8G04

Structure of signaling thrombopoietin-MPL receptor complex

  • Classification: CYTOKINE
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2023-01-31 Released: 2023-08-30 
  • Deposition Author(s): Tsutsumi, N., Jude, K.M., Gati, C., Garcia, K.C.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Howard Hughes Medical Institute (HHMI), Ludwig Institute for Cancer Research (LICR)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the thrombopoietin-MPL receptor complex is a blueprint for biasing hematopoiesis.

Tsutsumi, N.Masoumi, Z.James, S.C.Tucker, J.A.Winkelmann, H.Grey, W.Picton, L.K.Moss, L.Wilson, S.C.Caveney, N.A.Jude, K.M.Gati, C.Piehler, J.Hitchcock, I.S.Garcia, K.C.

(2023) Cell 186: 4189-4203.e22

  • DOI: https://doi.org/10.1016/j.cell.2023.07.037
  • Primary Citation of Related Structures:  
    8G04

  • PubMed 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 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 mod ) with a spectrum of signaling activities, from neutral antagonists to partial- and super-agonists. Partial agonist TPO mod 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 mod in hematology research and clinical HSC transplantation.


  • Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan. Electronic address: ntsutsumi@okayama-u.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombopoietin171Homo sapiensMutation(s): 0 
Gene Names: THPOMGDF
UniProt & NIH Common Fund Data Resources
Find proteins for P40225 (Homo sapiens)
Explore P40225 
Go to UniProtKB:  P40225
PHAROS:  P40225
GTEx:  ENSG00000090534 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40225
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombopoietin receptor
B, C
636Homo sapiensMutation(s): 0 
Gene Names: MPLTPOR
UniProt & NIH Common Fund Data Resources
Find proteins for P40238 (Homo sapiens)
Explore P40238 
Go to UniProtKB:  P40238
PHAROS:  P40238
GTEx:  ENSG00000117400 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40238
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth B]
E [auth B]
F [auth B]
J [auth C]
K [auth C]
D [auth B],
E [auth B],
F [auth B],
J [auth C],
K [auth C],
L [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
G [auth B]
H [auth B]
I [auth B]
M [auth C]
N [auth C]
G [auth B],
H [auth B],
I [auth B],
M [auth C],
N [auth C],
O [auth C]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
B, C
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR37AI051321
Howard Hughes Medical Institute (HHMI)United States--
Ludwig Institute for Cancer Research (LICR)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references, Refinement description