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- PDB-8qy6: Structure of interleukin 6 (gp130 P496L mutant). -

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Basic information

Entry
Database: PDB / ID: 8qy6
TitleStructure of interleukin 6 (gp130 P496L mutant).
Components
  • Interleukin-6 receptor subunit alpha
  • Interleukin-6 receptor subunit beta
  • Interleukin-6Interleukin 6
KeywordsIMMUNE SYSTEM / interleukin / gp130
Function / homology
Function and homology information


oncostatin-M receptor activity / ciliary neurotrophic factor binding / positive regulation of interleukin-21 production / regulation of astrocyte activation / IL-6-type cytokine receptor ligand interactions / glucagon secretion / leukemia inhibitory factor receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling ...oncostatin-M receptor activity / ciliary neurotrophic factor binding / positive regulation of interleukin-21 production / regulation of astrocyte activation / IL-6-type cytokine receptor ligand interactions / glucagon secretion / leukemia inhibitory factor receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling / triglyceride mobilization / interleukin-6 receptor activity / interleukin-6 binding / regulation of glucagon secretion / negative regulation of interleukin-1-mediated signaling pathway / Interleukin-6 signaling / hepatic immune response / Interleukin-35 Signalling / regulation of vascular endothelial growth factor production / oncostatin-M receptor complex / negative regulation of primary miRNA processing / oncostatin-M-mediated signaling pathway / ciliary neurotrophic factor receptor activity / ciliary neurotrophic factor receptor binding / negative regulation of interleukin-6-mediated signaling pathway / leukemia inhibitory factor signaling pathway / T follicular helper cell differentiation / interleukin-11 receptor activity / interleukin-11 binding / germinal center B cell differentiation / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / regulation of microglial cell activation / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / positive regulation of extracellular matrix disassembly / positive regulation of type B pancreatic cell apoptotic process / positive regulation of receptor signaling pathway via STAT / positive regulation of apoptotic DNA fragmentation / response to peptidoglycan / hepatocyte proliferation / neutrophil apoptotic process / interleukin-6 receptor binding / regulation of Notch signaling pathway / negative regulation of collagen biosynthetic process / positive regulation of activation of Janus kinase activity / interleukin-11-mediated signaling pathway / inflammatory response to wounding / T-helper 17 cell lineage commitment / positive regulation of T-helper 2 cell cytokine production / positive regulation of B cell activation / positive regulation of glomerular mesangial cell proliferation / endocrine pancreas development / negative regulation of interleukin-8 production / positive regulation of acute inflammatory response / regulation of neuroinflammatory response / vascular endothelial growth factor production / negative regulation of chemokine production / positive regulation of neuroinflammatory response / positive regulation of astrocyte differentiation / positive regulation of leukocyte chemotaxis / intestinal epithelial cell development / positive regulation of platelet aggregation / neutrophil mediated immunity / positive regulation of cytokine production involved in inflammatory response / cytokine receptor activity / negative regulation of bone resorption / CD163 mediating an anti-inflammatory response / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of fat cell differentiation / neuronal cell body membrane / maintenance of blood-brain barrier / glycogen metabolic process / Interleukin-6 signaling / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / protein tyrosine kinase activator activity / negative regulation of cytosolic calcium ion concentration / cytokine binding / positive regulation of smooth muscle cell migration / positive regulation of interleukin-17 production / MAPK3 (ERK1) activation / growth factor binding / Interleukin-10 signaling / MAPK1 (ERK2) activation / monocyte chemotaxis / positive regulation of interleukin-10 production / regulation of insulin secretion / humoral immune response / negative regulation of lipid storage / positive regulation of immunoglobulin production / Transcriptional Regulation by VENTX / positive regulation of vascular endothelial growth factor production / positive regulation of epithelial to mesenchymal transition / positive regulation of osteoblast differentiation / regulation of angiogenesis / coreceptor activity / positive regulation of chemokine production / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway
Similarity search - Function
Interleukin-6 / Interleukin-6/G-CSF/MGF family / Interleukin-6/GCSF/MGF, conserved site / Interleukin-6 / G-CSF / MGF signature. / Interleukin-6/GCSF/MGF / Interleukin-6 homologues / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain ...Interleukin-6 / Interleukin-6/G-CSF/MGF family / Interleukin-6/GCSF/MGF, conserved site / Interleukin-6 / G-CSF / MGF signature. / Interleukin-6/GCSF/MGF / Interleukin-6 homologues / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / Four-helical cytokine-like, core / Immunoglobulin / Immunoglobulin domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-6 / Interleukin-6 receptor subunit alpha / Interleukin-6 receptor subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsGardner, S. / Bubeck, D. / Jin, Y.
Funding support United Kingdom, European Union, 4items
OrganizationGrant numberCountry
Wellcome Trust202323/Z/16 United Kingdom
European Research Council (ERC)C-206-STGEuropean Union
Engineering and Physical Sciences Research CouncilEP/X035603/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011178/1 United Kingdom
Citation
Journal: To Be Published
Title: Structure of interleukin 6 (gp130 P496L mutant).
Authors: Gardner, S. / Bubeck, D. / Jin, Y.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-6 receptor subunit beta
B: Interleukin-6
C: Interleukin-6 receptor subunit alpha
E: Interleukin-6
F: Interleukin-6 receptor subunit alpha
D: Interleukin-6 receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,52118
Polymers355,8356
Non-polymers4,68612
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "D"
d_1ens_2chain "E"
d_2ens_2chain "B"
d_1ens_3chain "F"
d_2ens_3chain "C"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1LEULEUTHRTHRAA24 - 60724 - 607
d_12ens_1NAGNAGNAGNAGGG1
d_13ens_1NAGNAGNAGNAGGG2
d_14ens_1NAGNAGNAGNAGHH1
d_15ens_1NAGNAGNAGNAGHH2
d_16ens_1NAGNAGNAGNAGII1
d_17ens_1NAGNAGNAGNAGII2
d_18ens_1NAGNAGNAGNAGJJ1
d_19ens_1NAGNAGNAGNAGJJ2
d_110ens_1NAGNAGNAGNAGKK1
d_111ens_1NAGNAGNAGNAGKK2
d_112ens_1NAGNAGNAGNAGAQ1001
d_21ens_1LEULEUTHRTHRDF24 - 60724 - 607
d_22ens_1NAGNAGNAGNAGLL1
d_23ens_1NAGNAGNAGNAGLL2
d_24ens_1NAGNAGNAGNAGMM1
d_25ens_1NAGNAGNAGNAGMM2
d_26ens_1NAGNAGNAGNAGNN1
d_27ens_1NAGNAGNAGNAGNN2
d_28ens_1NAGNAGNAGNAGOO1
d_29ens_1NAGNAGNAGNAGOO2
d_210ens_1NAGNAGNAGNAGPP1
d_211ens_1NAGNAGNAGNAGPP2
d_212ens_1NAGNAGNAGNAGDR1001
d_11ens_2LEULEUMETMETED19 - 18447 - 212
d_21ens_2LEULEUMETMETBB19 - 18447 - 212
d_11ens_3GLUGLUTRPTRPFE96 - 296115 - 315
d_21ens_3GLUGLUTRPTRPCC96 - 296115 - 315

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.9999847611, 0.00517443955486, -0.00192425148701), (-0.00516631968503, -0.999977829905, -0.00420105225627), (-0.00194594691714, -0.00419104693851, 0.999989324151)474.519848309, 477.358699521, 1.75382933125
2given(-0.999885480052, -0.0136106635338, -0.00661639017353), (0.0135132752, -0.999802859785, 0.0145476100549), (-0.00681308844263, 0.0144565349621, 0.999872287056)479.438447682, 468.077330211, -2.08924200025
3given(-0.999686318042, 0.00610331606038, -0.0242902254414), (-0.00652494035714, -0.999828766658, 0.017316538824), (-0.0241803778354, 0.0174695992104, 0.999554962186)479.549858741, 471.348829258, 0.409008730032

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Components

#1: Protein Interleukin-6 receptor subunit beta /


Mass: 102568.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il6st / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q00560
#2: Protein Interleukin-6 / Interleukin 6


Mass: 23743.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P05231
#3: Protein Interleukin-6 receptor subunit alpha /


Mass: 51605.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL6R / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P08887
#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.: 10
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: 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.: 2 / 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

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: IL-6 signalling complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2250 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_4933 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 491673 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 25.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003615670
ELECTRON MICROSCOPYf_angle_d0.754521318
ELECTRON MICROSCOPYf_chiral_restr0.05212436
ELECTRON MICROSCOPYf_plane_restr0.0092694
ELECTRON MICROSCOPYf_dihedral_angle_d7.41431952
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints1.49667366283E-11
ens_2d_2DEELECTRON MICROSCOPYNCS constraints8.90959817019E-13
ens_3d_2EFELECTRON MICROSCOPYNCS constraints6.01966905256E-13

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