[English] 日本語
Yorodumi
- PDB-4kc3: Cytokine/receptor binary complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kc3
TitleCytokine/receptor binary complex
Components
  • Interleukin-1 receptor-like 1
  • Interleukin-33
KeywordsIMMUNE SYSTEM / beta-trefoil / Ig-like domain
Function / homology
Function and homology information


interleukin-33 binding / interleukin-33 receptor binding / negative regulation of macrophage proliferation / : / : / positive regulation of cellular defense response / Interleukin-33 signaling / interleukin-33 receptor activity / positive regulation of MHC class I biosynthetic process / negative regulation of immunoglobulin production ...interleukin-33 binding / interleukin-33 receptor binding / negative regulation of macrophage proliferation / : / : / positive regulation of cellular defense response / Interleukin-33 signaling / interleukin-33 receptor activity / positive regulation of MHC class I biosynthetic process / negative regulation of immunoglobulin production / interleukin-1 receptor activity / microglial cell activation involved in immune response / negative regulation of T-helper 1 type immune response / negative regulation of inflammatory response to wounding / negative regulation of leukocyte migration / antibacterial innate immune response / microglial cell proliferation / interleukin-33-mediated signaling pathway / positive regulation of type 2 immune response / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / positive regulation of neuroinflammatory response / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / cytokine receptor activity / type 2 immune response / positive regulation of immunoglobulin production / positive regulation of interleukin-4 production / negative regulation of type II interferon production / macrophage differentiation / positive regulation of oligodendrocyte differentiation / transport vesicle / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / cytokine activity / positive regulation of cytokine production / positive regulation of interleukin-6 production / response to wounding / cellular response to mechanical stimulus / positive regulation of inflammatory response / protein import into nucleus / positive regulation of tumor necrosis factor production / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / PIP3 activates AKT signaling / chromosome / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / gene expression / defense response to virus / Ub-specific processing proteases / immune response / inflammatory response / external side of plasma membrane / focal adhesion / intracellular membrane-bounded organelle / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Interleukin-33 / : / Interleukin 33 / Interleukin-1 receptor type I/II / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily ...Interleukin-33 / : / Interleukin 33 / Interleukin-1 receptor type I/II / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-33 / Interleukin-1 receptor-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2702 Å
AuthorsLiu, X. / Wang, X.Q.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural insights into the interaction of IL-33 with its receptors.
Authors: Liu, X. / Hammel, M. / He, Y. / Tainer, J.A. / Jeng, U.S. / Zhang, L. / Wang, S. / Wang, X.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interleukin-33
B: Interleukin-1 receptor-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8765
Polymers53,2122
Non-polymers6643
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint3 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)329.924, 329.924, 43.731
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein Interleukin-33 / IL-33 / Interleukin-1 family member 11 / IL-1F11 / Nuclear factor from high endothelial venules / NF-HEV


Mass: 18155.857 Da / Num. of mol.: 1 / Fragment: UNP residues 112-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL33, C9orf26, IL1F11, NFHEV / Production host: Escherichia coli (E. coli) / References: UniProt: O95760
#2: Protein Interleukin-1 receptor-like 1 / Protein ST2


Mass: 35056.531 Da / Num. of mol.: 1 / Fragment: UNP residues 19-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1RL1, DER4, ST2, T1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q01638
#3: 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.: 3
Source method: isolated from a genetically manipulated source
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 protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 12% PEG3350, 100 mM Sodium Malonate pH 4.5, 7% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.27→50 Å / Num. all: 14029 / Num. obs: 14000 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KLL and 1IRA

3kll

1ira


Resolution: 3.2702→32.007 Å / SU ML: 0.46 / σ(F): 0 / Phase error: 33.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2831 703 5.02 %
Rwork0.2384 --
obs0.2407 14000 99.79 %
all-14029 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2702→32.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 42 0 3354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113434
X-RAY DIFFRACTIONf_angle_d1.7244642
X-RAY DIFFRACTIONf_dihedral_angle_d20.4811260
X-RAY DIFFRACTIONf_chiral_restr0.121518
X-RAY DIFFRACTIONf_plane_restr0.006588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2702-3.52240.34471520.28522625X-RAY DIFFRACTION100
3.5224-3.87640.31581490.26262649X-RAY DIFFRACTION100
3.8764-4.4360.28361430.20512662X-RAY DIFFRACTION100
4.436-5.58410.22891410.22362658X-RAY DIFFRACTION100
5.5841-32.00870.29581180.24692703X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8348-0.7483-0.68385.1309-0.47113.5437-0.3597-0.5739-0.52130.44290.3974-0.4357-0.3846-0.03370.00011.35150.2251-0.01581.1346-0.05191.126946.7239-41.20217.5061
22.86971.51970.04525.27722.32713.57650.0130.26660.3243-0.22760.19960.3471-0.42480.22690.00021.51930.0522-0.00510.9489-0.15151.056239.1812-18.59928.7233
31.6353-0.5281-0.66810.80610.54061.9026-0.20050.3291-1.0933-0.98860.1212-0.40580.08220.48310.04061.20470.01410.25641.24-0.26381.819749.662-60.27982.2924
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B and resid 21:186
3X-RAY DIFFRACTION3chain B and resid 194:299

+
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