[English] 日本語
Yorodumi
- EMDB-75245: Cryo-tomogram of a solid-like NLRP3 inflammasome condensate at th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-75245
TitleCryo-tomogram of a solid-like NLRP3 inflammasome condensate at the MTOC
Map dataCryo-tomogram reveals solid-like NLRP3 inflammasome condensate at the MTOC following LPS and 10-min nigericin treatment
Sample
  • Cell: Differentiated human THP-1 cells treated with LPS, followed by 10 min of nigericin
KeywordsNLRP3 inflammasome / MTOC / pyroptosis / IMMUNE SYSTEM
Biological speciesHuman THP-1 cells (human)
Methodelectron tomography / cryo EM
AuthorsWang J / Wu M / Xiao L / Du G / Chen M / Magupalli VG / Dahlberg PD / Wu H / Jensen GJ
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127401 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR079766 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM150905 United States
Chan Zuckerberg Initiative2021-234593 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI177778 United States
CitationJournal: To Be Published
Title: Human NLRP3 inflammasome activation leads to formation of condensate at the microtubule organizing center
Authors: Wang J / Man W / Xiao L / Du G / Chen M / Magupalli VG / Dahlberg PD / Wu H / Jensen GJ
History
DepositionJan 23, 2026-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_75245.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-tomogram reveals solid-like NLRP3 inflammasome condensate at the MTOC following LPS and 10-min nigericin treatment
Voxel sizeX=Y=Z: 13.86 Å
Density
Minimum - Maximum-0.9666121 - 1.8001552
Average (Standard dev.)0.6254006 (±0.18068558)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions14401024350
Spacing10241440350
CellA: 14192.641 Å / B: 19958.4 Å / C: 4851.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Differentiated human THP-1 cells treated with LPS, followed by 10...

EntireName: Differentiated human THP-1 cells treated with LPS, followed by 10 min of nigericin
Components
  • Cell: Differentiated human THP-1 cells treated with LPS, followed by 10 min of nigericin

-
Supramolecule #1: Differentiated human THP-1 cells treated with LPS, followed by 10...

SupramoleculeName: Differentiated human THP-1 cells treated with LPS, followed by 10 min of nigericin
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Human THP-1 cells (human)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
Details: Roswell Park Memorial Institute (RPMI) Medium supplemented with heat inactivated 10% FBS, 10mM HEPES, 1mM sodium pyruvate, 0.05mM 2-mercaptoethanol, 100units/mL of penicillin and streptomycin
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1000
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.3 / Focused ion beam - Duration: 300 / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 3000 / Focused ion beam - Final thickness: 180
Focused ion beam - Details: Cryo-FIB milling was guided by fluorescence. The value given for _em_focused_ion_beam.instrument is Aquilos2 Dual-Beam system with customized integrated ENZEL fluorescent ...Focused ion beam - Details: Cryo-FIB milling was guided by fluorescence. The value given for _em_focused_ion_beam.instrument is Aquilos2 Dual-Beam system with customized integrated ENZEL fluorescent light microscope. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 160.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 42
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION

+
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