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- PDB-8v2c: Cryo-EM structure of mouse type II OSM receptor complex: model fo... -

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Basic information

Entry
Database: PDB / ID: 8v2c
TitleCryo-EM structure of mouse type II OSM receptor complex: model for assembly core region
Components
  • Interleukin-6 receptor subunit beta
  • Oncostatin-M
  • Oncostatin-M-specific receptor subunit beta
KeywordsCYTOKINE/RECEPTOR / cytokine 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 / leukemia inhibitory factor receptor activity / interleukin-6 receptor activity / interleukin-6 binding ...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 / 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-6 receptor complex / interleukin-27-mediated signaling pathway / negative regulation of hormone secretion / interleukin-6 receptor binding / interleukin-11-mediated signaling pathway / regulation of Notch signaling pathway / positive regulation of astrocyte differentiation / intestinal epithelial cell development / peripheral nervous system development / cell surface receptor signaling pathway via STAT / glycogen metabolic process / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / cytokine binding / behavioral response to pain / protein tyrosine kinase activator activity / positive regulation of osteoblast differentiation / positive regulation of T cell proliferation / coreceptor activity / positive regulation of apoptotic signaling pathway / cytokine activity / cytokine-mediated signaling pathway / cell body / response to heat / scaffold protein binding / negative regulation of neuron apoptotic process / cell surface receptor signaling pathway / positive regulation of MAPK cascade / immune response / membrane raft / external side of plasma membrane / neuronal cell body / positive regulation of cell population proliferation / dendrite / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsZhou, Y. / Franklin, M.C.
Funding support1items
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, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.0Nov 20, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 20, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 20, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 20, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 20, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oncostatin-M
B: Interleukin-6 receptor subunit beta
C: Oncostatin-M-specific receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,82211
Polymers173,0373
Non-polymers2,7868
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Oncostatin-M


Mass: 20645.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Osm / Production host: Escherichia coli (E. coli) / References: UniProt: P53347
#2: Protein Interleukin-6 receptor subunit beta


Mass: 70033.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il6st / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q00560
#3: Protein Oncostatin-M-specific receptor subunit beta


Mass: 82357.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Osmr / Production host: Homo sapiens (human) / References: UniProt: O70458
#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.: 5
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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
Has protein modificationY

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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: Mouse OSM in complex with gp130 and OSMR / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Buffer solutionpH: 7.5
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 FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 270829 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024700
ELECTRON MICROSCOPYf_angle_d0.4016379
ELECTRON MICROSCOPYf_dihedral_angle_d25.237672
ELECTRON MICROSCOPYf_chiral_restr0.04746
ELECTRON MICROSCOPYf_plane_restr0.003802

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