[English] 日本語
Yorodumi
- EMDB-28596: CryoEM Structure of NLRP3 NACHT domain in complex with G2394 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28596
TitleCryoEM Structure of NLRP3 NACHT domain in complex with G2394
Map data
Sample
  • Complex: NLRP3 NACHT domain
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 3
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: (6S,8R)-N-[(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)carbamoyl]-6-(methylamino)-6,7-dihydro-5H-pyrazolo[5,1-b][1,3]oxazine-3-sulfonamide
KeywordsNLRP3 / NACHT / inhibitor / HYDROLASE
Function / homology
Function and homology information


detection of biotic stimulus / molecular sensor activity / phosphatidylinositol phosphate binding / positive regulation of T-helper 2 cell differentiation / NLRP3 inflammasome complex assembly / positive regulation of T-helper 2 cell cytokine production / interphase microtubule organizing center / positive regulation of type 2 immune response / NLRP3 inflammasome complex / cysteine-type endopeptidase activator activity ...detection of biotic stimulus / molecular sensor activity / phosphatidylinositol phosphate binding / positive regulation of T-helper 2 cell differentiation / NLRP3 inflammasome complex assembly / positive regulation of T-helper 2 cell cytokine production / interphase microtubule organizing center / positive regulation of type 2 immune response / NLRP3 inflammasome complex / cysteine-type endopeptidase activator activity / osmosensory signaling pathway / peptidoglycan binding / 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 / pyroptotic inflammatory response / positive regulation of interleukin-4 production / microtubule organizing center / negative regulation of acute inflammatory response / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / signaling adaptor activity / protein maturation / positive regulation of interleukin-1 beta production / molecular condensate scaffold activity / defense response / positive regulation of non-canonical NF-kappaB signal transduction / Cytoprotection by HMOX1 / ADP binding / protein homooligomerization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to virus / negative regulation of inflammatory response / Metalloprotease DUBs / positive regulation of inflammatory response / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / regulation of inflammatory response / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / molecular adaptor activity / sequence-specific DNA binding / inflammatory response / Golgi membrane / innate immune response / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / extracellular region / ATP binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm
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. ...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 / PAAD/DAPIN/Pyrin domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / 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: 3.5 Å
AuthorsMurray JM / Johnson MC
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: J Med Chem / Year: 2022
Title: Overcoming Preclinical Safety Obstacles to Discover ()--((1,2,3,5,6,7-Hexahydro--indacen-4-yl)carbamoyl)-6-(methylamino)-6,7-dihydro-5-pyrazolo[5,1-][1,3]oxazine-3-sulfonamide (GDC-2394): A ...Title: Overcoming Preclinical Safety Obstacles to Discover ()--((1,2,3,5,6,7-Hexahydro--indacen-4-yl)carbamoyl)-6-(methylamino)-6,7-dihydro-5-pyrazolo[5,1-][1,3]oxazine-3-sulfonamide (GDC-2394): A Potent and Selective NLRP3 Inhibitor.
Authors: Christopher McBride / Lynnie Trzoss / Davide Povero / Milos Lazic / Geza Ambrus-Aikelin / Angelina Santini / Rama Pranadinata / Gretchen Bain / Ryan Stansfield / Jeffrey A Stafford / James ...Authors: Christopher McBride / Lynnie Trzoss / Davide Povero / Milos Lazic / Geza Ambrus-Aikelin / Angelina Santini / Rama Pranadinata / Gretchen Bain / Ryan Stansfield / Jeffrey A Stafford / James Veal / Ryan Takahashi / Justin Ly / Shu Chen / Liling Liu / Marika Nespi / Robert Blake / Arna Katewa / Tracy Kleinheinz / Swathi Sujatha-Bhaskar / Nandhini Ramamoorthi / Jessica Sims / Brent McKenzie / Mark Chen / Mark Ultsch / Matthew Johnson / Jeremy Murray / Claudio Ciferri / Steven T Staben / Michael J Townsend / Craig E Stivala /
Abstract: Inappropriate activation of the NLRP3 inflammasome has been implicated in multiple inflammatory and autoimmune diseases. Herein, we aimed to develop novel NLRP3 inhibitors that could minimize the ...Inappropriate activation of the NLRP3 inflammasome has been implicated in multiple inflammatory and autoimmune diseases. Herein, we aimed to develop novel NLRP3 inhibitors that could minimize the risk of drug-induced liver injury. Lipophilic ligand efficiency was used as a guiding metric to identify a series of 6,7-dihydro-5H-pyrazolo[5,1-][1,3]oxazinesulfonylureas. A leading compound from this series was advanced into safety studies in cynomolgus monkeys, and renal toxicity, due to compound precipitation, was observed. To overcome this obstacle, we focused on improving the solubility of our compounds, specifically by introducing basic amine substituents into the scaffold. This led to the identification of GDC-2394, a potent and selective NLRP3 inhibitor, with an in vitro and in vivo safety profile suitable for advancement into human clinical trials.
History
DepositionOct 17, 2022-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28596.png

Downloads & links

-
Map

FileDownload / File: emd_28596.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.11 Å/pix.
x 78 pix.
= 86.525 Å		1.11 Å/pix.
x 84 pix.
= 93.181 Å		1.11 Å/pix.
x 93 pix.
= 103.165 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.1093 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.8268428 - 4.4969797
Average (Standard dev.)-0.000000000010355 (±0.31531385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin126113100
Dimensions849378
Spacing788493
CellA: 86.5254 Å / B: 93.1812 Å / C: 103.1649 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_28596_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_28596_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : NLRP3 NACHT domain

EntireName: NLRP3 NACHT domain
Components
  • Complex: NLRP3 NACHT domain
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 3
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: (6S,8R)-N-[(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)carbamoyl]-6-(methylamino)-6,7-dihydro-5H-pyrazolo[5,1-b][1,3]oxazine-3-sulfonamide

-
Supramolecule #1: NLRP3 NACHT domain

SupramoleculeName: NLRP3 NACHT domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: NACHT domain only
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120 KDa

-
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.38034 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: KDYRKKYRKY VRSRFQCIED RNARLGESVS LNKRYTRLRL IKEHRSQQER EQELLAIGKT KTCESPVSPI KMELLFDPDD EHSEPVHTV VFQGAAGIGK TILARKMMLD WASGTLYQDR FDYLFYIHCR EVSLVTQRSL GDLIMSCCPD PNPPIHKIVR K PSRILFLM ...String:
KDYRKKYRKY VRSRFQCIED RNARLGESVS LNKRYTRLRL IKEHRSQQER EQELLAIGKT KTCESPVSPI KMELLFDPDD EHSEPVHTV VFQGAAGIGK TILARKMMLD WASGTLYQDR FDYLFYIHCR EVSLVTQRSL GDLIMSCCPD PNPPIHKIVR K PSRILFLM DGFDELQGAF DEHIGPLCTD WQKAERGDIL LSSLIRKKLL PEASLLITTR PVALEKLQHL LDHPRHVEIL GF SEAKRKE YFFKYFSDEA QARAAFSLIQ ENEVLFTMCF IPLVCWIVCT GLKQQMESGK SLAQTSKTTT AVYVFFLSSL LQP RGGSQE HGLCAHLWGL CSLAADGIWN QKILFEESDL RNHGLQKADV SAFLRMNLFQ KEVDCEKFYS FIHMTFQEFF AAMY YLLEE EKEGRTNVPG SRLKLPSRDV TVLLENYGKF EKGYLIFVVR FLFGLVNQER TSYLEKKLSC KISQQIRLEL LKWIE VKAK AKKLQIQPSQ LELFYCLYEM QEEDFVQRAM DYFPKIEINL STRMDHMVSS FCIENCHRV

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

-
Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
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

-
Macromolecule #4: (6S,8R)-N-[(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)carbamoyl]-6-(me...

MacromoleculeName: (6S,8R)-N-[(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)carbamoyl]-6-(methylamino)-6,7-dihydro-5H-pyrazolo[5,1-b][1,3]oxazine-3-sulfonamide
type: ligand / ID: 4 / Number of copies: 1 / Formula: WTN
Molecular weightTheoretical: 431.509 Da
Chemical component information

ChemComp-WTN:
(6S,8R)-N-[(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)carbamoyl]-6-(methylamino)-6,7-dihydro-5H-pyrazolo[5,1-b][1,3]oxazine-3-sulfonamide

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
0.15 MNaClsodium chloride
20.0 mMTris-HClTris buffer
10.0 %glycerolgycerol
1.0 mMTCEP(tris(2-carboxyethyl)phosphine)

Details: 0.15M NaCl, 20mM Tris pH 7.5, 10% glycerol, 1mM TCEP, 2.5mM ATP, 2mM MgCl2.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 25 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Pressure: 0.007 kPa
Details: Holey gold grids (UltrAuFoil 25 nm R 1.2/1.3) were glow discharged for 20 seconds using a Solarus plasma cleaner (Gatan, Pleasanton, CA, USA), and grids were blotted and plunge frozen in ...Details: Holey gold grids (UltrAuFoil 25 nm R 1.2/1.3) were glow discharged for 20 seconds using a Solarus plasma cleaner (Gatan, Pleasanton, CA, USA), and grids were blotted and plunge frozen in liquid ethane using a Vitrobot (ThermoFisher Scientific, Waltham, MA), operating at 4C, 100 relative humidity, blot force 7, and with a 4 second blot time.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III
Detailsmono disperse

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 3.0 sec. / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1054244
Startup modelType of model: OTHER / Details: cisTEM ab initio
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 231263
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cisTEM (ver. 2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 2 / Software - Name: RELION (ver. 3.1) / Details: 94,527 monomers, 68,368 dimers
FSC plot (resolution estimation)

-
Atomic model buiding 1

SoftwareName: Coot
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8etr:
CryoEM Structure of NLRP3 NACHT domain in complex with G2394

+
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