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Yorodumi- EMDB-27230: Cryo-EM structure of human CLCF1 in complex with CRLF1 and CNTFR alpha -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27230 | |||||||||
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Title | Cryo-EM structure of human CLCF1 in complex with CRLF1 and CNTFR alpha | |||||||||
Map data | main map | |||||||||
Sample |
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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 / ciliary neurotrophic factor receptor complex / brainstem development / sex differentiation ...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 / ciliary neurotrophic factor receptor complex / brainstem development / sex differentiation / positive regulation of astrocyte differentiation / negative regulation of motor neuron apoptotic process / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / motor neuron apoptotic process / ureteric bud development / cytokine receptor activity / positive regulation of immunoglobulin production / extrinsic component of membrane / suckling behavior / cytokine binding / cell surface receptor signaling pathway via JAK-STAT / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / 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 / external side of plasma membrane / signaling receptor binding / positive regulation of cell population proliferation / signal transduction / extracellular space / extracellular region / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Zhou Y / Franklin MC | |||||||||
Funding support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27230.map.gz | 107.3 MB | EMDB map data format | |
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Header (meta data) | emd-27230-v30.xml emd-27230.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
Images | emd_27230.png | 77.5 KB | ||
Others | emd_27230_half_map_1.map.gz emd_27230_half_map_2.map.gz | 194.3 MB 194.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27230 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27230 | HTTPS FTP |
-Validation report
Summary document | emd_27230_validation.pdf.gz | 1003 KB | Display | EMDB validaton report |
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Full document | emd_27230_full_validation.pdf.gz | 1002.6 KB | Display | |
Data in XML | emd_27230_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_27230_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27230 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27230 | HTTPS FTP |
-Related structure data
Related structure data | 8d7hMC 8d6aC 8d74C 8d7eC 8d7rC 8d82C 8d85C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27230.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | main map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map A
File | emd_27230_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_27230_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human CLCF1 in complex with in complex with CRLF1 and CNTFR alpha
Entire | Name: Human CLCF1 in complex with in complex with CRLF1 and CNTFR alpha |
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Components |
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-Supramolecule #1: Human CLCF1 in complex with in complex with CRLF1 and CNTFR alpha
Supramolecule | Name: Human CLCF1 in complex with in complex with CRLF1 and CNTFR alpha type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Ciliary neurotrophic factor receptor subunit alpha
Macromolecule | Name: Ciliary neurotrophic factor receptor subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 39.170848 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: 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 |
-Macromolecule #2: Cardiotrophin-like cytokine factor 1
Macromolecule | Name: Cardiotrophin-like cytokine factor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.122336 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: 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 |
-Macromolecule #3: Cytokine receptor-like factor 1
Macromolecule | Name: Cytokine receptor-like factor 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 44.026652 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: 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 |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Final reconstruction | Applied 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 |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |