Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 16.85 kDa 
• Atom Count: 1101 
• Modelled Residue Count: 120 
• Deposited Residue Count: 140 
• Unique protein chains: 2

2VNF

MOLECULAR BASIS OF HISTONE H3K4ME3 RECOGNITION BY ING4

• PDB DOI: 10.2210/pdb2VNF/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-02-04 Released: 2008-04-01 
• Deposition Author(s): Palacios, A., Munoz, I.G., Pantoja-Uceda, D., Marcaida, M.J., Torres, D., Martin-Garcia, J.M., Luque, I., Montoya, G., Blanco, F.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.227 
• R-Value Work: 0.156 
• R-Value Observed: 0.160 

Literature

Molecular Basis of Histone H3K4Me3 Recognition by Ing4

Palacios, A., Munoz, I.G., Pantoja-Uceda, D., Marcaida, M.J., Torres, D., Martin-Garcia, J.M., Luque, I., Montoya, G., Blanco, F.J.

(2008) J Biol Chem 283: 15956

• PubMed: 18381289 
• DOI: 10.1074/jbc.M710020200
• Primary Citation of Related Structures:  
  2VNF


• PubMed Abstract: 
  

The inhibitors of growth (ING) family of tumor suppressors consists of five homologous proteins involved in chromatin remodeling. They form part of different acetylation and deacetylation complexes and are thought to direct them to specific regions of the chromatin, through the recognition of H3K4me3 (trimethylated K4 in the histone 3 tail) by their conserved plant homeodomain (PHD). We have determined the crystal structure of ING4-PHD bound to H3K4me3, which reveals a tight complex stabilized by numerous interactions. NMR shows that there is a reduction in the backbone mobility on the regions of the PHD that participate in the peptide binding, and binding affinities differ depending on histone tail lengths Thermodynamic analysis reveals that the discrimination in favor of methylated lysine is entropy-driven, contrary to what has been described for chromodomains. The molecular basis of H3K4me3 recognition by ING4 differs from that of ING2, which is consistent with their different affinities for methylated histone tails. These differences suggest a distinct role in transcriptional regulation for these two ING family members because of the antagonistic effect of the complexes that they recruit onto chromatin. Our results illustrate the versatility of PHD fingers as readers of the histone code.

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Organizational Affiliation: 

Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 800, 48160 Derio, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INHIBITOR OF GROWTH PROTEIN 4	A, C	60	Homo sapiens	Mutation(s): 0  Gene Names: ING4, My036
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNL4 (Homo sapiens) Explore Q9UNL4  Go to UniProtKB:  Q9UNL4
PHAROS:  Q9UNL4 GTEx:  ENSG00000111653

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H3	B, D	10	Homo sapiens	Mutation(s): 0  Gene Names:  H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTU	I [auth C]	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C4 H10 O2 S2 VHJLVAABSRFDPM-ZXZARUISSA-N
DTT	F [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
ZN	G [auth A], H [auth A], J [auth C], K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	B, D	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.227 
• R-Value Work: 0.156 
• R-Value Observed: 0.160 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.516	α = 90
b = 68.516	β = 90
c = 28.174	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-02-04 
• Released Date: 2008-04-01 
Deposition Author(s): Palacios, A., Munoz, I.G., Pantoja-Uceda, D., Marcaida, M.J., Torres, D., Martin-Garcia, J.M., Luque, I., Montoya, G., Blanco, F.J.

Revision History  

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2016-12-28
  Changes: Database references, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance