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- EMDB-18743: Structure of interleukin 6 (gp130 P496L mutant). -

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Basic information

Entry
Database: EMDB / ID: EMD-18743
TitleStructure of interleukin 6 (gp130 P496L mutant).
Map dataSharpened map.
Sample
  • Complex: IL-6 signalling complex
    • Protein or peptide: Interleukin-6 receptor subunit beta
    • Protein or peptide: Interleukin-6
    • Protein or peptide: Interleukin-6 receptor subunit alpha
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinterleukin / gp130 / IMMUNE SYSTEM
Function / homology
Function and homology information


oncostatin-M receptor activity / ciliary neurotrophic factor binding / regulation of astrocyte activation / IL-6-type cytokine receptor ligand interactions / glucagon secretion / leukemia inhibitory factor receptor activity / positive regulation of interleukin-21 production / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling ...oncostatin-M receptor activity / ciliary neurotrophic factor binding / regulation of astrocyte activation / IL-6-type cytokine receptor ligand interactions / glucagon secretion / leukemia inhibitory factor receptor activity / positive regulation of interleukin-21 production / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling / triglyceride mobilization / interleukin-6 receptor activity / interleukin-6 binding / regulation of glucagon secretion / Interleukin-6 signaling / hepatic immune response / negative regulation of interleukin-1-mediated signaling pathway / Interleukin-35 Signalling / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / oncostatin-M receptor complex / : / ciliary neurotrophic factor receptor binding / T follicular helper cell differentiation / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor-mediated signaling pathway / germinal center B cell differentiation / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / interleukin-6 receptor complex / positive regulation of extracellular matrix disassembly / positive regulation of receptor signaling pathway via STAT / positive regulation of apoptotic DNA fragmentation / positive regulation of type B pancreatic cell apoptotic process / response to peptidoglycan / regulation of microglial cell activation / hepatocyte proliferation / neutrophil apoptotic process / cell surface receptor signaling pathway via STAT / regulation of Notch signaling pathway / interleukin-6 receptor binding / negative regulation of collagen biosynthetic process / endocrine pancreas development / interleukin-11-mediated signaling pathway / positive regulation of B cell activation / inflammatory response to wounding / T-helper 17 cell lineage commitment / positive regulation of T-helper 2 cell cytokine production / negative regulation of interleukin-8 production / positive regulation of acute inflammatory response / regulation of neuroinflammatory response / positive regulation of glomerular mesangial cell proliferation / vascular endothelial growth factor production / negative regulation of chemokine production / positive regulation of astrocyte differentiation / positive regulation of neuroinflammatory response / positive regulation of leukocyte chemotaxis / intestinal epithelial cell development / neutrophil mediated immunity / positive regulation of platelet aggregation / positive regulation of cytokine production involved in inflammatory response / cytokine receptor activity / negative regulation of bone resorption / positive regulation of leukocyte adhesion to vascular endothelial cell / CD163 mediating an anti-inflammatory response / positive regulation of immunoglobulin production / glycogen metabolic process / Interleukin-6 signaling / maintenance of blood-brain barrier / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / protein tyrosine kinase activator activity / negative regulation of fat cell differentiation / negative regulation of cytosolic calcium ion concentration / neuronal cell body membrane / positive regulation of smooth muscle cell migration / MAPK3 (ERK1) activation / monocyte chemotaxis / cytokine binding / positive regulation of interleukin-17 production / Interleukin-10 signaling / MAPK1 (ERK2) activation / positive regulation of interleukin-10 production / humoral immune response / negative regulation of lipid storage / Transcriptional Regulation by VENTX / positive regulation of vascular endothelial growth factor production / regulation of angiogenesis / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of epithelial to mesenchymal transition / positive regulation of T cell proliferation / response to glucocorticoid / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of chemokine production / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway / regulation of insulin secretion / response to cytokine
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 / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. ...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 / Long hematopoietin receptor, soluble alpha chain, conserved site / 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 / 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 speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 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-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18743.png

Downloads & links

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Map

FileDownload / File: emd_18743.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map.
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 448 pix.
= 474.88 Å		1.06 Å/pix.
x 448 pix.
= 474.88 Å		1.06 Å/pix.
x 448 pix.
= 474.88 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-6.8499417 - 9.055699000000001
Average (Standard dev.)-0.0012016726 (±0.07312185)
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_18743_msk_1.map
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Additional map: Unsharpened map.

Fileemd_18743_additional_1.map
AnnotationUnsharpened map.
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Additional map: Locally filtered map.

Fileemd_18743_additional_2.map
AnnotationLocally filtered map.
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Half map: Half map 2.

Fileemd_18743_half_map_1.map
AnnotationHalf map 2.
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Histogram

Histogram (log scale)

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Half map: Half map 1.

Fileemd_18743_half_map_2.map
AnnotationHalf map 1.
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Sample components

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Entire : IL-6 signalling complex

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

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Supramolecule #1: IL-6 signalling complex

SupramoleculeName: IL-6 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-6 receptor subunit beta

MacromoleculeName: Interleukin-6 receptor subunit beta / type: protein_or_peptide / ID: 1 / 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 #2: Interleukin-6

MacromoleculeName: Interleukin-6 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.743189 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNSFSTSAFG PVAFSLGLLL VLPAAFPAPV PPGEDSKDVA APHRQPLTSS ERIDKQIRYI LDGISALRKE TCNKSNMCES SKEALAENN LNLPKMAEKD GCFQSGFNEE TCLVKIITGL LEFEVYLEYL QNRFESSEEQ ARAVQMSTKV LIQFLQKKAK N LDAITTPD ...String:
MNSFSTSAFG PVAFSLGLLL VLPAAFPAPV PPGEDSKDVA APHRQPLTSS ERIDKQIRYI LDGISALRKE TCNKSNMCES SKEALAENN LNLPKMAEKD GCFQSGFNEE TCLVKIITGL LEFEVYLEYL QNRFESSEEQ ARAVQMSTKV LIQFLQKKAK N LDAITTPD PTTNASLLTK LQAQNQWLQD MTTHLILRSF KEFLQSSLRA LRQM

UniProtKB: Interleukin-6

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Macromolecule #3: Interleukin-6 receptor subunit alpha

MacromoleculeName: Interleukin-6 receptor subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.605348 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLAVGCALLA ALLAAPGAAL APRRCPAQEV ARGVLTSLPG DSVTLTCPGV EPEDNATVHW VLRKPAAGSH PSRWAGMGRR LLLRSVQLH DSGNYSCYRA GRPAGTVHLL VDVPPEEPQL SCFRKSPLSN VVCEWGPRST PSLTTKAVLL VRKFQNSPAE D FQEPCQYS ...String:
MLAVGCALLA ALLAAPGAAL APRRCPAQEV ARGVLTSLPG DSVTLTCPGV EPEDNATVHW VLRKPAAGSH PSRWAGMGRR LLLRSVQLH DSGNYSCYRA GRPAGTVHLL VDVPPEEPQL SCFRKSPLSN VVCEWGPRST PSLTTKAVLL VRKFQNSPAE D FQEPCQYS QESQKFSCQL AVPEGDSSFY IVSMCVASSV GSKFSKTQTF QGCGILQPDP PANITVTAVA RNPRWLSVTW QD PHSWNSS FYRLRFELRY RAERSKTFTT WMVKDLQHHC VIHDAWSGLR HVVQLRAQEE FGQGEWSEWS PEAMGTPWTE SRS PPAENE VSTPMQALTT NKDDDNILFR DSANATSLPV QDSSSVPLPT FLVAGGSLAF GTLLCIAIVL RFKKTWKLRA LKEG KTSMH PPYSLGQLVP ERPRPTPVLV PLISPPVSPS SLGSDNTSSH NRPDARDPRS PYDISNTDYF FPR

UniProtKB: Interleukin-6 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: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 491673
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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