4X3K: Chromobox protein homolog 7

Crystal structure of chromobox homolog 7 (CBX7) chromodomain with H3K27me3 peptide. Determined by X-ray diffraction at 1.45 Å resolution. Released 4 Mar 2015.

Method: X-ray diffraction
Resolution: 1.45 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 1,380
Mol. weight: 17.17 kDa
Ligands: NI
Released: 4 Mar 2015

Explore 4X3K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4X3K contains 8 α-helices and 11 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: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	10-12	3	1
β-strand	13-22	10	2
β-strand	25-32	8	2
α-helix	37-39	3
β-strand	41-44	4	2
α-helix	45-47	3
α-helix	51-65	15

Chain B: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	8-9	2
β-strand	10-12	3	3
β-strand	13-22	10	4
β-strand	25-32	8	4
α-helix	37-39	3
β-strand	41-44	4	4
α-helix	45-47	3
β-strand	48	1	3
α-helix	51-64	14

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-4	3	1

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-4	3	3
α-helix	5-6	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromobox protein homolog 7	A, B	protein	64	Mus musculus	Q8VDS3 (AlphaFold model)
H3K27me3 peptide	C, D	protein	7	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4X3K_1 Chromobox protein homolog 7 (chains A, B)
GSHMGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE
RDRA

Sequence of entity 2 (C, D), FASTA

>4X3K_2 H3K27me3 peptide (chains C, D)
KAARKSA

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	2

Water and common crystallization additives (K) are not listed.

Primary citation

Small-Molecule Modulators of Methyl-Lysine Binding for the CBX7 Chromodomain. Ren, C., Morohashi, K., Plotnikov, A.N. et al. Chem Biol (2015) 22:161-168. DOI 10.1016/j.chembiol.2014.11.021 · PubMed

Other PDB entries of the same protein (UniProt Q8VDS3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4X3S 1.6 Å, Crystal structure of chromobox homology 7 (CBX7) with SETDB1-1170me3 Peptide
4X3U 1.63 Å, Crystal structure of chromobox homolog 7 (CBX7) chromodomain with Suramin
4X3T 2.14 Å, Crystal structure of chromobox homolog 7 (CBX7) chromodomain with MS37452
5EJW 2.6 Å, Crystal structure of chromobox homolog 7 (CBX7) chromodomain with MS351
2KVM Solution structure of the CBX7 chromodomain in complex with a H3K27me2 peptide

Browse structure collections

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