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- PDB-22pl: Structure of the IL-31/IL-31RA/OSMRB complex -

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Basic information

Entry
Database: PDB / ID: 22pl
TitleStructure of the IL-31/IL-31RA/OSMRB complex
Components
  • Interleukin-31
  • Interleukin-31 receptor subunit alpha
  • Oncostatin-M-specific receptor subunit beta
KeywordsCYTOKINE / IL-31
Function / homology
Function and homology information


type I oncostatin-M receptor complex / negative regulation of macrophage activation / ciliary neurotrophic factor receptor binding / oncostatin-M-mediated signaling pathway / positive regulation of acute inflammatory response / homeostatic process / cytokine receptor binding / IL-6-type cytokine receptor ligand interactions / cytokine receptor activity / growth factor binding ...type I oncostatin-M receptor complex / negative regulation of macrophage activation / ciliary neurotrophic factor receptor binding / oncostatin-M-mediated signaling pathway / positive regulation of acute inflammatory response / homeostatic process / cytokine receptor binding / IL-6-type cytokine receptor ligand interactions / cytokine receptor activity / growth factor binding / positive regulation of tyrosine phosphorylation of STAT protein / cytokine binding / macrophage differentiation / monocyte differentiation / cell surface receptor signaling pathway via JAK-STAT / immune system process / response to cytokine / cell surface receptor protein tyrosine kinase signaling pathway / cytokine activity / defense response / cytokine-mediated signaling pathway / MAPK cascade / presynaptic membrane / signaling receptor complex / transcription coactivator activity / apical plasma membrane / external side of plasma membrane / axon / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / : / extracellular region / membrane / plasma membrane
Similarity search - Function
Interleukin-31 / Interleukin 31 / Leukemia inhibitory factor receptor, D2 domain / : / Leukemia inhibitory factor receptor D2 domain / Leukemia inhibitory factor receptor, Ig-like domain / : / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Leukemia inhibitory factor receptor D4 domain ...Interleukin-31 / Interleukin 31 / Leukemia inhibitory factor receptor, D2 domain / : / Leukemia inhibitory factor receptor D2 domain / Leukemia inhibitory factor receptor, Ig-like domain / : / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Leukemia inhibitory factor receptor D4 domain / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / 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
Interleukin-31 / Interleukin-31 receptor subunit alpha / Oncostatin-M-specific receptor subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsFeng, Y. / Dong, X.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural basis of extracellular receptor assemblies mediated by IL-31
Authors: Feng, Y. / Qian, G.F. / Dong, X.C.
History
DepositionJan 19, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: 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-31
B: Interleukin-31 receptor subunit alpha
C: Oncostatin-M-specific receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4107
Polymers76,9573
Non-polymers1,4534
Water00
1


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

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Interleukin-31 / IL-31


Mass: 15856.054 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL31 / Production host: Homo sapiens (human) / References: UniProt: Q6EBC2
#2: Protein Interleukin-31 receptor subunit alpha / IL-31 receptor subunit alpha / IL-31R subunit alpha / IL-31R-alpha / IL-31RA / Cytokine receptor- ...IL-31 receptor subunit alpha / IL-31R subunit alpha / IL-31R-alpha / IL-31RA / Cytokine receptor-like 3 / GLM-R / hGLM-R / Gp130-like monocyte receptor / Gp130-like receptor / ZcytoR17


Mass: 24864.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL31RA, CRL3, GPL, UNQ6368/PRO21073/PRO21384 / Production host: Homo sapiens (human) / References: UniProt: Q8NI17
#3: Protein Oncostatin-M-specific receptor subunit beta / Interleukin-31 receptor subunit beta / IL-31 receptor subunit beta / IL-31R subunit beta / IL-31R- ...Interleukin-31 receptor subunit beta / IL-31 receptor subunit beta / IL-31R subunit beta / IL-31R-beta / IL-31RB


Mass: 36236.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OSMR, OSMRB / Production host: Homo sapiens (human) / References: UniProt: Q99650

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Sugars , 3 types, 4 molecules

#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.: 1
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: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 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.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

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Details

Has ligand of interestY
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: IL-31/IL-31RA/OSMRB complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 246851 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024941
ELECTRON MICROSCOPYf_angle_d0.5576700
ELECTRON MICROSCOPYf_dihedral_angle_d4.401666
ELECTRON MICROSCOPYf_chiral_restr0.042771
ELECTRON MICROSCOPYf_plane_restr0.005841

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