8VTT

Meis1 homeobox domain bound to neomycin fragment

• PDB DOI: https://doi.org/10.2210/pdb8VTT/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., Sadek, H.A.
• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.257 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 

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.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors.

Biological Assembly 7  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 7 assigned by authors.

Biological Assembly 8  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 8 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.84 kDa 
• Atom Count: 3,854 
• Modelled Residue Count: 447 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox protein Meis1	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RIO (Subject of Investigation/LOI)	I [auth D]	RIBOSTAMYCIN C17 H34 N4 O10 NSKGQURZWSPSBC-VVPCINPTSA-N
SO4	J [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.257 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 
• Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.757	α = 90
b = 77.757	β = 90
c = 213.298	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-14 
Deposition Author(s): Tomchick, D.R., Ahmed, M.S., Nguyen, N.U.N., Sadek, H.A.

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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

Revision History  

• Version 1.0: 2024-02-14
  Type: Initial release