2JMJ: PHD domain from the yeast YNG1 protein

NMR solution structure of the PHD domain from the yeast YNG1 protein in complex with H3(1-9)K4me3 peptide. Determined by solution NMR. Released 3 Jul 2007.

Method: Solution NMR
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 558
Mol. weight: 11.51 kDa
Ligands: ZN
Released: 3 Jul 2007

Explore 2JMJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2JMJ contains 1 α-helix and 5 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	1
β-strand	34	1	1
β-strand	39-40	2	2
β-strand	52-53	2	2
α-helix	71-78	8

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-4	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein YNG1	A	protein	90	Saccharomyces cerevisiae	Q08465 (AlphaFold model)
Histone H3	P	protein	9		P61830 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2JMJ_1 Protein YNG1 (chains A)
GPLGSHMASEFINQGDVTEGNNNQEEVYCFCRNVSYGPMVACDNPACPFEWFHYGCVGLK
QAPKGKWYCSKDCKEIANQRSKSKRQKRRK

Sequence of entity 2 (P), FASTA

>2JMJ_2 Histone H3 (chains P)
ARTKQTARK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Taverna, S.D., Ilin, S., Rogers, R.S. et al. Mol Cell (2006) 24:785-796. DOI 10.1016/j.molcel.2006.10.026 · PubMed

Other PDB entries of the same protein (UniProt Q08465 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8U77 1.93 Å, Crystal structure of Taf14 in complex with Yng1
9VKW 3.13 Å, Cryo-EM structure of the NuA3 complex bound to Ace-coenzyme A
9UUS 3.2 Å, The NuA3 histone acetyltransferase complex bound to acetyl-CoA and H3 tail
9UUO 3.68 Å, The NuA3 histone acetyltransferase complex
2JMI NMR solution structure of PHD finger fragment of Yeast Yng1 protein in free state

Browse structure collections

About this viewer

MolViewer shows 2JMJ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.