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Yorodumi- PDB-8u18: Cryo-EM structure of murine Thrombopoietin receptor ectodomain in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8u18 | |||||||||
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Title | Cryo-EM structure of murine Thrombopoietin receptor ectodomain in complex with Tpo | |||||||||
Components |
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Keywords | CYTOKINE/RECEPTOR / Receptor / cytokine / signalling / haematopoiesis / CYTOKINE-RECEPTOR complex | |||||||||
Function / homology | Function and homology information thrombopoietin receptor activity / basophil homeostasis / regulation of chemokine production / monocyte homeostasis / thrombopoietin-mediated signaling pathway / positive regulation of hematopoietic stem cell proliferation / cell surface receptor signaling pathway via STAT / regulation of stem cell division / positive regulation of lymphocyte proliferation / megakaryocyte differentiation ...thrombopoietin receptor activity / basophil homeostasis / regulation of chemokine production / monocyte homeostasis / thrombopoietin-mediated signaling pathway / positive regulation of hematopoietic stem cell proliferation / cell surface receptor signaling pathway via STAT / regulation of stem cell division / positive regulation of lymphocyte proliferation / megakaryocyte differentiation / positive regulation of megakaryocyte differentiation / positive regulation of platelet formation / eosinophil homeostasis / regulation of stem cell proliferation / myeloid cell differentiation / neutrophil homeostasis / definitive hemopoiesis / platelet formation / megakaryocyte development / homeostasis of number of cells / immunoglobulin mediated immune response / cytokine activity / hormone activity / nuclear membrane / cell population proliferation / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / DNA-binding transcription factor activity / external side of plasma membrane / signaling receptor binding / neuronal cell body / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / Golgi apparatus / cell surface / extracellular space / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Sarson-Lawrence, K.S. / Hardy, J.M. / Leis, A. / Babon, J.J. / Kershaw, N.J. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Nat Commun / Year: 2024 Title: Cryo-EM structure of the extracellular domain of murine Thrombopoietin Receptor in complex with Thrombopoietin. Authors: Kaiseal T G Sarson-Lawrence / Joshua M Hardy / Josephine Iaria / Dina Stockwell / Kira Behrens / Tamanna Saiyed / Cyrus Tan / Leila Jebeli / Nichollas E Scott / Toby A Dite / Nicos A Nicola ...Authors: Kaiseal T G Sarson-Lawrence / Joshua M Hardy / Josephine Iaria / Dina Stockwell / Kira Behrens / Tamanna Saiyed / Cyrus Tan / Leila Jebeli / Nichollas E Scott / Toby A Dite / Nicos A Nicola / Andrew P Leis / Jeffrey J Babon / Nadia J Kershaw / Abstract: Thrombopoietin (Tpo) is the primary regulator of megakaryocyte and platelet numbers and is required for haematopoetic stem cell maintenance. Tpo functions by binding its receptor (TpoR, a homodimeric ...Thrombopoietin (Tpo) is the primary regulator of megakaryocyte and platelet numbers and is required for haematopoetic stem cell maintenance. Tpo functions by binding its receptor (TpoR, a homodimeric Class I cytokine receptor) and initiating cell proliferation or differentiation. Here we characterise the murine Tpo:TpoR signalling complex biochemically and structurally, using cryo-electron microscopy. Tpo uses opposing surfaces to recruit two copies of receptor, forming a 1:2 complex. Although it binds to the same, membrane-distal site on both receptor chains, it does so with significantly different affinities and its highly glycosylated C-terminal domain is not required. In one receptor chain, a large insertion, unique to TpoR, forms a partially structured loop that contacts cytokine. Tpo binding induces the juxtaposition of the two receptor chains adjacent to the cell membrane. The therapeutic agent romiplostim also targets the cytokine-binding site and the characterisation presented here supports the future development of improved TpoR agonists. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u18.cif.gz | 193.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u18.ent.gz | 147 KB | Display | PDB format |
PDBx/mmJSON format | 8u18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u18_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8u18_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8u18_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 8u18_validation.cif.gz | 59.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/8u18 ftp://data.pdbj.org/pub/pdb/validation_reports/u1/8u18 | HTTPS FTP |
-Related structure data
Related structure data | 41805MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 56559.676 Da / Num. of mol.: 2 Fragment: extracellular domain,leucine zipper,extracellular domain,leucine zipper Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: Mpl, Tpor, GCN4 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q08351, UniProt: A0A8H8ULK5 #2: Protein | | Mass: 19611.674 Da / Num. of mol.: 1 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Thpo / Cell line (production host): FreeStyle 293-F / Production host: Homo sapiens (human) / References: UniProt: P40226 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / #5: Sugar | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Value: 0.131698 MDa / Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.55 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: TpoR1-479-LeuZ and TPON were combined with a molar ratio of 1:1.5 and applied to superdex 200 10/300 increased column equilibrated in TBS pH7.5. The resultant peaks were analysed by SDS-PAGE ...Details: TpoR1-479-LeuZ and TPON were combined with a molar ratio of 1:1.5 and applied to superdex 200 10/300 increased column equilibrated in TBS pH7.5. The resultant peaks were analysed by SDS-PAGE and SEC-MALS, and those corresponding to the complex were pooled and concentrated to 0.55 mg/ml. CTAB (Hexadecyl-trimethylammonium bromide) was added right before plunge freezing to a concentration of 0.005% (w/v). | ||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 K Details: Blot time of 4 s, blot force of 6 and no wait time or drain time. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3600 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.38 sec. / Electron dose: 50.57 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6130 |
EM imaging optics | Energyfilter name: GIF Bioquantum |
-Processing
EM software |
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Image processing | Details: Movies were aligned using patch motion correction and defocus values were estimated using patch CTF estimation. Images with significant astigmatism, ice contamination, or drift were removed ...Details: Movies were aligned using patch motion correction and defocus values were estimated using patch CTF estimation. Images with significant astigmatism, ice contamination, or drift were removed resulting in 5,297 micrographs. | ||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: Defocus values were estimated using patch CTF estimation and CTF correction was performed during 3D reccnstruction. Type: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2353523 Details: Templates for picking were generated using a gaussian based picking approach, followed by 2D classification and selection of high-quality 2D classes for template picking. | ||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 745000 / Algorithm: BACK PROJECTION Details: Final map was generated using Non-uniform refinement followed by 3DFlex refinement in cryoSPARC. Map was sharpened by deepEMhancer. Num. of class averages: 73 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: ChimeraX was used to perform rigid-body fitting of domains and modelling was performed using Coot and ISOLDE. Refinement was carried out in PHENIX. | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Details: Multimer complex of the complete assembly was produced using AlphaFold2 on Google CoLab Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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