8VU5 | pdb_00008vu5

Cryo-EM structure of MPL bound to TPO


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of MPL activation by thrombopoietin.

Mafi, A.Bratkowski, M.Geng, J.Brito, A.A.Sridar, J.Hu, D.Darcy, A.T.Nanavati, D.Brown, N.J.Rathinaswamy, M.K.Kutskova, Y.Eaton, D.Hao, Q.Paddock, M.

(2024) Blood Vessel Thromb Hemost 1: 100018-100018

  • DOI: https://doi.org/10.1016/j.bvth.2024.100018
  • Primary Citation of Related Structures:  
    8VU5

  • PubMed Abstract: 

    Myeloproliferative leukemia protein (MPL), also known as thrombopoietin (TPO) receptor, is a class I cytokine receptor that is expressed on hematopoietic progenitors, promoting growth and differentiation toward the megakaryocyte lineage and is critical for normal platelet production. Mutations in MPL, TPO, or Janus kinase 2 (JAK2) have been implicated in multiple diseases from congenital thrombocytopenias to myeloproliferative neoplasms. The ligand for MPL, TPO, stimulates platelet production by inducing MPL dimerization and results in an active conformation that allows downstream JAK2/STAT5 signaling. Despite the biological importance of this pathway, the molecular signaling mechanism remained unclear. Here, we present a 3.39-Å cryo-electron microscopy structure of the ectodomain of mouse MPL bound to TPO. The structure revealed both low and high affinity sites between MPL and TPO that contain several pathologic mutations. To better understand TPO-driven MPL signaling, we expanded upon this structure by molecular dynamic (MD) simulations to model the full-length human MPL/TPO complex, and showed that MPL D4-D4 domain interactions are functionally relevant in activity assays. To build on our understanding of downstream activation, we added JAK2 to the MPL/TPO complex by MD simulations. This ternary complex illustrates JAK2 dimerization through the pseudokinase domain, illustrates residues important for MPL interactions, and reveals the constitutive activation mechanism of patient mutant V617F. The model also suggests the mechanism of JAK2 tyrosine kinase domain transphosphorylation. Overall, our studies illuminate TPO/MPL/JAK2 signaling mechanisms and provide additional insight into the nature of receptor signaling, which will further benefit human health.


  • Organizational Affiliation
    • Calico Life Sciences LLC, South San Francisco, CA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombopoietin170Mus musculusMutation(s): 0 
Gene Names: Thpo
UniProt & NIH Common Fund Data Resources
Find proteins for P40226 (Mus musculus)
Explore P40226 
Go to UniProtKB:  P40226
IMPC:  MGI:101875
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40226
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombopoietin receptor
B, C
463Mus musculusMutation(s): 0 
Gene Names: MplTpor
UniProt & NIH Common Fund Data Resources
Find proteins for Q08351 (Mus musculus)
Explore Q08351 
Go to UniProtKB:  Q08351
IMPC:  MGI:97076
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08351
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-05-21
    Changes: Data collection
  • Version 1.3: 2025-08-20
    Changes: Data collection, Database references