[English] 日本語
Yorodumi
- PDB-3bpl: Crystal structure of the IL4-IL4R-Common Gamma ternary complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bpl
TitleCrystal structure of the IL4-IL4R-Common Gamma ternary complex
Components
  • Cytokine receptor common gamma chain
  • Interleukin-4 receptor alpha chain
  • Interleukin-4Interleukin 4
KeywordsCytokine/Cytokine receptor / IL4 / IL13 / receptor / cytokine / B-cell activation / Glycoprotein / Growth factor / Secreted / Immune response / Membrane / Phosphoprotein / Transmembrane / Disease mutation / Host-virus interaction / SCID / Cytokine-receptor COMPLEX / Cytokine-Cytokine receptor COMPLEX
Function / homology
Function and homology information


interleukin-4 receptor activity / interleukin-7-mediated signaling pathway / mature B cell differentiation / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / production of molecular mediator involved in inflammatory response / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / positive regulation of eosinophil chemotaxis ...interleukin-4 receptor activity / interleukin-7-mediated signaling pathway / mature B cell differentiation / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / production of molecular mediator involved in inflammatory response / interleukin-4 receptor binding / positive regulation of isotype switching to IgE isotypes / positive regulation of eosinophil chemotaxis / B cell costimulation / negative regulation of T-helper 1 cell differentiation / negative regulation of complement-dependent cytotoxicity / T-helper 1 cell differentiation / negative regulation of macrophage activation / negative regulation of chronic inflammatory response / Interleukin-18 signaling / regulation of isotype switching / negative regulation of neuroinflammatory response / positive regulation of T-helper 2 cell differentiation / positive regulation of T cell differentiation in thymus / positive regulation of cellular respiration / negative regulation of epithelial cell migration / negative regulation of T-helper 17 cell differentiation / dendritic cell differentiation / positive regulation of T-helper 2 cell cytokine production / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / positive regulation of isotype switching to IgG isotypes / positive regulation of amyloid-beta clearance / neuroinflammatory response / interleukin-4-mediated signaling pathway / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-2-mediated signaling pathway / myeloid dendritic cell differentiation / macrophage activation / positive regulation of mast cell degranulation / positive regulation of mononuclear cell migration / regulation of phosphorylation / type 2 immune response / STAT3 nuclear events downstream of ALK signaling / positive regulation of macrophage activation / activation of Janus kinase activity / interleukin-15-mediated signaling pathway / positive regulation of MHC class II biosynthetic process / T-helper 2 cell differentiation / Interleukin-15 signaling / cytokine receptor activity / Interleukin-2 signaling / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of T cell differentiation / positive regulation of B cell differentiation / positive regulation of interleukin-13 production / positive regulation of myoblast fusion / positive regulation of ATP biosynthetic process / cytokine binding / defense response to protozoan / negative regulation of osteoclast differentiation / positive regulation of interleukin-10 production / positive regulation of macroautophagy / immunoglobulin mediated immune response / positive regulation of immunoglobulin production / negative regulation of acute inflammatory response / centriolar satellite / negative regulation of tumor necrosis factor production / regulation of immune response / Interleukin receptor SHC signaling / coreceptor activity / positive regulation of phagocytosis / negative regulation of endothelial cell apoptotic process / positive regulation of B cell proliferation / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of defense response to virus by host / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of T cell proliferation / cholesterol metabolic process / Interleukin-7 signaling / T cell activation / B cell differentiation / innate immune response in mucosa / cytokine activity / negative regulation of extrinsic apoptotic signaling pathway / microglial cell activation / growth factor activity / negative regulation of inflammatory response / positive regulation of receptor-mediated endocytosis / cytokine-mediated signaling pathway / T cell differentiation in thymus / gene expression / positive regulation of cold-induced thermogenesis / RAF/MAP kinase cascade / Interleukin-4 and Interleukin-13 signaling / receptor complex / endosome / positive regulation of cell migration / immune response / external side of plasma membrane / negative regulation of DNA-templated transcription
Similarity search - Function
Interleukin-4 receptor alpha, N-terminal / Interleukin-4 receptor alpha chain, N-terminal / : / : / Cytokine receptor-like factor 2-like, D1 domain / Cytokine receptor-like factor 2-like, D2 domain / Interleukin-4 / Interleukin 4 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site ...Interleukin-4 receptor alpha, N-terminal / Interleukin-4 receptor alpha chain, N-terminal / : / : / Cytokine receptor-like factor 2-like, D1 domain / Cytokine receptor-like factor 2-like, D2 domain / Interleukin-4 / Interleukin 4 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site / Interleukins -4 and -13 signature. / Interleukins 4 and 13 / Short hematopoietin receptor family 1 signature. / Interleukin-6 receptor alpha chain, binding / Short hematopoietin receptor, family 1, conserved site / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / 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
Interleukin-4 / Interleukin-4 receptor subunit alpha / Cytokine receptor common subunit gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsGarcia, K.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Molecular and Structural Basis of Cytokine Receptor Pleiotropy in the Interleukin-4/13 System.
Authors: Laporte, S.L. / Juo, Z.S. / Vaclavikova, J. / Colf, L.A. / Qi, X. / Heller, N.M. / Keegan, A.D. / Garcia, K.C.
History
DepositionDec 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_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 2.1Oct 20, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interleukin-4
B: Interleukin-4 receptor alpha chain
C: Cytokine receptor common gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0318
Polymers62,3723
Non-polymers1,6595
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.578, 86.652, 175.671
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 3 types, 3 molecules ABC

#1: Protein Interleukin-4 / Interleukin 4 / IL-4 / B-cell stimulatory factor 1 / BSF-1 / Lymphocyte stimulatory factor 1 / Binetrakin / Pitrakinra


Mass: 14989.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL4 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P05112
#2: Protein Interleukin-4 receptor alpha chain / IL-4R-alpha / CD124 antigen / Soluble interleukin-4 receptor alpha chain


Mass: 23470.332 Da / Num. of mol.: 1 / Fragment: Extracellular domain, residues 27-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL4R, 582J2.1, IL4RA / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P24394
#3: Protein Cytokine receptor common gamma chain / Gamma-C / Interleukin-2 receptor gamma chain / IL-2R gamma chain / p64 / CD132 antigen


Mass: 23912.684 Da / Num. of mol.: 1 / Fragment: Extracellular domain, residues 56-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RG / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P31785

-
Sugars , 3 types, 5 molecules

#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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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.: 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

-
Non-polymers , 1 types, 137 molecules

#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG8K, 8% ethylene glycol, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.93→50 Å / Num. obs: 17699 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 11.3
Reflection shellResolution: 2.93→3.06 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1724 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.93→40 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.85 / SU B: 33.594 / SU ML: 0.334 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29711 888 5 %RANDOM
Rwork0.22228 ---
obs0.226 16770 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.186 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2---0.86 Å20 Å2
3---1.86 Å2
Refinement stepCycle: LAST / Resolution: 2.93→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4289 0 108 137 4534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214532
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.9566183
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.95519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.33424.045220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22815739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3061526
X-RAY DIFFRACTIONr_chiral_restr0.0820.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023412
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2610.21979
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.23040
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2195
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3190.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5181.52673
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2824257
X-RAY DIFFRACTIONr_scbond_it2.14532131
X-RAY DIFFRACTIONr_scangle_it3.2874.51926
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.93→3.008 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.55 55 -
Rwork0.369 1029 -
obs--84.42 %
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)
12.5042-0.8490.88681.268-0.61381.39060.07090.2268-0.04-0.1601-0.03-0.07420.04710.0372-0.0409-0.0491-0.01050.01510.0095-0.0098-0.043427.1978-15.0147-28.8314
22.19080.9748-1.22660.7153-0.71071.37780.0250.063-0.0175-0.04170.0597-0.0058-0.0384-0.0781-0.0848-0.04470.0272-0.0098-0.02070.00190.04354.4649-19.236-7.5233
31.25060.43930.72652.53491.69542.0926-0.0863-0.13190.1287-0.01050.1939-0.069-0.10620.1231-0.10760.0052-0.01120.002-0.0568-0.0373-0.036321.98966.31731.5042
45.46670.1597-2.11164.6915-1.22073.712-0.16830.08880.0735-0.5249-0.2051-0.41550.31720.3620.3734-0.04660.08540.13840.00690.1915-0.174744.34928.8345-44.1824
50.7907-0.5558-1.01012.41031.86814.49540.08630.15690.18530.00350.014-0.018-0.21470.0389-0.1003-0.0187-0.04320.0566-0.17910.06-0.004428.270817.9579-15.8535
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1283 - 128
2X-RAY DIFFRACTION2BB-2 - 931 - 96
3X-RAY DIFFRACTION3BB94 - 19997 - 202
4X-RAY DIFFRACTION4CC34 - 1261 - 93
5X-RAY DIFFRACTION5CC127 - 22794 - 194

+
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