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- EMDB-27246: Cryo-EM map of human IL-27 signaling complex with full extracellu... -

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Basic information

Entry
Database: EMDB / ID: EMD-27246
TitleCryo-EM map of human IL-27 signaling complex with full extracellular domains
Map dataIL-27 Full Map
Sample
  • Complex: Human IL-27 in complex with IL-27R alpha and gp130Interleukin 27
    • 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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.14 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-
UpdateMar 29, 2023-
Current statusMar 29, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27246.png

Downloads & links

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Map

FileDownload / File: emd_27246.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIL-27 Full Map
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.27891365 - 0.6490562
Average (Standard dev.)0.00014768288 (±0.014380161)
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

Fileemd_27246_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_27246_half_map_2.map
Annotationhalf map B
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 gp130Interleukin 27
Components
  • Complex: Human IL-27 in complex with IL-27R alpha and gp130Interleukin 27
    • 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 / Chimera: Yes / 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

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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

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Macromolecule #3: Interleukin-27 receptor subunit alpha

MacromoleculeName: Interleukin-27 receptor subunit alpha / type: protein_or_peptide / ID: 3
Details: The model of IL-27R alpha D3-D5 predicted by AlphaFold was rigid-body refined against the EM density
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

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Macromolecule #4: Interleukin-6 receptor subunit beta

MacromoleculeName: Interleukin-6 receptor subunit beta / type: protein_or_peptide / ID: 4
Details: The model of gp130 D4-D6 derived from PDB:3L5H was rigid-body refined against the EM density
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

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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 / N-Acetylglucosamine

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

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 139752

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