4U68: Rhino chromodomain

Crystal structure of Rhino chromodomain in complex with H3K9me3. Determined by X-ray diffraction at 1.8 Å resolution. Released 5 Aug 2015.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Drosophila melanogaster
Chains: 6
Atoms: 1,853
Mol. weight: 28.95 kDa
Released: 5 Aug 2015

Explore 4U68 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4U68 contains 12 α-helices and 15 β-strands across 6 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	24-25	2	1
β-strand	26-35	10	2
β-strand	38-45	8	2
α-helix	50-52	3
β-strand	54-57	4	2
α-helix	58-60	3
α-helix	62-64	3
α-helix	65-85	21

Chain B: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	24-25	2	3
β-strand	26-35	10	4
β-strand	38-45	8	4
α-helix	50-52	3
β-strand	54-57	4	4
α-helix	58-60	3
α-helix	62-64	3
α-helix	65-79	15

Chain C: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	24-25	2	5
β-strand	26-35	10	6
β-strand	38-45	8	6
α-helix	50-52	3
β-strand	54-57	4	6
α-helix	58-60	3
α-helix	62-64	3
α-helix	65-78	14

Chains D, E and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6-7	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rhino	A, B, C	protein	75	Drosophila melanogaster	Q7JXA8 (AlphaFold model)
H3K9me3	D, E, F	protein	11	Drosophila melanogaster	P68431 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>4U68_1 Rhino (chains A, B, C)
GPGSHVEEYVVEKILGKRFVNGRPQVLVKWSGFPNENNTWEPLENVGNCMKLVSDFESEV
FRLHRKAAAKSVGKS

Sequence of entity 2 (D, E, F), FASTA

>4U68_2 H3K9me3 (chains D, E, F)
KQTARKSTGGK

Primary citation

Structural insights into Rhino-mediated germline piRNA cluster formation. Yu, B.W., Cassani, M., Wang, M. et al. Cell Res (2015) 25:525-528. DOI 10.1038/cr.2015.10 · PubMed

Other PDB entries of the same protein (UniProt Q7JXA8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4QUC 1.5 Å, Crystal structure of chromodomain of Rhino
5XYV 2.1 Å, Crystal structure of drosophila melanogaster Rhino chromoshadow domain in complex with…
4QUF 2.5 Å, crystal structure of chromodomain of Rhino with H3K9me3

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