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- EMDB-27247: Cryo-EM map of human IL-27 signaling complex: focused refinement ... -

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Basic information

Entry
Database: EMDB / ID: EMD-27247
TitleCryo-EM map of human IL-27 signaling complex: focused refinement on the interaction core region
Map dataIL27_complex_local_refined_map
Sample
  • Complex: Human IL-27 in complex with IL-27R alpha and gp130
    • Protein or peptide: Interleukin-27 subunit beta
    • Protein or peptide: Interleukin-27 subunit alpha
    • Protein or peptide: Interleukin-27 receptor subunit alpha
    • Protein or peptide: Interleukin-6 receptor subunit beta
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscytokine signaling / IL-27 / IL-27R alpha / gp130 / EBI3 / p28 / CYTOKINE
Function / homology
Function and homology information


interleukin-27 receptor binding / regulation of T-helper 1 cell differentiation / negative regulation of T cell extravasation / negative regulation of T-helper 17 type immune response / interleukin-27 receptor activity / ciliary neurotrophic factor receptor activity / oncostatin-M-mediated signaling pathway / negative regulation of type 2 immune response / leukemia inhibitory factor signaling pathway / regulation of isotype switching to IgG isotypes ...interleukin-27 receptor binding / regulation of T-helper 1 cell differentiation / negative regulation of T cell extravasation / negative regulation of T-helper 17 type immune response / interleukin-27 receptor activity / ciliary neurotrophic factor receptor activity / oncostatin-M-mediated signaling pathway / negative regulation of type 2 immune response / leukemia inhibitory factor signaling pathway / regulation of isotype switching to IgG isotypes / negative regulation of interleukin-6-mediated signaling pathway / oncostatin-M receptor complex / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor receptor binding / ciliary neurotrophic factor-mediated signaling pathway / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / interleukin-6 receptor complex / response to Gram-positive bacterium / positive regulation of T-helper 1 type immune response / interleukin-11-mediated signaling pathway / T-helper 17 cell lineage commitment / positive regulation of alpha-beta T cell proliferation / positive regulation of adaptive immune response / positive regulation of acute inflammatory response / positive regulation of astrocyte differentiation / intestinal epithelial cell development / positive regulation of platelet aggregation / negative regulation of interleukin-17 production / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-35 Signalling / cytokine receptor activity / T-helper 1 type immune response / Interleukin-6 signaling / glycogen metabolic process / regulation of T cell proliferation / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / protein tyrosine kinase activator activity / positive regulation of cardiac muscle hypertrophy / MAPK3 (ERK1) activation / growth factor binding / cytokine binding / MAPK1 (ERK2) activation / negative regulation of interleukin-6 production / humoral immune response / negative regulation of tumor necrosis factor production / positive regulation of vascular endothelial growth factor production / positive regulation of osteoblast differentiation / coreceptor activity / T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of defense response to virus by host / positive regulation of T cell proliferation / response to cytokine / cytokine activity / cytokine-mediated signaling pathway / positive regulation of type II interferon production / transmembrane signaling receptor activity / scaffold protein binding / negative regulation of neuron apoptotic process / receptor complex / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / inflammatory response / immune response / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / innate immune response / signaling receptor binding / neuronal cell body / dendrite / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Interleukin-27 alpha / : / : / Type I cytokine receptor, cytokine-binding domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / 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 ...Interleukin-27 alpha / : / : / Type I cytokine receptor, cytokine-binding domain / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / 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
Interleukin-6 receptor subunit beta / Interleukin-27 subunit beta / Interleukin-27 receptor subunit alpha / Interleukin-27 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsZhou Y / Franklin MC
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: Sci Adv / Year: 2023
Title: Structural insights into the assembly of gp130 family cytokine signaling complexes.
Authors: Yi Zhou / Panayiotis E Stevis / Jing Cao / Kei Saotome / Jiaxi Wu / Arielle Glatman Zaretsky / Sokol Haxhinasto / George D Yancopoulos / Andrew J Murphy / Mark W Sleeman / William C Olson / Matthew C Franklin /
Abstract: The interleukin-6 (IL-6) family cytokines signal through gp130 receptor homodimerization or heterodimerization with a second signaling receptor and play crucial roles in various cellular processes. ...The interleukin-6 (IL-6) family cytokines signal through gp130 receptor homodimerization or heterodimerization with a second signaling receptor and play crucial roles in various cellular processes. We determined cryo-electron microscopy structures of five signaling complexes of this family, containing full receptor ectodomains bound to their respective ligands ciliary neurotrophic factor, cardiotrophin-like cytokine factor 1 (CLCF1), leukemia inhibitory factor, IL-27, and IL-6. Our structures collectively reveal similarities and differences in the assembly of these complexes. The acute bends at both signaling receptors in all complexes bring the membrane-proximal domains to a ~30 angstrom range but with distinct distances and orientations. We also reveal how CLCF1 engages its secretion chaperone cytokine receptor-like factor 1. Our data provide valuable insights for therapeutically targeting gp130-mediated signaling.
History
DepositionJun 7, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27247.png

Downloads & links

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Map

FileDownload / File: emd_27247.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIL27_complex_local_refined_map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 380 pix.
= 326.8 Å		0.86 Å/pix.
x 380 pix.
= 326.8 Å		0.86 Å/pix.
x 380 pix.
= 326.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.44878912 - 0.9344496
Average (Standard dev.)0.0000014061776 (±0.01880992)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 326.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A for the local refined map

Fileemd_27247_half_map_1.map
Annotationhalf map A for the local_refined_map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B for the local refined map

Fileemd_27247_half_map_2.map
Annotationhalf map B for the local_refined_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 : Human IL-27 in complex with IL-27R alpha and gp130

EntireName: Human IL-27 in complex with IL-27R alpha and gp130
Components
  • Complex: Human IL-27 in complex with IL-27R alpha and gp130
    • Protein or peptide: Interleukin-27 subunit beta
    • Protein or peptide: Interleukin-27 subunit alpha
    • Protein or peptide: Interleukin-27 receptor subunit alpha
    • Protein or peptide: Interleukin-6 receptor subunit beta
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human IL-27 in complex with IL-27R alpha and gp130

SupramoleculeName: Human IL-27 in complex with IL-27R alpha and gp130 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Interleukin-27 subunit beta

MacromoleculeName: Interleukin-27 subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.338732 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: RKGPPAALTL PRVQCRASRY PIAVDCSWTL PPAPNSTSPV SFIATYRLGM AARGHSWPCL QQTPTSTSCT ITDVQLFSMA PYVLNVTAV HPWGSSSSFV PFITEHIIKP DPPEGVRLSP LAERQLQVQW EPPGSWPFPE IFSLKYWIRY KRQGAARFHR V GPIEATSF ...String:
RKGPPAALTL PRVQCRASRY PIAVDCSWTL PPAPNSTSPV SFIATYRLGM AARGHSWPCL QQTPTSTSCT ITDVQLFSMA PYVLNVTAV HPWGSSSSFV PFITEHIIKP DPPEGVRLSP LAERQLQVQW EPPGSWPFPE IFSLKYWIRY KRQGAARFHR V GPIEATSF ILRAVRPRAR YYVQVAAQDL TDYGELSDWS LPATATMSLG K

UniProtKB: Interleukin-27 subunit beta

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Macromolecule #2: Interleukin-27 subunit alpha

MacromoleculeName: Interleukin-27 subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.87773 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: FPRPPGRPQL SLQELRREFT VSLHLARKLL SEVRGQAHRF AESHLPGVNL YLLPLGEQLP DVSLTFQAWR RLSDPERLCF ISTTLQPFH ALLGGLGTQG RWTNMERMQL WAMRLDLRDL QRHLRFQVLA AGFNLPEEEE EEEEEEEEER KGLLPGALGS A LQGPAQVS ...String:
FPRPPGRPQL SLQELRREFT VSLHLARKLL SEVRGQAHRF AESHLPGVNL YLLPLGEQLP DVSLTFQAWR RLSDPERLCF ISTTLQPFH ALLGGLGTQG RWTNMERMQL WAMRLDLRDL QRHLRFQVLA AGFNLPEEEE EEEEEEEEER KGLLPGALGS A LQGPAQVS WPQLLSTYRL LHSLELVLSR AVRELLLLSK AGHSVWPLGF PTLSPQPEQK LISEEDLGGE QKLISEEDLH HH HHH

UniProtKB: Interleukin-27 subunit alpha

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Macromolecule #3: Interleukin-27 receptor subunit alpha

MacromoleculeName: Interleukin-27 receptor subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.944184 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QGSAGPLQCY GVGPLGDLNC SWEPLGDLGA PSELHLQSQK YRSNKTQTVA VAAGRSWVAI PREQLTMSDK LLVWGTKAGQ PLWPPVFVN LETQMKPNAP RLGPDVDFSE DDPLEATVHW APPTWPSHKV LICQFHYRRC QEAAWTLLEP ELKTIPLTPV E IQDLELAT ...String:
QGSAGPLQCY GVGPLGDLNC SWEPLGDLGA PSELHLQSQK YRSNKTQTVA VAAGRSWVAI PREQLTMSDK LLVWGTKAGQ PLWPPVFVN LETQMKPNAP RLGPDVDFSE DDPLEATVHW APPTWPSHKV LICQFHYRRC QEAAWTLLEP ELKTIPLTPV E IQDLELAT GYKVYGRCRM EKEEDLWGEW SPILSFQTPP SAPKDVWVSG NLCGTPGGEE PLLLWKAPGP CVQVSYKVWF WV GGRELSP EGITCCCSLI PSGAEWARVS AVNATSWEPL TNLSLVCLDS ASAPRSVAVS SIAGSTELLV TWQPGPGEPL EHV VDWARD GDPLEKLNWV RLPPGNLSAL LPGNFTVGVP YRITVTAVSA SGLASASSVW GFREELAPLV GPTLWRLQDA PPGT PAIAW GEVPRHQLRG HLTHYTLCAQ SGTSPSVCMN VSGNTQSVTL PDLPWGPCEL WVTASTIAGQ GPPGPILRLH LPDNT LRWK EQKLISEEDL GGEQKLISEE DLHHHHHH

UniProtKB: Interleukin-27 receptor subunit alpha

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Macromolecule #4: Interleukin-6 receptor subunit beta

MacromoleculeName: Interleukin-6 receptor subunit beta / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.233203 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: ELLDPCGYIS PESPVVQLHS NFTAVCVLKE KCMDYFHVNA NYIVWKTNHF TIPKEQYTII NRTASSVTFT DIASLNIQLT CNILTFGQL EQNVYGITII SGLPPEKPKN LSCIVNEGKK MRCEWDGGRE THLETNFTLK SEWATHKFAD CKAKRDTPTS C TVDYSTVY ...String:
ELLDPCGYIS PESPVVQLHS NFTAVCVLKE KCMDYFHVNA NYIVWKTNHF TIPKEQYTII NRTASSVTFT DIASLNIQLT CNILTFGQL EQNVYGITII SGLPPEKPKN LSCIVNEGKK MRCEWDGGRE THLETNFTLK SEWATHKFAD CKAKRDTPTS C TVDYSTVY FVNIEVWVEA ENALGKVTSD HINFDPVYKV KPNPPHNLSV INSEELSSIL KLTWTNPSIK SVIILKYNIQ YR TKDASTW SQIPPEDTAS TRSSFTVQDL KPFTEYVFRI RCMKEDGKGY WSDWSEEASG ITYEDRPSKA PSFWYKIDPS HTQ GYRTVQ LVWKTLPPFE ANGKILDYEV TLTRWKSHLQ NYTVNATKLT VNLTNDRYLA TLTVRNLVGK SDAAVLTIPA CDFQ ATHPV MDLKAFPKDN MLWVEWTTPR ESVKKYILEW CVLSDKAPCI TDWQQEDGTV HRTYLRGNLA ESKCYLITVT PVYAD GPGS PESIKAYLKQ APPSKGPTVR TKKVGKNEAV LEWDQLPVDV QNGFIRNYTI FYRTIIGNET AVNVDSSHTE YTLSSL TSD TLYMVRMAAY TDEGGKDGPE FTFTTPKFAQ GEIEEQKLIS EEDLGGEQKL ISEEDLHHHH HH

UniProtKB: Interleukin-6 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: 5 / 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 139752
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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