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- EMDB-68584: Structure of the IL-31/IL-31RA/OSMRB complex -

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Basic information

Entry
Database: EMDB / ID: EMD-68584
TitleStructure of the IL-31/IL-31RA/OSMRB complex
Map data
Sample
  • Complex: IL-31/IL-31RA/OSMRB complex
    • Protein or peptide: Interleukin-31
    • Protein or peptide: Interleukin-31 receptor subunit alpha
    • Protein or peptide: Oncostatin-M-specific receptor subunit beta
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsIL-31 / cytokine
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsFeng Y / Dong XC
Funding support China, 1 items
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 GF / Dong XC
History
DepositionJan 19, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68584.png

Downloads & links

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Map

FileDownload / File: emd_68584.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 288 pix.
= 231.264 Å		0.8 Å/pix.
x 288 pix.
= 231.264 Å		0.8 Å/pix.
x 288 pix.
= 231.264 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.803 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.31835425 - 0.5186564
Average (Standard dev.)0.00022626818 (±0.0074182493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 231.26399 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68584_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68584_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : IL-31/IL-31RA/OSMRB complex

EntireName: IL-31/IL-31RA/OSMRB complex
Components
  • Complex: IL-31/IL-31RA/OSMRB complex
    • Protein or peptide: Interleukin-31
    • Protein or peptide: Interleukin-31 receptor subunit alpha
    • Protein or peptide: Oncostatin-M-specific receptor subunit beta
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: IL-31/IL-31RA/OSMRB complex

SupramoleculeName: IL-31/IL-31RA/OSMRB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Interleukin-31

MacromoleculeName: Interleukin-31 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.856054 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SHTLPVRLLR PSDDVQKIVE ELQSLSKMLL KDVEEEKGVL VSQNYTLPCL SPDAQPPNNI HSPAIRAYLK TIRQLDNKSV IDEIIEHLD KLIFQDAPET NISVPTDTHE CKRFILTISQ QFSECMDLAL KSLTSGAQQA TT

UniProtKB: Interleukin-31

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Macromolecule #2: Interleukin-31 receptor subunit alpha

MacromoleculeName: Interleukin-31 receptor subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.864186 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ALPAKPENIS CVYYYRKNLT CTWSPGKETS YTQYTVKRTY AFGEKHDNCT TNSSTSENRA SCSFFLPRIT IPDNYTIEVE AENGDGVIK SHMTYWRLEN IAKTEPPKIF RVKPVLGIKR MIQIEWIKPE LAPVSSDLKY TLRFRTVNST SWMEVNFAKN R KDKNQTYN ...String:
ALPAKPENIS CVYYYRKNLT CTWSPGKETS YTQYTVKRTY AFGEKHDNCT TNSSTSENRA SCSFFLPRIT IPDNYTIEVE AENGDGVIK SHMTYWRLEN IAKTEPPKIF RVKPVLGIKR MIQIEWIKPE LAPVSSDLKY TLRFRTVNST SWMEVNFAKN R KDKNQTYN LTGLQPFTEY VIALRCAVKE SKFWSDWSQE KMGMTEEEHH HHHH

UniProtKB: Interleukin-31 receptor subunit alpha

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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: Homo sapiens (human)
Molecular weightTheoretical: 36.236543 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ERLPLTPVSL KVSTNSTRQS LHLQWTVHNL PYHQELKMVF QIQISRIETS NVIWVGNYST TVKWNQVLHW SWESELPLEC ATHFVRIKS LVDDAKFPEP NFWSNWSSWE EVSVQDSTGQ DILFVFPKDK LVEEGTNVTI CYVSRNIQNN VSCYLEGKQI H GEQLDPHV ...String:
ERLPLTPVSL KVSTNSTRQS LHLQWTVHNL PYHQELKMVF QIQISRIETS NVIWVGNYST TVKWNQVLHW SWESELPLEC ATHFVRIKS LVDDAKFPEP NFWSNWSSWE EVSVQDSTGQ DILFVFPKDK LVEEGTNVTI CYVSRNIQNN VSCYLEGKQI H GEQLDPHV TAFNLNSVPF IRNKGTNIYC EASQGNVSEG MKGIVLFVSK VLEEPKDFSC ETEDFKTLHC TWDPGTDTAL GW SKQPSQS YTLFESFSGE KKLCTHKNWC NWQITQDSQE TYNFTLIAEN YLRKRSVNIL FNLTHRVYHH HHHH

UniProtKB: Oncostatin-M-specific receptor subunit beta

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
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: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 246851
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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