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- PDB-8qy4: Structure of interleukin 11 (gp130 P496L mutant). -

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Basic information

Entry
Database: PDB / ID: 8qy4
TitleStructure of interleukin 11 (gp130 P496L mutant).
Components
  • Interleukin-11 receptor subunit alpha
  • Interleukin-11Interleukin 11
  • Interleukin-6 receptor subunit beta
KeywordsIMMUNE SYSTEM / interleukin / gp130
Function / homology
Function and homology information


interleukin-11 receptor binding / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / oncostatin-M receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling / triglyceride mobilization / interleukin-6 receptor activity / interleukin-6 binding ...interleukin-11 receptor binding / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / oncostatin-M receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling / triglyceride mobilization / interleukin-6 receptor activity / interleukin-6 binding / Interleukin-6 signaling / Interleukin-35 Signalling / oncostatin-M receptor complex / 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 / interleukin-11 receptor activity / interleukin-11 binding / megakaryocyte differentiation / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / head development / negative regulation of hormone secretion / regulation of Notch signaling pathway / interleukin-6 receptor binding / interleukin-11-mediated signaling pathway / developmental process / positive regulation of astrocyte differentiation / intestinal epithelial cell development / IL-6-type cytokine receptor ligand interactions / cytokine receptor activity / neuronal cell body membrane / glycogen metabolic process / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / negative regulation of cytosolic calcium ion concentration / protein tyrosine kinase activator activity / cytokine binding / fat cell differentiation / positive regulation of smooth muscle cell migration / growth factor binding / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / B cell differentiation / response to cytokine / cytokine activity / growth factor activity / cytokine-mediated signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / positive regulation of peptidyl-serine phosphorylation / cell body / scaffold protein binding / cell population proliferation / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / receptor complex / membrane raft / external side of plasma membrane / neuronal cell body / dendrite / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Interleukin-11, mammalian / Interleukin-11 / Interleukin 11 / 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 ...Interleukin-11, mammalian / Interleukin-11 / Interleukin 11 / 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 / Fibronectin type III domain / Fibronectin type 3 domain / 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-11 / Interleukin-6 receptor subunit beta / Interleukin-11 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 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 11 (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-11
C: Interleukin-6 receptor subunit beta
D: Interleukin-11
F: Interleukin-6 receptor subunit beta
B: Interleukin-11 receptor subunit alpha
E: Interleukin-11 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,33922
Polymers338,5806
Non-polymers4,75816
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 "B"
d_2ens_2chain "E"
d_1ens_3chain "C"
d_2ens_3chain "F"

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_1PROPROLEULEUAA35 - 19935 - 199
d_21ens_1PROPROLEULEUDC35 - 19935 - 199
d_11ens_2PROPROTHRTHRBE112 - 317112 - 317
d_12ens_2NAGNAGNAGNAGII1
d_13ens_2NAGNAGNAGNAGII2
d_14ens_2NAGNAGNAGNAGJJ1
d_15ens_2NAGNAGNAGNAGJJ2
d_21ens_2PROPROTHRTHREF112 - 317112 - 317
d_22ens_2NAGNAGNAGNAGKK1
d_23ens_2NAGNAGNAGNAGKK2
d_24ens_2NAGNAGNAGNAGLL1
d_25ens_2NAGNAGNAGNAGLL2
d_11ens_3LEULEUTHRTHRCB25 - 60725 - 607
d_12ens_3NAGNAGNAGNAGGG1
d_13ens_3NAGNAGNAGNAGGG2
d_14ens_3NAGNAGNAGNAGCM1001
d_15ens_3NAGNAGNAGNAGCN1002
d_16ens_3NAGNAGNAGNAGCO1003
d_17ens_3NAGNAGNAGNAGCP1004
d_18ens_3NAGNAGNAGNAGCQ1005
d_21ens_3LEULEUTHRTHRFD25 - 60725 - 607
d_22ens_3NAGNAGNAGNAGHH1
d_23ens_3NAGNAGNAGNAGHH2
d_24ens_3NAGNAGNAGNAGFR1001
d_25ens_3NAGNAGNAGNAGFS1002
d_26ens_3NAGNAGNAGNAGFT1003
d_27ens_3NAGNAGNAGNAGFU1004
d_28ens_3NAGNAGNAGNAGFV1005

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.999990008453, 0.00439868322267, -0.000796605286919), (-0.0043970034382, -0.99998813169, -0.00209829437618), (-0.000805825564829, -0.00209477073479, 0.999997481287)473.868467771, 476.355191676, 0.734085733312
2given(-0.99997905264, -0.00589651779862, -0.00266933699387), (0.00587692794244, -0.99995617134, 0.00728814903376), (-0.00271219470091, 0.00727230886511, 0.999969878308)477.141569233, 471.677519603, -1.3264822899
3given(-0.999997965158, 0.00154926137421, -0.00129207897269), (-0.00154924890706, -0.999998799856, -1.06497278327E-5), (-0.00129209392122, -8.64795422592E-6, 0.999999165209)474.826997094, 475.27100001, 0.212740626921

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Components

#1: Protein Interleukin-11 / Interleukin 11


Mass: 21455.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL11 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P20809
#2: 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
#3: Protein Interleukin-11 receptor subunit alpha /


Mass: 45266.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL11RA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q14626
#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.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-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.: 10 / 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-11 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: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 487147 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 41.99 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003715534
ELECTRON MICROSCOPYf_angle_d0.870321238
ELECTRON MICROSCOPYf_chiral_restr0.05462454
ELECTRON MICROSCOPYf_plane_restr0.01032684
ELECTRON MICROSCOPYf_dihedral_angle_d12.45595574
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints8.27248501355E-13
ens_2d_2MCELECTRON MICROSCOPYNCS constraints3.52978435707E-11
ens_3d_2BCELECTRON MICROSCOPYNCS constraints8.7348019437E-12

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