGFL HNM PKEEEEEEKE GRHLDMVQCV LPSSSHAACS HGLVNSHLTS SFCRGLFSVL STSQSLTELD LSDNSLGDPG MRVLCET LQ HPGCNIRRLW LGRCGLSHEC CFDISLVLSS NQKLVELDLS DNALGDFGIR LLCVGLKHLL CNLKKLWLVS CCLTSACC Q DLASVLSTSH SLTRLYVGEN ALGDSGVAIL CEKAKNPQCN LQKLGLVNSG LTSVCCSALS SVLSTNQNLT HLYLRGNTL GDKGIKLLCE GLLHPDCKLQ VLELDNCNLT SHCCWDLSTL LTSSQSLRKL SLGNNDLGDL GVMMFCEVLK QQSCLLQNLG LSEMYFNYE TKSALETLQE EKPELTVVFE PSWGSGGDYK DDDDK

-
Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / 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

Concentration0.075 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Cs-corrected microscope
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 99.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 871597
CTF correctionSoftware - Name: CTFFIND
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 124523
Initial angle assignmentType: OTHER / Software - Name: SPHIRE
Final angle assignmentType: OTHER / Software - Name: SPHIRE

+
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://pdbjlvh1.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