7VRF: Oxpecker chromodomain

Crystal structure of Oxpecker chromodomain in complex with H3K9me3. Determined by X-ray diffraction at 1.7 Å resolution. Released 26 Oct 2022.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Drosophila melanogaster
Chains: 4
Atoms: 1,252
Mol. weight: 19.54 kDa
Released: 26 Oct 2022

Explore 7VRF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VRF contains 8 α-helices and 10 β-strands across 4 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: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	21-23	3	1
β-strand	24-33	10	2
β-strand	36-43	8	2
α-helix	48-50	3
β-strand	52-55	4	2
α-helix	56-58	3
α-helix	60-62	3
α-helix	63-78	16

Chain B: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	21-23	3	3
β-strand	24-33	10	4
β-strand	36-43	8	4
α-helix	48-50	3
β-strand	52-55	4	4
α-helix	56-58	3
α-helix	60-62	3
α-helix	63-76	14

Chains C and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6-8	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Oxpecker	A, B	protein	71	Drosophila melanogaster	A1ZAW9 (AlphaFold model)
H3K9me3	C, D	protein	11	Drosophila melanogaster	P02299 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7VRF_1 Oxpecker (chains A, B)
NVKEKSSEYIVEKFLGKRYLRGRPQYLTKWEGYPIEQCTWEPLENLGKCMTLIADYEAEL
FQQSREKKNDQ

Sequence of entity 2 (C, D), FASTA

>7VRF_2 H3K9me3 (chains C, D)
KQTARKSTGGK

Primary citation

Structural insights into the chromodomain of Oxpecker in complex with histone H3 lysine 9 trimethylation reveal a transposon silencing mechanism by heterodimerization. Jin, Z., Yu, B., Huang, Y. Biochem Biophys Res Commun (2023) 652:95-102. DOI 10.1016/j.bbrc.2023.02.045 · PubMed

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