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- EMDB-42905: Cryo-EM structure of mouse type II OSM receptor complex: model fo... -

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Basic information

Entry
Database: EMDB / ID: EMD-42905
TitleCryo-EM structure of mouse type II OSM receptor complex: model for assembly core region
Map data
Sample
  • Complex: Mouse OSM in complex with gp130 and OSMR
    • Protein or peptide: Oncostatin-M
    • Protein or peptide: Interleukin-6 receptor subunit beta
    • Protein or peptide: Oncostatin-M-specific receptor subunit beta
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscytokine signaling / OSM / gp130 / OSMR / CYTOKINE / CYTOKINE-RECEPTOR complex
Function / homology
Function and homology information


oncostatin-M receptor binding / oncostatin-M receptor activity / meiotic nuclear division / IL-6-type cytokine receptor ligand interactions / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling / triglyceride mobilization / leukemia inhibitory factor receptor activity / interleukin-6 receptor activity ...oncostatin-M receptor binding / oncostatin-M receptor activity / meiotic nuclear division / IL-6-type cytokine receptor ligand interactions / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interleukin-27 signaling / triglyceride mobilization / leukemia inhibitory factor receptor activity / interleukin-6 receptor activity / interleukin-6 binding / Interleukin-6 signaling / Interleukin-35 Signalling / oncostatin-M-mediated signaling pathway / negative regulation of meiotic nuclear division / oncostatin-M receptor complex / ciliary neurotrophic factor receptor binding / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / interleukin-6 receptor complex / negative regulation of hormone secretion / regulation of Notch signaling pathway / interleukin-6 receptor binding / interleukin-11-mediated signaling pathway / positive regulation of astrocyte differentiation / peripheral nervous system development / intestinal epithelial cell development / cytokine receptor activity / glycogen metabolic process / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / negative regulation of cytosolic calcium ion concentration / neuronal cell body membrane / protein tyrosine kinase activator activity / positive regulation of smooth muscle cell migration / cytokine binding / behavioral response to pain / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of T cell proliferation / cytokine activity / positive regulation of apoptotic signaling pathway / cytokine-mediated signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-serine phosphorylation / response to heat / cell body / scaffold protein binding / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / receptor complex / cell surface receptor signaling pathway / immune response / 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 / identical protein binding / plasma membrane
Similarity search - Function
Oncostatin-M / Leukemia inhibitory factor receptor, D2 domain / : / Leukemia inhibitory factor receptor D2 domain / Leukemia inhibitory factor receptor, Ig-like domain / Leukemia inhibitory factor /oncostatin / Leukemia inhibitory factor /oncostatin, conserved site / LIF / OSM family / LIF / OSM family signature. / leukemia inhibitory factor ...Oncostatin-M / Leukemia inhibitory factor receptor, D2 domain / : / Leukemia inhibitory factor receptor D2 domain / Leukemia inhibitory factor receptor, Ig-like domain / Leukemia inhibitory factor /oncostatin / Leukemia inhibitory factor /oncostatin, conserved site / LIF / OSM family / LIF / OSM family signature. / leukemia inhibitory factor / 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, 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-like fold
Similarity search - Domain/homology
Oncostatin-M-specific receptor subunit beta / Oncostatin-M / Interleukin-6 receptor subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsZhou Y / Franklin MC
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2024
Title: Structures of complete extracellular assemblies of type I and type II Oncostatin M receptor complexes.
Authors: Yi Zhou / Panayiotis E Stevis / Jing Cao / George Ehrlich / Jennifer Jones / Ashique Rafique / Mark W Sleeman / William C Olson / Matthew C Franklin /
Abstract: Oncostatin M (OSM) is a unique Interleukin 6 (IL-6) family cytokine that plays pivotal roles in numerous biological events by signaling via two types of receptor complexes. While type I OSM receptor ...Oncostatin M (OSM) is a unique Interleukin 6 (IL-6) family cytokine that plays pivotal roles in numerous biological events by signaling via two types of receptor complexes. While type I OSM receptor complex is formed by glycoprotein 130 (gp130) heterodimerization with Leukemia Inhibitory Factor receptor (LIFR), type II OSM receptor complex is composed of gp130 and OSM receptor (OSMR). OSM is an important contributor to multiple inflammatory diseases and cancers while OSM inhibition has been shown to be effective at reducing symptoms, making OSM an attractive therapeutic target. Using cryogenic electron microscopy (cryo-EM), we characterize full extracellular assemblies of human type I OSM receptor complex and mouse type II OSM receptor complex. The juxtamembrane domains of both complexes are situated in close proximity due to acute bends of the receptors. The rigid N-terminal extension of OSM contributes to gp130 binding and OSM signaling. Neither glycosylation nor pro-domain cleavage of OSM affects its activity. Mutagenesis identifies multiple OSM and OSMR residues crucial for complex formation and signaling. Our data reveal the structural basis for the assemblies of both type I and type II OSM receptor complexes and provide insights for modulation of OSM signaling in therapeutics.
History
DepositionNov 22, 2023-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42905.png

Downloads & links

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Map

FileDownload / File: emd_42905.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 360 pix.
= 309.6 Å		0.86 Å/pix.
x 360 pix.
= 309.6 Å		0.86 Å/pix.
x 360 pix.
= 309.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.3640255 - 0.94973284
Average (Standard dev.)-0.000011983255 (±0.016498465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 309.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42905_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: #2

Fileemd_42905_half_map_2.map
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Sample components

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Entire : Mouse OSM in complex with gp130 and OSMR

EntireName: Mouse OSM in complex with gp130 and OSMR
Components
  • Complex: Mouse OSM in complex with gp130 and OSMR
    • Protein or peptide: Oncostatin-M
    • Protein or peptide: Interleukin-6 receptor subunit beta
    • Protein or peptide: Oncostatin-M-specific receptor subunit beta
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Mouse OSM in complex with gp130 and OSMR

SupramoleculeName: Mouse OSM in complex with gp130 and OSMR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Macromolecule #1: Oncostatin-M

MacromoleculeName: Oncostatin-M / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 20.645201 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ANRGCSNSSS QLLSQLQNQA NLTGNTESLL EPYIRLQNLN TPDLRAACTQ HSVAFPSEDT LRQLSKPHFL STVYTTLDRV LYQLDALRQ KFLKTPAFPK LDSARHNILG IRNNVFCMAR LLNHSLEIPE PTQTDSGASR STTTPDVFNT KIGSCGFLWG Y HRFMGSVG RVFREWDDGS TRSRR

UniProtKB: Oncostatin-M

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 70.033594 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QLLEPCGYIY PEFPVVQRGS NFTAICVLKE ACLQHYYVNA SYIVWKTNHA AVPREQVTVI NRTTSSVTFT DVVLPSVQLT CNILSFGQI EQNVYGVTML SGFPPDKPTN LTCIVNEGKN MLCQWDPGRE TYLETNYTLK SEWATEKFPD CQSKHGTSCM V SYMPTYYV ...String:
QLLEPCGYIY PEFPVVQRGS NFTAICVLKE ACLQHYYVNA SYIVWKTNHA AVPREQVTVI NRTTSSVTFT DVVLPSVQLT CNILSFGQI EQNVYGVTML SGFPPDKPTN LTCIVNEGKN MLCQWDPGRE TYLETNYTLK SEWATEKFPD CQSKHGTSCM V SYMPTYYV NIEVWVEAEN ALGKVSSESI NFDPVDKVKP TPPYNLSVTN SEELSSILKL SWVSSGLGGL LDLKSDIQYR TK DASTWIQ VPLEDTMSPR TSFTVQDLKP FTEYVFRIRS IKDSGKGYWS DWSEEASGTT YEDRPSRPPS FWYKTNPSHG QEY RSVRLI WKALPLSEAN GKILDYEVIL TQSKSVSQTY TVTGTELTVN LTNDRYVASL AARNKVGKSA AAVLTIPSPH VTAA YSVVN LKAFPKDNLL WVEWTPPPKP VSKYILEWCV LSENAPCVED WQQEDATVNR THLRGRLLES KCYQITVTPV FATGP GGSE SLKAYLKQAA PARGPTVRTK KVGKNEAVLA WDQIPVDDQN GFIRNYSISY RTSVGKEMVV HVDSSHTEYT LSSLSS DTL YMVRMAAYTD EGGKDGPEFT FTTPKFAQGE IEEQKLISEE DLGGEQKLIS EEDLHHHHHH

UniProtKB: Interleukin-6 receptor subunit beta

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Macromolecule #3: Oncostatin-M-specific receptor subunit beta

MacromoleculeName: Oncostatin-M-specific receptor subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 82.357742 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVLEEPLPLT PEIHKVSFQL KLQEVNLEWT VPALTHEELN MIFQIEISRL NISNTIWVEN YSTTVKREEA VRWNWTSDIP LECVKHFIR IRALVDDTKS LPQSSWGNWS SWKEVNAKVS VEPDKSLIFP KDKVLEEGSN VTICLMYGQN VYNVSCKLQD E PIHGEQLD ...String:
EVLEEPLPLT PEIHKVSFQL KLQEVNLEWT VPALTHEELN MIFQIEISRL NISNTIWVEN YSTTVKREEA VRWNWTSDIP LECVKHFIR IRALVDDTKS LPQSSWGNWS SWKEVNAKVS VEPDKSLIFP KDKVLEEGSN VTICLMYGQN VYNVSCKLQD E PIHGEQLD SHVSLLKLNN VVFLSDTGTN INCQATKGPK RIFGTVLFVS KVLEEPKNVS CETRDFKTLD CSWEPGVDTT LT WRKQRFQ NYTLCESFSK RCEVSNYRNS YTWQITEGSQ EMYNFTLTAE NQLRKRSVNI NFNLTHRVHP KAPQDVTLKI IGA TKANMT WKVHSHGNNY TLLCQVKLQY GEVIHEHNVS VHMSANYLFS DLDPDTKYKA FVRCASANHF WKWSDWTQKE FSTP ETAPS QALDVWRQVW SENGRRIVTL FWKPLLKSQA NGKIISYNIV VENEAKPTES EHYCVWAPAL STNLSLDLQP YKIRI TTNN SMGASPESLM VLSNDSGHEE VKEKTIKGIK DAFNISWEPV SGDTMGYVVD WCAHSQDQRC DLQWKNLGPN TTSTTI TSD DFKPGVRYNF RIFERSVEHK ARLVEKQRGY TQELAPLVNP KVEIPYSTPN SFVLRWPDYD SDFQAGFIKG YLVYVKS KE MQCNQPWERT LLPDNSVLCK YDINGSETKT LTVENLQPES LYEFFVTPYT SAGPGPNETF TKVTTPDARS HML

UniProtKB: Oncostatin-M-specific receptor subunit beta

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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: 3 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 270829
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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