[English] 日本語
Yorodumi
- PDB-9i7x: Cryo-EM structure of human IL-36gamma in complex with the IL-36R ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9i7x
TitleCryo-EM structure of human IL-36gamma in complex with the IL-36R and IL-1RAcP ectodomains
Components
  • Interleukin-1 receptor accessory protein
  • Interleukin-1 receptor-like 2
  • Interleukin-36 gamma
KeywordsIMMUNE SYSTEM / cytokine / receptor complex / inflammation / IL-1 family
Function / homology
Function and homology information


interleukin-33 receptor activity / interleukin-1, type I, activating receptor activity / Interleukin-33 signaling / Interleukin-36 pathway / interleukin-1 receptor activity / negative regulation of interleukin-1 alpha production / trans-synaptic signaling by trans-synaptic complex / Interleukin-38 signaling / microglial cell activation involved in immune response / Receptor-type tyrosine-protein phosphatases ...interleukin-33 receptor activity / interleukin-1, type I, activating receptor activity / Interleukin-33 signaling / Interleukin-36 pathway / interleukin-1 receptor activity / negative regulation of interleukin-1 alpha production / trans-synaptic signaling by trans-synaptic complex / Interleukin-38 signaling / microglial cell activation involved in immune response / Receptor-type tyrosine-protein phosphatases / negative regulation of interleukin-1-mediated signaling pathway / synaptic membrane adhesion / interleukin-33-mediated signaling pathway / regulation of postsynaptic density assembly / positive regulation of interleukin-5 production / positive regulation of interleukin-13 production / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / positive regulation of synapse assembly / interleukin-1 receptor binding / interleukin-1-mediated signaling pathway / positive regulation of cytokine production involved in inflammatory response / negative regulation of interleukin-1 beta production / positive regulation of interleukin-4 production / monocyte differentiation / regulation of presynapse assembly / cellular defense response / coreceptor activity / cytokine activity / negative regulation of inflammatory response / positive regulation of interleukin-6 production / cytokine-mediated signaling pathway / positive regulation of inflammatory response / Interleukin-1 signaling / PIP3 activates AKT signaling / cell-cell signaling / cellular response to lipopolysaccharide / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein-containing complex assembly / positive regulation of MAPK cascade / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / immune response / inflammatory response / innate immune response / glutamatergic synapse / cell surface / signal transduction / : / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
Interleukin-1 receptor type 1 / Interleukin-1 receptor antagonist/Interleukin-36 / Interleukin-1 receptor type I/II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF ...Interleukin-1 receptor type 1 / Interleukin-1 receptor antagonist/Interleukin-36 / Interleukin-1 receptor type I/II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / TIR domain / Immunoglobulin domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-1 receptor-like 2 / Interleukin-1 receptor accessory protein / Interleukin-36 gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsAndries, J. / Felix, J. / Clancy, D.M. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1S83421N Belgium
CitationJournal: To Be Published
Title: Structural basis of pro-inflammatory signaling via the IL-36 receptor mediated by IL-36g and IL-37
Authors: Andries, J. / Toul, M. / Felix, J. / Clancy, D.M. / Savvides, S.N.
History
DepositionFeb 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interleukin-1 receptor accessory protein
B: Interleukin-36 gamma
C: Interleukin-1 receptor-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,20813
Polymers93,7923
Non-polymers2,41510
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable, isothermal titration calorimetry, gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Interleukin-1 receptor accessory protein / IL-1 receptor accessory protein / IL-1RAcP / Interleukin-1 receptor 3 / IL-1R-3 / IL-1R3


Mass: 40339.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1RAP, C3orf13, IL1R3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q9NPH3, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#2: Protein Interleukin-36 gamma / IL-1-related protein 2 / IL-1RP2 / Interleukin-1 epsilon / IL-1 epsilon / Interleukin-1 family ...IL-1-related protein 2 / IL-1RP2 / Interleukin-1 epsilon / IL-1 epsilon / Interleukin-1 family member 9 / IL-1F9 / Interleukin-1 homolog 1 / IL-1H1


Mass: 17045.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL36G, IL1E, IL1F9, IL1H1, IL1RP2, UNQ2456/PRO5737 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NZH8
#3: Protein Interleukin-1 receptor-like 2 / IL-36 receptor / IL-36R / Interleukin-1 receptor-related protein 2 / IL-1Rrp2 / IL1R-rp2


Mass: 36407.152 Da / Num. of mol.: 1 / Mutation: C154S, C262S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1RL2, IL1RRP2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q9HB29, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Ternary complex of IL-36gamma with the IL-36R and IL-1RAcP ectodomains
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.0927 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4 / Details: DDM was added before application on grids
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2150 mMsodium chlorideNaCl1
30.1 mMdodecyl maltosideDDM1
SpecimenConc.: 3.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295.15 K

-
Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 3.37 sec. / Electron dose: 61.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8828

-
Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2SerialEMimage acquisition
4cryoSPARC4.2.1CTF correction
7UCSF ChimeraXmodel fitting
8NAMDmodel fitting
9Cootmodel fitting
11cryoSPARC4.2.1initial Euler assignment
12cryoSPARC4.2.1final Euler assignment
13cryoSPARC4.2.1classification
14cryoSPARC4.2.13D reconstruction
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 771846
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 201760 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Details: NAMDINATOR was used for flexible fitting of the AlphaFold model in the final cryo-EM map
Atomic model buildingSource name: AlphaFold / Type: in silico model

+
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