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- EMDB-43526: Cryo-EM structure of MPL bound to TPO -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-43526
TitleCryo-EM structure of MPL bound to TPO
Map data
Sample
  • Complex: Thrombopoietin bound to thrombopoietin receptor
    • Protein or peptide: Thrombopoietin
    • Protein or peptide: Thrombopoietin receptor
KeywordsReceptor / cytokine / complex / platelet synthesis / SIGNALING PROTEIN
Function / homology
Function and homology information


thrombopoietin receptor activity / regulation of chemokine production / positive regulation of hematopoietic stem cell proliferation / regulation of stem cell division / megakaryocyte differentiation / positive regulation of megakaryocyte differentiation / thrombopoietin-mediated signaling pathway / regulation of stem cell proliferation / myeloid cell differentiation / definitive hemopoiesis ...thrombopoietin receptor activity / regulation of chemokine production / positive regulation of hematopoietic stem cell proliferation / regulation of stem cell division / megakaryocyte differentiation / positive regulation of megakaryocyte differentiation / thrombopoietin-mediated signaling pathway / regulation of stem cell proliferation / myeloid cell differentiation / definitive hemopoiesis / platelet formation / homeostasis of number of cells / cytokine activity / hormone activity / positive regulation of protein phosphorylation / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / positive regulation of gene expression / negative regulation of apoptotic process / cell surface / Golgi apparatus / extracellular space / plasma membrane
Similarity search - Function
Thrombopoietin / Erythropoietin/thrombopoietin / Erythropoietin/thrombopoeitin, conserved site / Erythropoietin/thrombopoietin / Erythropoietin / thrombopoeitin signature. / Long hematopoietin receptor, single chain, conserved site / Long hematopoietin receptor, single chain family signature. / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Four-helical cytokine-like, core ...Thrombopoietin / Erythropoietin/thrombopoietin / Erythropoietin/thrombopoeitin, conserved site / Erythropoietin/thrombopoietin / Erythropoietin / thrombopoeitin signature. / Long hematopoietin receptor, single chain, conserved site / Long hematopoietin receptor, single chain family signature. / Growth hormone/erythropoietin receptor, ligand binding / Erythropoietin receptor, ligand binding / Four-helical cytokine-like, core / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Thrombopoietin / Thrombopoietin receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsBratkowski M / Hao Q / Paddock M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Blood Vessels, Thrombosis & Hemostasis / Year: 2024
Title: Structural basis of MPL activation by thrombopoietin
Authors: Mafi A / Bratkowski M / Geng J / Brito AA / Sridar J / Hu D / Darcy AT / Nanavati D / Brown NJ / Rathinaswamy MK / Kutskova Y / Eaton D / Hao Q / Paddock M
History
DepositionJan 28, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43526.png

Downloads & links

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Map

FileDownload / File: emd_43526.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.08 Å		0.82 Å/pix.
x 320 pix.
= 262.08 Å		0.82 Å/pix.
x 320 pix.
= 262.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.819 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.112
Minimum - Maximum-0.9299605 - 1.6195757
Average (Standard dev.)-0.0003228938 (±0.018341277)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43526_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43526_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43526_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Thrombopoietin bound to thrombopoietin receptor

EntireName: Thrombopoietin bound to thrombopoietin receptor
Components
  • Complex: Thrombopoietin bound to thrombopoietin receptor
    • Protein or peptide: Thrombopoietin
    • Protein or peptide: Thrombopoietin receptor

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Supramolecule #1: Thrombopoietin bound to thrombopoietin receptor

SupramoleculeName: Thrombopoietin bound to thrombopoietin receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 122 KDa

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Macromolecule #1: Thrombopoietin

MacromoleculeName: Thrombopoietin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 18.365381 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SPVAPACDPR LLNKLLRDSH LLHSRLSQCP DVDPLSIPVL LPAVDFSLGE WKTQTEQSKA QDILGAVSLL LEGVMAARGQ LEPSCLSSL LGQLSGQVRL LLGALQGLLG TQLPLQGRTT AHKDPNALFL SLQQLLRGKV RFLLLVEGPT LCVRRTLPTT A VPSENLYF QG

UniProtKB: Thrombopoietin

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Macromolecule #2: Thrombopoietin receptor

MacromoleculeName: Thrombopoietin receptor / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 52.030488 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QDVFLLALGT EPLNCFSQTF EDLTCFWDEE EAAPSGTYQL LYAYRGEKPR ACPLYSQSVP TFGTRYVCQF PAQDEVRLFF PLHLWVKNV SLNQTLIQRV LFVDSVGLPA PPRVIKARGG SQPGELQIHW EAPAPEISDF LRHELRYGPT DSSNATAPSV I QLLSTETC ...String:
QDVFLLALGT EPLNCFSQTF EDLTCFWDEE EAAPSGTYQL LYAYRGEKPR ACPLYSQSVP TFGTRYVCQF PAQDEVRLFF PLHLWVKNV SLNQTLIQRV LFVDSVGLPA PPRVIKARGG SQPGELQIHW EAPAPEISDF LRHELRYGPT DSSNATAPSV I QLLSTETC CPTLWMPNPV PVLDQPPCVH PTASQPHGPA PFLTVKGGSC LVSGLQAGKS YWLQLRSQPD GVSLRGSWGP WS FPVTVDL PGDAVTIGLQ CFTLDLKMVT CQWQQQDRTS SQGFFRHSRT RCCPTDRDPT WEKCEEEEPR PGSQPALVSR CHF KSRNDS VIHILVEVTT AQGAVHSYLG SPFWIHQAVL LPTPSLHWRE VSSGRLELEW QHQSSWAAQE TCYQLRYTGE GRED WKVLE PSLGARGGTL ELRPRARYSL QLRARLNGPT YQGPWSAWSP PARVSTGSET AWENLYFQ

UniProtKB: Thrombopoietin receptor

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.18 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 207077
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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