8VTS | pdb_00008vts

Meis1 homeobox domain bound to paromomycin fragment

PDB DOI: https://doi.org/10.2210/pdb8VTS/pdb

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), 0.211 (DCC)
R-Value Work:
0.191 (Depositor), 0.191 (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

PubMed: 39183959 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s44161-024-00450-y
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 63.66 kDa
Atom Count: 4,282
Modeled Residue Count: 447
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox protein Meis1	A, B, C, D, E A, B, C, D, E, F, G, H	67	Mus musculus	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q60954
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RIO (Subject of Investigation/LOI) Query on RIO Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth B] MOL2 format, chain L [auth D] MOL2 format, chain J [auth B] mmCIF format, chain L [auth D] mmCIF format, chain J [auth B]	J [auth B], L [auth D]	RIBOSTAMYCIN C₁₇ H₃₄ N₄ O₁₀ NSKGQURZWSPSBC-VVPCINPTSA-N		Interactions Focus chain J [auth B] Focus chain L [auth D] Interactions & Density Focus chain J [auth B] Focus chain L [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth F] MOL2 format, chain O [auth F] mmCIF format, chain O [auth F]	O [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain O [auth F] Interactions & Density Focus chain O [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Q [auth H] SDF format, chain M [auth D] SDF format, chain I [auth B] MOL2 format, chain Q [auth H] MOL2 format, chain M [auth D] MOL2 format, chain I [auth B] mmCIF format, chain Q [auth H] mmCIF format, chain M [auth D] mmCIF format, chain I [auth B]	I [auth B], M [auth D], Q [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain M [auth D] Focus chain Q [auth H] Interactions & Density Focus chain I [auth B] Focus chain M [auth D] Focus chain Q [auth H]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain P [auth G] SDF format, chain N [auth E] SDF format, chain K [auth C] MOL2 format, chain P [auth G] MOL2 format, chain N [auth E] MOL2 format, chain K [auth C] mmCIF format, chain P [auth G] mmCIF format, chain N [auth E] mmCIF format, chain K [auth C]	K [auth C], N [auth E], P [auth G]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain N [auth E] Focus chain P [auth G] Interactions & Density Focus chain K [auth C] Focus chain N [auth E] Focus chain P [auth G]

Experimental Data & Validation

Experimental Data

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

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.621	α = 90
b = 77.621	β = 90
c = 213.724	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-14

Deposition Author(s):

Tomchick, D.R.

Ahmed, M.S.

Nguyen, N.U.N.

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL137415-02
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL147276-01
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL149137-01
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP160520
Leducq Foundation	France	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM119336
American Heart Association	United States	856552
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM127390
Robert A. Welch Foundation	United States	I-1505
Leukemia & Lymphoma Society	United States	6629-21
European Research Council (ERC)	European Union	787971
British Heart Foundation	United Kingdom	RG/19/11/34633
European Commission	European Union	825670
European Commission	European Union	874764