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- EMDB-27231: Cryo-EM map of human CLCF1 signaling complex with full extracellu... -

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Basic information

Entry
Database: EMDB / ID: EMD-27231
TitleCryo-EM map of human CLCF1 signaling complex with full extracellular domains
Map dataCLCF1 signaling complex map
Sample
  • Complex: Human CLCF1 in complex with CNTFR alpha, gp130, and LIFR
    • Protein or peptide: Cardiotrophin-like cytokine factor 1
    • Protein or peptide: Ciliary neurotrophic factor receptor subunit alpha
    • Protein or peptide: Leukemia inhibitory factor receptor
    • Protein or peptide: Interleukin-6 receptor subunit beta
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


CRLF-CLCF1 complex / CNTFR-CLCF1 complex / skeletal muscle organ development / leukemia inhibitory factor receptor activity / oncostatin-M receptor activity / oncostatin-M-mediated signaling pathway / ciliary neurotrophic factor receptor activity / negative regulation of interleukin-6-mediated signaling pathway / leukemia inhibitory factor signaling pathway / interleukin-27 receptor activity ...CRLF-CLCF1 complex / CNTFR-CLCF1 complex / skeletal muscle organ development / leukemia inhibitory factor receptor activity / oncostatin-M receptor activity / oncostatin-M-mediated signaling pathway / ciliary neurotrophic factor receptor activity / negative regulation of interleukin-6-mediated signaling pathway / leukemia inhibitory factor signaling pathway / interleukin-27 receptor activity / oncostatin-M receptor complex / positive regulation of isotype switching to IgE isotypes / ciliary neurotrophic factor receptor binding / interleukin-11 receptor activity / interleukin-11 binding / RUNX1 regulates transcription of genes involved in interleukin signaling / interleukin-6 receptor activity / interleukin-6 binding / ciliary neurotrophic factor-mediated signaling pathway / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / interleukin-6 receptor complex / brainstem development / interleukin-11-mediated signaling pathway / T-helper 17 cell lineage commitment / sex differentiation / positive regulation of adaptive immune response / positive regulation of acute inflammatory response / positive regulation of astrocyte differentiation / intestinal epithelial cell development / negative regulation of motor neuron apoptotic process / positive regulation of platelet aggregation / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / motor neuron apoptotic process / cytokine receptor activity / positive regulation of immunoglobulin production / extrinsic component of membrane / glycogen metabolic process / interleukin-6-mediated signaling pathway / Interleukin-6 signaling / positive regulation of Notch signaling pathway / suckling behavior / protein tyrosine kinase activator activity / positive regulation of cardiac muscle hypertrophy / cytokine binding / MAPK3 (ERK1) activation / growth factor binding / MAPK1 (ERK2) activation / cell surface receptor signaling pathway via JAK-STAT / positive regulation of vascular endothelial growth factor production / positive regulation of osteoblast differentiation / coreceptor activity / positive regulation of T cell proliferation / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / B cell differentiation / response to cytokine / cytokine activity / growth factor activity / cytokine-mediated signaling pathway / nervous system development / scaffold protein binding / negative regulation of neuron apoptotic process / cell surface receptor signaling pathway / receptor complex / membrane raft / apical plasma membrane / external side of plasma membrane / signaling receptor binding / neuronal cell body / dendrite / positive regulation of cell population proliferation / negative regulation of apoptotic process / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Plethodontid receptivity factor PRF/cardiotrophin-like / Plethodontid receptivity factor PRF / : / Leukemia inhibitory factor receptor, Ig-like domain / Leukemia inhibitory factor receptor, D2 domain / Leukemia inhibitory factor receptor, N-terminal / Leukemia inhibitory factor receptor D2 domain / Leukemia inhibitory factor receptor N-terminal domain / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding ...Plethodontid receptivity factor PRF/cardiotrophin-like / Plethodontid receptivity factor PRF / : / Leukemia inhibitory factor receptor, Ig-like domain / Leukemia inhibitory factor receptor, D2 domain / Leukemia inhibitory factor receptor, N-terminal / Leukemia inhibitory factor receptor D2 domain / Leukemia inhibitory factor receptor N-terminal domain / 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, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / 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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Ciliary neurotrophic factor receptor subunit alpha / Interleukin-6 receptor subunit beta / Leukemia inhibitory factor receptor / Cardiotrophin-like cytokine factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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_27231.png

Downloads & links

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Map

FileDownload / File: emd_27231.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCLCF1 signaling complex map
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.4242069 - 0.8031161
Average (Standard dev.)-7.486671e-05 (±0.018158928)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_27231_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_27231_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 CLCF1 in complex with CNTFR alpha, gp130, and LIFR

EntireName: Human CLCF1 in complex with CNTFR alpha, gp130, and LIFR
Components
  • Complex: Human CLCF1 in complex with CNTFR alpha, gp130, and LIFR
    • Protein or peptide: Cardiotrophin-like cytokine factor 1
    • Protein or peptide: Ciliary neurotrophic factor receptor subunit alpha
    • Protein or peptide: Leukemia inhibitory factor receptor
    • Protein or peptide: Interleukin-6 receptor subunit beta
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human CLCF1 in complex with CNTFR alpha, gp130, and LIFR

SupramoleculeName: Human CLCF1 in complex with CNTFR alpha, gp130, and LIFR
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cardiotrophin-like cytokine factor 1

MacromoleculeName: Cardiotrophin-like cytokine factor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.122336 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: LNRTGDPGPG PSIQKTYDLT RYLEHQLRSL AGTYLNYLGP PFNEPDFNPP RLGAETLPRA TVDLEVWRSL NDKLRLTQNY EAYSHLLCY LRGLNRQAAT AELRRSLAHF CTSLQGLLGS IAGVMAALGY PLPQPLPGTE PTWTPGPAHS DFLQKMDDFW L LKELQTWL ...String:
LNRTGDPGPG PSIQKTYDLT RYLEHQLRSL AGTYLNYLGP PFNEPDFNPP RLGAETLPRA TVDLEVWRSL NDKLRLTQNY EAYSHLLCY LRGLNRQAAT AELRRSLAHF CTSLQGLLGS IAGVMAALGY PLPQPLPGTE PTWTPGPAHS DFLQKMDDFW L LKELQTWL WRSAKDFNRL KKKMQPPAAA VTLHLGAHGF HHHHHH

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Macromolecule #2: Ciliary neurotrophic factor receptor subunit alpha

MacromoleculeName: Ciliary neurotrophic factor receptor subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.12357 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: QRHSPQEAPH VQYERLGSDV TLPCGTANWD AAVTWRVNGT DLAPDLLNGS QLVLHGLELG HSGLYACFHR DSWHLRHQVL LHVGLPPRE PVLSCRSNTY PKGFYCSWHL PTPTYIPNTF NVTVLHGSKI MVCEKDPALK NRCHIRYMHL FSTIKYKVSI S VSNALGHN ...String:
QRHSPQEAPH VQYERLGSDV TLPCGTANWD AAVTWRVNGT DLAPDLLNGS QLVLHGLELG HSGLYACFHR DSWHLRHQVL LHVGLPPRE PVLSCRSNTY PKGFYCSWHL PTPTYIPNTF NVTVLHGSKI MVCEKDPALK NRCHIRYMHL FSTIKYKVSI S VSNALGHN ATAITFDEFT IVKPDPPENV VARPVPSNPR RLEVTWQTPS TWPDPESFPL KFFLRYRPLI LDQWQHVELS DG TAHTITD AYAGKEYIIQ VAAKDNEIGT WSDWSVAAHA TPWTEEPRHL TTEAQAAETT TSTTSSLAPP PTTKICDPGE LGS GGGP

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Macromolecule #3: Leukemia inhibitory factor receptor

MacromoleculeName: Leukemia inhibitory factor receptor / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.834812 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QKKGAPHDLK CVTNNLQVWN CSWKAPSGTG RGTDYEVCIE NRSRSCYQLE KTSIKIPALS HGDYEITINS LHDFGSSTSK FTLNEQNVS LIPDTPEILN LSADFSTSTL YLKWNDRGSV FPHRSNVIWE IKVLRKESME LVKLVTHNTT LNGKDTLHHW S WASDMPLE ...String:
QKKGAPHDLK CVTNNLQVWN CSWKAPSGTG RGTDYEVCIE NRSRSCYQLE KTSIKIPALS HGDYEITINS LHDFGSSTSK FTLNEQNVS LIPDTPEILN LSADFSTSTL YLKWNDRGSV FPHRSNVIWE IKVLRKESME LVKLVTHNTT LNGKDTLHHW S WASDMPLE CAIHFVEIRC YIDNLHFSGL EEWSDWSPVK NISWIPDSQT KVFPQDKVIL VGSDITFCCV SQEKVLSALI GH TNCPLIH LDGENVAIKI RNISVSASSG TNVVFTTEDN IFGTVIFAGY PPDTPQQLNC ETHDLKEIIC SWNPGRVTAL VGP RATSYT LVESFSGKYV RLKRAEAPTN ESYQLLFQML PNQEIYNFTL NAHNPLGRSQ STILVNITEK VYPHTPTSFK VKDI NSTAV KLSWHLPGNF AKINFLCEIE IKKSNSVQEQ RNVTIKGVEN SSYLVALDKL NPYTLYTFRI RCSTETFWKW SKWSN KKQH LTTEASPSKG PDTWREWSSD GKNLIIYWKP LPINEANGKI LSYNVSCSSD EETQSLSEIP DPQHKAEIRL DKNDYI ISV VAKNSVGSSP PSKIASMEIP NDDLKIEQVV GMGKGILLTW HYDPNMTCDY VIKWCNSSRS EPCLMDWRKV PSNSTET VI ESDEFRPGIR YNFFLYGCRN QGYQLLRSMI GYIEELAPIV APNFTVEDTS ADSILVKWED IPVEELRGFL RGYLFYFG K GERDTSKMRV LESGRSDIKV KNITDISQKT LRIADLQGKT SYHLVLRAYT DGGVGPEKSM YVVTKENSEQ KLISEEDLG GEQKLISEED LHHHHHH

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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

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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: 6 / 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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92463
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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