5T1I: CBX3 chromo shadow domain

CBX3 chromo shadow domain in complex with histone H3 peptide. Determined by X-ray diffraction at 1.6 Å resolution. Released 14 Sept 2016.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 3
Atoms: 1,246
Mol. weight: 17.14 kDa
Released: 14 Sept 2016

Explore 5T1I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5T1I contains 9 α-helices and 11 β-strands across 3 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: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	112-114	3
α-helix	116-119	4
α-helix	121-122	2
β-strand	123-130	8	1
β-strand	137-142	6	1
β-strand	149-152	4	1
α-helix	153-159	7
α-helix	161-169	9
β-strand	172-174	3	2

Chain B: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	116-119	4
α-helix	121-122	2
β-strand	123-130	8	3
β-strand	137-142	6	3
β-strand	149-152	4	3
α-helix	153-159	7
α-helix	161-171	11
β-strand	172-174	3	2

Chain C: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	42	1	1
β-strand	44-48	5	2
β-strand	50	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromobox protein homolog 3	A, B	protein	68	Homo sapiens	Q13185 (AlphaFold model)
Histone H3.1	C	protein	15	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5T1I_1 Chromobox protein homolog 3 (chains A, B)
GAADKPRGFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFY
EERLTWHS

Sequence of entity 2 (C), FASTA

>5T1I_2 Histone H3.1 (chains C)
PHRYRPGTVALREIR

Primary citation

Peptide recognition by heterochromatin protein 1 (HP1) chromoshadow domains revisited: Plasticity in the pseudosymmetric histone binding site of human HP1. Liu, Y., Qin, S., Lei, M. et al. J Biol Chem (2017) 292:5655-5664. DOI 10.1074/jbc.M116.768374 · PubMed

Other PDB entries of the same protein (UniProt Q13185 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KUP 1.77 Å, Crystal Structure of the CBX3 Chromo Shadow Domain
9OSC 1.77 Å, Crystal structure of HP1gamma chromoshadow domain in complex with KAP1 peptide
8JZW 1.8 Å, Cystal structure of HP1 in complex with TRIM66 peptide
3TZD 1.81 Å, Crystal structure of the complex of Human Chromobox Homolog 3 (CBX3)
6HW2 1.94 Å, The Crystal Structure of CaV beta4c in complex with HP1gamma chromo shadow domains
3DM1 2.4 Å, Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide
2L11 Solution NMR structure of the Cbx3 in complex with H3K9me3 peptide

Browse structure collections

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