+Open data
-Basic information
Entry | Database: PDB / ID: 8g04 | ||||||||||||
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Title | Structure of signaling thrombopoietin-MPL receptor complex | ||||||||||||
Components |
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Keywords | CYTOKINE / TPO / TpoR / receptor / signaling / haematology | ||||||||||||
Function / homology | Function and homology information thrombopoietin receptor activity / basophil homeostasis / monocyte homeostasis / thrombopoietin-mediated signaling pathway / positive regulation of hematopoietic stem cell proliferation / cell surface receptor signaling pathway via STAT / positive regulation of lymphocyte proliferation / megakaryocyte differentiation / positive regulation of platelet formation / positive regulation of megakaryocyte differentiation ...thrombopoietin receptor activity / basophil homeostasis / monocyte homeostasis / thrombopoietin-mediated signaling pathway / positive regulation of hematopoietic stem cell proliferation / cell surface receptor signaling pathway via STAT / positive regulation of lymphocyte proliferation / megakaryocyte differentiation / positive regulation of platelet formation / positive regulation of megakaryocyte differentiation / eosinophil homeostasis / neutrophil homeostasis / megakaryocyte development / Platelet Aggregation (Plug Formation) / immunoglobulin mediated immune response / cytokine activity / growth factor activity / hormone activity / platelet aggregation / cellular response to hypoxia / nuclear membrane / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / neuron projection / external side of plasma membrane / signaling receptor binding / neuronal cell body / positive regulation of cell population proliferation / cell surface / Golgi apparatus / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
Authors | Tsutsumi, N. / Jude, K.M. / Gati, C. / Garcia, K.C. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Cell / Year: 2023 Title: Structure of the thrombopoietin-MPL receptor complex is a blueprint for biasing hematopoiesis. Authors: Naotaka Tsutsumi / Zahra Masoumi / Sophie C James / Julie A Tucker / Hauke Winkelmann / William Grey / Lora K Picton / Lucie Moss / Steven C Wilson / Nathanael A Caveney / Kevin M Jude / ...Authors: Naotaka Tsutsumi / Zahra Masoumi / Sophie C James / Julie A Tucker / Hauke Winkelmann / William Grey / Lora K Picton / Lucie Moss / Steven C Wilson / Nathanael A Caveney / Kevin M Jude / Cornelius Gati / Jacob Piehler / Ian S Hitchcock / K Christopher Garcia / Abstract: Thrombopoietin (THPO or TPO) is an essential cytokine for hematopoietic stem cell (HSC) maintenance and megakaryocyte differentiation. Here, we report the 3.4 Å resolution cryoelectron microscopy ...Thrombopoietin (THPO or TPO) is an essential cytokine for hematopoietic stem cell (HSC) maintenance and megakaryocyte differentiation. Here, we report the 3.4 Å resolution cryoelectron microscopy structure of the extracellular TPO-TPO receptor (TpoR or MPL) signaling complex, revealing the basis for homodimeric MPL activation and providing a structural rationalization for genetic loss-of-function thrombocytopenia mutations. The structure guided the engineering of TPO variants (TPO) with a spectrum of signaling activities, from neutral antagonists to partial- and super-agonists. Partial agonist TPO decoupled JAK/STAT from ERK/AKT/CREB activation, driving a bias for megakaryopoiesis and platelet production without causing significant HSC expansion in mice and showing superior maintenance of human HSCs in vitro. These data demonstrate the functional uncoupling of the two primary roles of TPO, highlighting the potential utility of TPO in hematology research and clinical HSC transplantation. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g04.cif.gz | 205.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g04.ent.gz | 155.6 KB | Display | PDB format |
PDBx/mmJSON format | 8g04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8g04_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8g04_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8g04_validation.xml.gz | 44.4 KB | Display | |
Data in CIF | 8g04_validation.cif.gz | 63.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/8g04 ftp://data.pdbj.org/pub/pdb/validation_reports/g0/8g04 | HTTPS FTP |
-Related structure data
Related structure data | 29644MC 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: 18381.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: THPO, MGDF / Production host: Homo sapiens (human) / References: UniProt: P40225 | ||||||
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#2: Protein | Mass: 71493.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MPL, TPOR / Production host: Homo sapiens (human) / References: UniProt: P40238 #3: Sugar | ChemComp-NAG / #4: Sugar | ChemComp-MAN / Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Thrombopoietin signaling complex with two thrombopoietin receptor chains Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.16 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Buffer solution | pH: 7.2 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 281 K / Details: 3s blotting |
-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: 81000 X / Calibrated magnification: 46382 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10494 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 9537683 | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 329658 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1V7N Accession code: 1V7N / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||
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