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- EMDB-27230: Cryo-EM structure of human CLCF1 in complex with CRLF1 and CNTFR alpha -

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Basic information

Entry
Database: EMDB / ID: EMD-27230
TitleCryo-EM structure of human CLCF1 in complex with CRLF1 and CNTFR alpha
Map datamain map
Sample
  • Complex: Human CLCF1 in complex with in complex with CRLF1 and CNTFR alpha
    • Protein or peptide: Ciliary neurotrophic factor receptor subunit alpha
    • Protein or peptide: Cardiotrophin-like cytokine factor 1
    • Protein or peptide: Cytokine receptor-like factor 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscytokine signaling / CLCF1 / CNTFR alpha / CRLF1 / CYTOKINE
Function / homology
Function and homology information


CRLF-CLCF1 complex / CNTFR-CLCF1 complex / skeletal muscle organ development / ciliary neurotrophic factor receptor activity / positive regulation of isotype switching to IgE isotypes / ciliary neurotrophic factor receptor binding / ciliary neurotrophic factor-mediated signaling pathway / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor receptor complex ...CRLF-CLCF1 complex / CNTFR-CLCF1 complex / skeletal muscle organ development / ciliary neurotrophic factor receptor activity / positive regulation of isotype switching to IgE isotypes / ciliary neurotrophic factor receptor binding / ciliary neurotrophic factor-mediated signaling pathway / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor receptor complex / brainstem development / sex differentiation / positive regulation of astrocyte differentiation / negative regulation of motor neuron apoptotic process / suckling behavior / IL-6-type cytokine receptor ligand interactions / Interleukin-27 signaling / cytokine receptor activity / cell surface receptor signaling pathway via STAT / extrinsic component of membrane / ureteric bud development / motor neuron apoptotic process / positive regulation of immunoglobulin production / cytokine binding / cell surface receptor signaling pathway via JAK-STAT / positive regulation of B cell proliferation / B cell differentiation / cytokine activity / growth factor activity / cytokine-mediated signaling pathway / nervous system development / negative regulation of neuron apoptotic process / cell surface receptor signaling pathway / receptor complex / apical plasma membrane / signaling receptor binding / external side of plasma membrane / positive regulation of cell population proliferation / signal transduction / extracellular space / extracellular region / plasma membrane / cytosol
Similarity search - Function
Plethodontid receptivity factor PRF/cardiotrophin-like / Plethodontid receptivity factor PRF / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / : / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains family signature. / Four-helical cytokine-like, core / Fibronectin type III domain / Fibronectin type 3 domain ...Plethodontid receptivity factor PRF/cardiotrophin-like / Plethodontid receptivity factor PRF / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / : / Long hematopoietin receptor, soluble alpha chain, conserved site / Long hematopoietin receptor, soluble alpha chains 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
Cytokine receptor-like factor 1 / Ciliary neurotrophic factor receptor subunit alpha / Cardiotrophin-like cytokine factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27230.png

Downloads & links

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Map

FileDownload / File: emd_27230.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain 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: 0.09
Minimum - Maximum-0.6706305 - 1.2327871
Average (Standard dev.)0.000086570675 (±0.028487327)
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_27230_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_27230_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 in complex with CRLF1 and CNTFR alpha

EntireName: Human CLCF1 in complex with in complex with CRLF1 and CNTFR alpha
Components
  • Complex: Human CLCF1 in complex with in complex with CRLF1 and CNTFR alpha
    • Protein or peptide: Ciliary neurotrophic factor receptor subunit alpha
    • Protein or peptide: Cardiotrophin-like cytokine factor 1
    • Protein or peptide: Cytokine receptor-like factor 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human CLCF1 in complex with in complex with CRLF1 and CNTFR alpha

SupramoleculeName: Human CLCF1 in complex with in complex with CRLF1 and CNTFR alpha
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ciliary neurotrophic factor receptor subunit alpha

MacromoleculeName: Ciliary neurotrophic factor receptor subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.170848 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
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 EQKLIS EEDLGGEQKL ISEEDLHHHH HH

UniProtKB: Ciliary neurotrophic factor receptor subunit alpha

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Macromolecule #2: Cardiotrophin-like cytokine factor 1

MacromoleculeName: Cardiotrophin-like cytokine factor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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

UniProtKB: Cardiotrophin-like cytokine factor 1

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Macromolecule #3: Cytokine receptor-like factor 1

MacromoleculeName: Cytokine receptor-like factor 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.026652 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: AHTAVISPQD PTLLIGSSLL ATCSVHGDPP GATAEGLYWT LNGRRLPPEL SRVLNASTLA LALANLNGSR QRSGDNLVCH ARDGSILAG SCLYVGLPPE KPVNISCWSK NMKDLTCRWT PGAHGETFLH TNYSLKYKLR WYGQDNTCEE YHTVGPHSCH I PKDLALFT ...String:
AHTAVISPQD PTLLIGSSLL ATCSVHGDPP GATAEGLYWT LNGRRLPPEL SRVLNASTLA LALANLNGSR QRSGDNLVCH ARDGSILAG SCLYVGLPPE KPVNISCWSK NMKDLTCRWT PGAHGETFLH TNYSLKYKLR WYGQDNTCEE YHTVGPHSCH I PKDLALFT PYEIWVEATN RLGSARSDVL TLDILDVVTT DPPPDVHVSR VGGLEDQLSV RWVSPPALKD FLFQAKYQIR YR VEDSVDW KVVDDVSNQT SCRLAGLKPG TVYFVQVRCN PFGIYGSKKA GIWSEWSHPT AASTPRSERP GPGGGACEPR GGE PSSGPV RRELKQFLGW LKKHAYCSNL SFRLYDQWRA WMQKSHKTRN QDEGILPSGR RGTARGPARH HHHHHHHHH

UniProtKB: Cytokine receptor-like factor 1

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 4 / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 117773
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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