[English] 日本語
Yorodumi
- PDB-4nn5: Cytokine receptor complex - Crystal form 1A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nn5
TitleCytokine receptor complex - Crystal form 1A
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 binding / Interleukin-7 signaling / negative regulation of T cell mediated cytotoxicity / positive regulation of receptor signaling pathway via STAT / positive regulation of cytokine-mediated signaling pathway / positive regulation of T cell differentiation in thymus / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of interleukin-5 production / positive regulation of interleukin-13 production ...interleukin-7 receptor binding / Interleukin-7 signaling / negative regulation of T cell mediated cytotoxicity / positive regulation of receptor signaling pathway via STAT / positive regulation of cytokine-mediated signaling pathway / positive regulation of T cell differentiation in thymus / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of interleukin-5 production / positive regulation of interleukin-13 production / negative regulation of T cell apoptotic process / cytokine receptor activity / regulation of cell size / B cell proliferation / T cell homeostasis / positive regulation of interleukin-10 production / B cell homeostasis / hemopoiesis / T cell differentiation / lymph node development / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / cell morphogenesis / T cell mediated cytotoxicity / cytokine-mediated signaling pathway / positive regulation of inflammatory response / positive regulation of interleukin-6 production / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / Thymic stromal lymphopoietin / Thymic stromal lymphopoietin superfamily / Thymic stromal lymphopoietin / Immunoglobulin-like - #1870 / IL-7Ralpha, fibronectin type III domain / Fibronectin type III domain / : / : / Cytokine receptor-like factor 2-like, D1 domain ...Thymic stromal lymphopoietin / Thymic stromal lymphopoietin / Thymic stromal lymphopoietin superfamily / Thymic stromal lymphopoietin / Immunoglobulin-like - #1870 / IL-7Ralpha, fibronectin type III domain / Fibronectin type III domain / : / : / Cytokine receptor-like factor 2-like, D1 domain / Cytokine receptor-like factor 2-like, D2 domain / 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 / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / 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: 1.898 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 1.4Jul 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 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

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6345
Polymers63,3543
Non-polymers2802
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.060, 79.756, 52.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 3 types, 3 molecules ABC

#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: N122Q
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

-
Sugars , 1 types, 1 molecules

#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

-
Non-polymers , 2 types, 331 molecules

#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 14% PEG4000, 0.3 M sodium acetate, pH 4.5, 0.3 M calcium acetate, 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: 0.976293 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976293 Å / Relative weight: 1
ReflectionResolution: 1.898→49.25 Å / Num. all: 50432 / Num. obs: 50292 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 19.9
Reflection shellResolution: 1.898→2.01 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.9 / Num. unique all: 7921 / % possible all: 98.4

-
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 3DI2

3di2


Resolution: 1.898→49.25 Å / SU ML: 0.19 / Isotropic thermal model: ISOTROPIC + TLS / Cross valid method: FREE R / σ(F): 1.99 / Phase error: 18.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 2513 5 %RANDOM
Rwork0.1698 ---
obs0.1713 50285 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.7 Å2
Refinement stepCycle: LAST / Resolution: 1.898→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 0 18 330 4152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113931
X-RAY DIFFRACTIONf_angle_d1.2185337
X-RAY DIFFRACTIONf_dihedral_angle_d13.5341394
X-RAY DIFFRACTIONf_chiral_restr0.053596
X-RAY DIFFRACTIONf_plane_restr0.007678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.898-1.9340.25121330.21572521X-RAY DIFFRACTION95
1.934-1.97350.25691370.1942608X-RAY DIFFRACTION100
1.9735-2.01640.21771380.19322617X-RAY DIFFRACTION100
2.0164-2.06330.19111370.18162619X-RAY DIFFRACTION100
2.0633-2.11490.22031390.18192631X-RAY DIFFRACTION100
2.1149-2.17210.22431400.17222651X-RAY DIFFRACTION100
2.1721-2.2360.2081360.16662597X-RAY DIFFRACTION100
2.236-2.30820.19891390.16272645X-RAY DIFFRACTION100
2.3082-2.39070.22381390.16992629X-RAY DIFFRACTION100
2.3907-2.48640.19611390.17032648X-RAY DIFFRACTION100
2.4864-2.59950.21021400.1742648X-RAY DIFFRACTION100
2.5995-2.73660.23641400.18172664X-RAY DIFFRACTION100
2.7366-2.9080.24091390.18592644X-RAY DIFFRACTION100
2.908-3.13250.2451400.19152665X-RAY DIFFRACTION100
3.1325-3.44770.18341420.17732692X-RAY DIFFRACTION100
3.4477-3.94640.20231420.15282692X-RAY DIFFRACTION100
3.9464-4.97130.15051430.1342731X-RAY DIFFRACTION100
4.9713-49.26650.18651500.182870X-RAY DIFFRACTION100
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)
10.1281-0.00280.14020.3504-0.09010.1008-0.09440.1358-0.1129-0.2590.14070.0930.13770.0515-00.2745-0.04830.0190.2845-0.0040.245117.333515.801-0.789
21.2032-0.00640.97240.05580.04790.94920.67990.2196-0.16650.09170.12330.24090.3529-0.05210.27360.4123-0.1082-0.05490.25220.08260.547110.87992.78835.0738
30.0105-0.030.01470.1108-0.00550.03190.13550.031-0.146-0.52410.09860.22180.26670.01590.08980.3756-0.0323-0.11080.2919-0.07740.389413.82147.1484-5.6926
40.00350.00550.00960.04750.0460.0560.03910.171-0.2327-0.0112-0.09080.21890.2055-0.0313-0.1075-0.1598-0.4067-0.57860.26580.04070.96660.073510.974-5.0564
50.46290.3677-0.0650.6783-0.03420.17970.11420.35560.1386-0.8040.09710.8526-0.02580.05740.05710.3894-0.0913-0.12510.34320.0580.282810.795317.1896-7.4579
60.03720.0688-0.01990.44680.35481.39480.04650.0233-0.2161-0.10060.14620.33520.14370.00960.13220.205-0.0465-0.06480.20.050.387511.28697.67853.3551
70.223-0.15910.09870.16280.09310.14580.0997-0.04070.13350.10810.15580.2776-0.17950.0026-0.00010.248-0.02260.00030.22430.04150.22111.983941.69080.2143
80.2556-0.1187-0.20520.0503-0.01720.48370.10230.1871-0.0432-0.04620.01950.2893-0.2028-0.24590.0260.27240.0246-0.05180.23350.01760.28429.212844.0496-8.3947
90.0975-0.0350.00770.06690.04380.09970.09720.0151-0.0359-0.06720.0220.3985-0.0510.0096-0.00010.2159-0.00150.01830.24050.03610.39276.702638.6053-2.8398
100.0669-0.007-0.10980.05450.08170.13570.03750.06420.03320.0074-0.0531-0.0786-0.0258-0.050600.20150.00350.00670.26630.03680.201614.002441.3323-11.264
110.0108-0.05970.0280.0735-0.03250.0119-0.2282-0.08090.0107-0.0368-0.16680.06120.001-0.2853-00.19740.0053-0.02160.2906-0.00560.17114.899638.185215.0616
120.0417-0.0321-0.05240.03960.01880.0479-0.189-0.101-0.19690.35040.0097-0.08560.28890.007-0.00110.30280.0226-0.01540.29610.03240.176623.503338.383537.1782
13-0.0032-0.0140.06780.01010.01180.01650.1042-0.101-0.0514-0.1916-0.02430.05350.0987-0.25650.00010.32-0.06250.00680.32620.01390.270713.632129.223115.5468
140.1032-0.08310.12580.05590.00620.17010.00740.0806-0.03110.0031-0.02580.0466-0.07620.1177-00.2240.01830.00240.23890.00840.18126.281643.20522.443
150.03170.0269-0.00920.0243-0.00710.06690.1441-0.0954-0.10980.1406-0.1646-0.44420.02510.1218-00.28960.0057-0.01820.3092-0.00750.314929.266543.34234.5979
160.32140.24580.0020.2209-0.0820.24790.0105-0.0344-0.05110.05080.0337-0.04180.0563-0.0359-00.24220.022-0.02730.24250.01470.180721.455341.345919.8159
170.7269-0.4616-0.2840.82650.26961.1784-0.0249-0.3053-0.2738-0.16270.24340.29180.4721-0.13910.53650.3951-0.0819-0.12510.3210.14840.435215.6757-8.277818.1889
180.3901-0.15980.34930.2122-0.27620.607-0.0752-0.12510.08220.01120.0092-0.0352-0.1547-0.112800.27510.0227-0.04790.247-0.03770.261532.503217.63222.9758
190.0030.00990.0208-0.00260.00450.0006-0.0745-0.09230.34290.2933-0.1347-0.5404-0.28050.2631-0.00020.4508-0.0164-0.1260.4228-0.01810.52444.328221.893735.216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 72 )
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 84 )
5X-RAY DIFFRACTION5chain 'A' and (resid 85 through 117 )
6X-RAY DIFFRACTION6chain 'A' and (resid 118 through 140 )
7X-RAY DIFFRACTION7chain 'B' and (resid 36 through 59 )
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 81 )
9X-RAY DIFFRACTION9chain 'B' and (resid 82 through 104 )
10X-RAY DIFFRACTION10chain 'B' and (resid 105 through 125 )
11X-RAY DIFFRACTION11chain 'B' and (resid 126 through 135 )
12X-RAY DIFFRACTION12chain 'B' and (resid 136 through 149 )
13X-RAY DIFFRACTION13chain 'B' and (resid 150 through 162 )
14X-RAY DIFFRACTION14chain 'B' and (resid 163 through 186 )
15X-RAY DIFFRACTION15chain 'B' and (resid 187 through 199 )
16X-RAY DIFFRACTION16chain 'B' and (resid 200 through 232 )
17X-RAY DIFFRACTION17chain 'C' and (resid 28 through 114 )
18X-RAY DIFFRACTION18chain 'C' and (resid 115 through 207 )
19X-RAY DIFFRACTION19chain 'C' and (resid 208 through 219 )

+
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