8VTS | pdb_00008vts

Meis1 homeobox domain bound to paromomycin fragment

  • Classification: DNA BINDING PROTEIN
  • Organism(s): Mus musculus
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2024-01-27 Released: 2024-02-14 
  • Deposition Author(s): Tomchick, D.R., Ahmed, M.S., Nguyen, N.U.N.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), Cancer Prevention and Research Institute of Texas (CPRIT), Leducq Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), American Heart Association, Robert A. Welch Foundation, Leukemia & Lymphoma Society, European Research Council (ERC), British Heart Foundation, European Commission

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.211 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Identification of FDA-approved drugs that induce heart regeneration in mammals.

Ahmed, M.S.Nguyen, N.U.N.Nakada, Y.Hsu, C.C.Farag, A.Lam, N.T.Wang, P.Thet, S.Menendez-Montes, I.Elhelaly, W.M.Lou, X.Secco, I.Tomczyk, M.Zentilin, L.Pei, J.Cui, M.Dos Santos, M.Liu, X.Liu, Y.Zaha, D.Walcott, G.Tomchick, D.R.Xing, C.Zhang, C.C.Grishin, N.V.Giacca, M.Zhang, J.Sadek, H.A.

(2024) Nat Cardiovasc Res 3: 372-388

  • DOI: https://doi.org/10.1038/s44161-024-00450-y
  • Primary Citation of Related Structures:  
    8VTS, 8VTT

  • PubMed Abstract: 

    Targeting Meis1 and Hoxb13 transcriptional activity could be a viable therapeutic strategy for heart regeneration. In this study, we performd an in silico screening to identify FDA-approved drugs that can inhibit Meis1 and Hoxb13 transcriptional activity based on the resolved crystal structure of Meis1 and Hoxb13 bound to DNA. Paromomycin (Paro) and neomycin (Neo) induced proliferation of neonatal rat ventricular myocytes in vitro and displayed dose-dependent inhibition of Meis1 and Hoxb13 transcriptional activity by luciferase assay and disruption of DNA binding by electromobility shift assay. X-ray crystal structure revealed that both Paro and Neo bind to Meis1 near the Hoxb13-interacting domain. Administration of Paro-Neo combination in adult mice and in pigs after cardiac ischemia/reperfusion injury induced cardiomyocyte proliferation, improved left ventricular systolic function and decreased scar formation. Collectively, we identified FDA-approved drugs with therapeutic potential for induction of heart regeneration in mammals.


  • Organizational Affiliation
    • Division of Cardiology, Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homeobox protein Meis1
A, B, C, D, E
A, B, C, D, E, F, G, H
67Mus musculusMutation(s): 0 
Gene Names: Meis1
UniProt & NIH Common Fund Data Resources
Find proteins for Q60954 (Mus musculus)
Explore Q60954 
Go to UniProtKB:  Q60954
IMPC:  MGI:104717
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60954
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RIO (Subject of Investigation/LOI)
Query on RIO

Download Ideal Coordinates CCD File 
J [auth B],
L [auth D]
RIBOSTAMYCIN
C17 H34 N4 O10
NSKGQURZWSPSBC-VVPCINPTSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
O [auth F]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth B],
M [auth D],
Q [auth H]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
K [auth C],
N [auth E],
P [auth G]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.621α = 90
b = 77.621β = 90
c = 213.724γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL137415-02
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL147276-01
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL149137-01
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP160520
Leducq FoundationFrance--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM119336
American Heart AssociationUnited States856552
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM127390
Robert A. Welch FoundationUnited StatesI-1505
Leukemia & Lymphoma SocietyUnited States6629-21
European Research Council (ERC)European Union787971
British Heart FoundationUnited KingdomRG/19/11/34633
European CommissionEuropean Union825670
European CommissionEuropean Union874764

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Database references