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- EMDB-18741: Structure of interleukin 11 (gp130 P496L mutant). -

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Basic information

Entry
Database: EMDB / ID: EMD-18741
TitleStructure of interleukin 11 (gp130 P496L mutant).
Map dataSharpened map.
Sample
  • Complex: IL-11 signalling complex
    • Protein or peptide: Interleukin-11Interleukin 11
    • Protein or peptide: Interleukin-6 receptor subunit beta
    • Protein or peptide: Interleukin-11 receptor subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinterleukin / gp130 / IMMUNE SYSTEM
Function / homology
Function and homology information


interleukin-11 receptor binding / oncostatin-M receptor activity / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling / interleukin-6 receptor activity / triglyceride mobilization / interleukin-6 binding ...interleukin-11 receptor binding / oncostatin-M receptor activity / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling / interleukin-6 receptor activity / triglyceride mobilization / interleukin-6 binding / Interleukin-6 signaling / Interleukin-35 Signalling / oncostatin-M receptor complex / interleukin-11 receptor activity / interleukin-11 binding / 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 / 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 / interleukin-6 receptor binding / regulation of Notch signaling pathway / 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 / cytokine binding / positive regulation of Notch signaling pathway / protein tyrosine kinase activator activity / negative regulation of cytosolic calcium ion concentration / fat cell differentiation / positive regulation of smooth muscle cell migration / growth factor binding / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of T cell proliferation / B cell differentiation / cytokine activity / response to cytokine / growth factor activity / cytokine-mediated signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / cell body / positive regulation of peptidyl-serine phosphorylation / scaffold protein binding / negative regulation of neuron apoptotic process / cell population proliferation / positive regulation of MAPK cascade / receptor complex / membrane raft / external side of plasma membrane / dendrite / neuronal cell body / 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 / Long hematopoietin receptor, soluble alpha chain, conserved site / Interleukin-6 receptor alpha chain, binding / Long hematopoietin receptor, soluble alpha chains family signature. / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, Gp130 family 2, conserved site ...Interleukin-11, mammalian / Interleukin-11 / Interleukin 11 / Type I cytokine receptor, cytokine-binding domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Interleukin-6 receptor alpha chain, binding / Long hematopoietin receptor, soluble alpha chains family signature. / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsGardner S / Bubeck D / Jin Y
Funding support United Kingdom, European Union, 4 items
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
CitationJournal: 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, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18741.png

Downloads & links

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Map

FileDownload / File: emd_18741.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map.
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 1.01
Minimum - Maximum-5.2603135 - 9.202268999999999
Average (Standard dev.)-0.0005896182 (±0.06763965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 474.87997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18741_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map.

Fileemd_18741_additional_1.map
AnnotationUnsharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Locally filtered map.

Fileemd_18741_additional_2.map
AnnotationLocally filtered map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map 1.

Fileemd_18741_half_map_1.map
AnnotationHalf map 1.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2.

Fileemd_18741_half_map_2.map
AnnotationHalf map 2.
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : IL-11 signalling complex

EntireName: IL-11 signalling complex
Components
  • Complex: IL-11 signalling complex
    • Protein or peptide: Interleukin-11Interleukin 11
    • Protein or peptide: Interleukin-6 receptor subunit beta
    • Protein or peptide: Interleukin-11 receptor subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: IL-11 signalling complex

SupramoleculeName: IL-11 signalling complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Interleukin-11

MacromoleculeName: Interleukin-11 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.455186 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNCVCRLVLV VLSLWPDTAV APGPPPGPPR VSPDPRAELD STVLLTRSLL ADTRQLAAQL RDKFPADGDH NLDSLPTLAM SAGALGALQ LPGVLTRLRA DLLSYLRHVQ WLRRAGGSSL KTLEPELGTL QARLDRLLRR LQLLMSRLAL PQPPPDPPAP P LAPPSSAW ...String:
MNCVCRLVLV VLSLWPDTAV APGPPPGPPR VSPDPRAELD STVLLTRSLL ADTRQLAAQL RDKFPADGDH NLDSLPTLAM SAGALGALQ LPGVLTRLRA DLLSYLRHVQ WLRRAGGSSL KTLEPELGTL QARLDRLLRR LQLLMSRLAL PQPPPDPPAP P LAPPSSAW GGIRAAHAIL GGLHLTLDWA VRGLLLLKTR L

UniProtKB: Interleukin-11

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Macromolecule #2: Interleukin-6 receptor subunit beta

MacromoleculeName: Interleukin-6 receptor subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 102.568906 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSAPRIWLAQ ALLFFLTTES IGQLLEPCGY IYPEFPVVQR GSNFTAICVL KEACLQHYYV NASYIVWKTN HAAVPREQVT VINRTTSSV TFTDVVLPSV QLTCNILSFG QIEQNVYGVT MLSGFPPDKP TNLTCIVNEG KNMLCQWDPG RETYLETNYT L KSEWATEK ...String:
MSAPRIWLAQ ALLFFLTTES IGQLLEPCGY IYPEFPVVQR GSNFTAICVL KEACLQHYYV NASYIVWKTN HAAVPREQVT VINRTTSSV TFTDVVLPSV QLTCNILSFG QIEQNVYGVT MLSGFPPDKP TNLTCIVNEG KNMLCQWDPG RETYLETNYT L KSEWATEK FPDCQSKHGT SCMVSYMPTY YVNIEVWVEA ENALGKVSSE SINFDPVDKV KPTPPYNLSV TNSEELSSIL KL SWVSSGL GGLLDLKSDI QYRTKDASTW IQVPLEDTMS PRTSFTVQDL KPFTEYVFRI RSIKDSGKGY WSDWSEEASG TTY EDRPSR PPSFWYKTNP SHGQEYRSVR LIWKALPLSE ANGKILDYEV ILTQSKSVSQ TYTVTGTELT VNLTNDRYVA SLAA RNKVG KSAAAVLTIP SPHVTAAYSV VNLKAFPKDN LLWVEWTPPP KPVSKYILEW CVLSENAPCV EDWQQEDATV NRTHL RGRL LESKCYQITV TLVFATGPGG SESLKAYLKQ AAPARGPTVR TKKVGKNEAV LAWDQIPVDD QNGFIRNYSI SYRTSV GKE MVVHVDSSHT EYTLSSLSSD TLYMVRMAAY TDEGGKDGPE FTFTTPKFAQ GEIEAIVVPV CLAFLLTTLL GVLFCFN KR DLIKKHIWPN VPDPSKSHIA QWSPHTPPRH NFNSKDQMYS DGNFTDVSVV EIEANNKKPC PDDLKSVDLF KKEKVSTE G HSSGIGGSSC MSSSRPSISS NEENESAQST ASTVQYSTVV HSGYRHQVPS VQVFSRSEST QPLLDSEERP EDLQLVDSV DGGDEILPRQ PYFKQNCSQP EACPEISHFE RSNQVLSGNE EDFVRLKQQQ VSDHISQPYG SEQRRLFQEG STADALGTGA DGQMERFES VGMETTIDEE IPKSYLPQTV RQGGYMPQ

UniProtKB: Interleukin-6 receptor subunit beta

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Macromolecule #3: Interleukin-11 receptor subunit alpha

MacromoleculeName: Interleukin-11 receptor subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.266156 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSSSCSGLSR VLVAVATALV SASSPCPQAW GPPGVQYGQP GRSVKLCCPG VTAGDPVSWF RDGEPKLLQG PDSGLGHELV LAQADSTDE GTYICQTLDG ALGGTVTLQL GYPPARPVVS CQAADYENFS CTWSPSQISG LPTRYLTSYR KKTVLGADSQ R RSPSTGPW ...String:
MSSSCSGLSR VLVAVATALV SASSPCPQAW GPPGVQYGQP GRSVKLCCPG VTAGDPVSWF RDGEPKLLQG PDSGLGHELV LAQADSTDE GTYICQTLDG ALGGTVTLQL GYPPARPVVS CQAADYENFS CTWSPSQISG LPTRYLTSYR KKTVLGADSQ R RSPSTGPW PCPQDPLGAA RCVVHGAEFW SQYRINVTEV NPLGASTRLL DVSLQSILRP DPPQGLRVES VPGYPRRLRA SW TYPASWP CQPHFLLKFR LQYRPAQHPA WSTVEPAGLE EVITDAVAGL PHAVRVSARD FLDAGTWSTW SPEAWGTPST GTI PKEIPA WGQLHTQPEV EPQVDSPAPP RPSLQPHPRL LDHRDSVEQV AVLASLGILS FLGLVAGALA LGLWLRLRRG GKDG SPKPG FLASVIPVDR RPGAPNL

UniProtKB: Interleukin-11 receptor subunit alpha

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 487147
FSC plot (resolution estimation)

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