[English] 日本語
Yorodumi
- PDB-4nn7: Cytokine receptor complex - Crystal form 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nn7
TitleCytokine receptor complex - Crystal form 2
Components
  • Cytokine receptor-like factor 2
  • Interleukin-7 receptor subunit alpha
  • Thymic stromal lymphopoietin
KeywordsCYTOKINE/CYTOKINE RECEPTOR / four helical bundle fold / CHR domains / TSLP cytokine signaling / TSLPR and IL-7Ralpha receptors / cell surface / CYTOKINE-CYTOKINE RECEPTOR complex
Function / homology
Function and homology information


interleukin-7 receptor activity / Interleukin-7 signaling / negative regulation of T cell mediated cytotoxicity / positive regulation of T cell differentiation in thymus / positive regulation of receptor signaling pathway via STAT / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / negative regulation of T cell apoptotic process / cellular homeostasis / regulation of cell size ...interleukin-7 receptor activity / Interleukin-7 signaling / negative regulation of T cell mediated cytotoxicity / positive regulation of T cell differentiation in thymus / positive regulation of receptor signaling pathway via STAT / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / negative regulation of T cell apoptotic process / cellular homeostasis / regulation of cell size / T cell homeostasis / B cell homeostasis / B cell proliferation / T cell differentiation / lymph node development / cytokine activity / T cell mediated cytotoxicity / cell morphogenesis / T cell differentiation in thymus / gene expression / defense response to Gram-positive bacterium / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Thymic stromal lymphopoietin / Immunoglobulin-like - #1870 / Thymic stromal lymphopoietin / Thymic stromal lymphopoietin superfamily / Thymic stromal lymphopoietin / IL-7Ralpha, fibronectin type III domain / Fibronectin type III domain / : / : / Cytokine receptor-like factor 2-like, D2 domain ...Thymic stromal lymphopoietin / Immunoglobulin-like - #1870 / Thymic stromal lymphopoietin / Thymic stromal lymphopoietin superfamily / Thymic stromal lymphopoietin / IL-7Ralpha, fibronectin type III domain / Fibronectin type III domain / : / : / Cytokine receptor-like factor 2-like, D2 domain / Cytokine receptor-like factor 2, domain 1 / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Growth Hormone; Chain: A; / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-7 receptor subunit alpha / Cytokine receptor-like factor 2 / Thymic stromal lymphopoietin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.775 Å
AuthorsVerstraete, K. / van Schie, L. / Savvides, S.N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structural basis of the proinflammatory signaling complex mediated by TSLP.
Authors: Verstraete, K. / van Schie, L. / Vyncke, L. / Bloch, Y. / Tavernier, J. / Pauwels, E. / Peelman, F. / Savvides, S.N.
History
DepositionNov 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Apr 16, 2014Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thymic stromal lymphopoietin
B: Interleukin-7 receptor subunit alpha
C: Cytokine receptor-like factor 2


Theoretical massNumber of molelcules
Total (without water)63,3543
Polymers63,3543
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.789, 50.105, 249.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Thymic stromal lymphopoietin / TSLP / Thymic stroma-derived lymphopoietin


Mass: 15109.947 Da / Num. of mol.: 1 / Fragment: UNP residues 20-140 / Mutation: N123Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tslp / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q9JIE6
#2: Protein Interleukin-7 receptor subunit alpha / IL-7 receptor subunit alpha / IL-7R subunit alpha / IL-7R-alpha / IL-7RA


Mass: 25431.809 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 21-239)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il7r, IL7RA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3) / References: UniProt: P16872
#3: Protein Cytokine receptor-like factor 2 / Cytokine receptor-like molecule 2 / CRLM-2 / Thymic stromal lymphopoietin protein receptor / TSLP ...Cytokine receptor-like molecule 2 / CRLM-2 / Thymic stromal lymphopoietin protein receptor / TSLP receptor / TSLPR / Type I cytokine receptor delta 1


Mass: 22812.354 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 20-222) / Mutation: N53Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crlf2, CRLF2 (TSLPR), Crlm2, Tpte2, Tslpr / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q8CII9
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.77 Å3/Da / Density % sol: 30.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% pentaerythritol ethoxylate, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.77→50 Å / Num. all: 4995 / Num. obs: 4968 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Biso Wilson estimate: 98.8 Å2 / Rmerge(I) obs: 0.267 / Net I/σ(I): 9.17
Reflection shellResolution: 3.77→4 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 3 / Num. unique all: 790 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NN5

4nn5


Resolution: 3.775→49.127 Å / SU ML: 0.54 / Isotropic thermal model: ISOTROPIC / Cross valid method: FREE R / σ(F): 1.37 / Phase error: 29.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2865 249 5.02 %RANDOM
Rwork0.2765 ---
obs0.277 4962 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 101 Å2
Refinement stepCycle: LAST / Resolution: 3.775→49.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 0 0 3297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043398
X-RAY DIFFRACTIONf_angle_d0.8724679
X-RAY DIFFRACTIONf_dihedral_angle_d11.2171046
X-RAY DIFFRACTIONf_chiral_restr0.032556
X-RAY DIFFRACTIONf_plane_restr0.005601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.775-4.75490.32861200.28652277X-RAY DIFFRACTION99
4.7549-49.13110.26241290.27072436X-RAY DIFFRACTION100

+
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