6YIF: Chromosomal Passenger Complex

Structure of Chromosomal Passenger Complex (CPC) bound to phosphorylated Histone 3 peptide at 1.8 A. Determined by X-ray diffraction at 1.81 Å resolution. Released 13 May 2020.

Method: X-ray diffraction
Resolution: 1.81 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,117
Mol. weight: 32.65 kDa
Ligands: ZN
Released: 13 May 2020

Explore 6YIF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YIF contains 13 α-helices and 6 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: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	15-20	6
α-helix	35-40	6
β-strand	43-45	3	1
β-strand	55-57	3	1
β-strand	63-65	3	1
α-helix	73-80	8
α-helix	85-88	4
α-helix	93-95	3
β-strand	97	1	2
α-helix	98-133	36

Chain B: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	22-60	39
α-helix	63-66	4
β-strand	69	1	2
α-helix	70-74	5

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	10-26	17
α-helix	27-31	5
α-helix	32-40	9

Chain D: 0 helices, 1 β-strand

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Baculoviral IAP repeat-containing protein 5	A	protein	144	Homo sapiens	O15392 (AlphaFold model)
Borealin	B	protein	67	Homo sapiens	Q53HL2 (AlphaFold model)
Inner centromere protein	C	protein	51	Homo sapiens	Q9NQS7 (AlphaFold model)
Phosphorylated (Thr3) Histone H3	D	protein	12	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6YIF_1 Baculoviral IAP repeat-containing protein 5 (chains A)
GPMGAPTLPPAWQPFLKDHRISTFKNWPFLEGCACTPERMAEAGFIHCPTENEPDLAQCF
FCFKELEGWEPDDDPIEEHKKHSSGCAFLSVKKQFEELTLGEFLKLDRERAKNKIAKETN
NKKKEFEETAKKVRRAIEQLAAMD

Sequence of entity 2 (B), FASTA

>6YIF_2 Borealin (chains B)
VAKTNSLRRRKLASFLKDFDREVEIRIKQIESDRQNLLKEVDNLYNIEILRLPKALREMN
WLDYFAL

Sequence of entity 3 (C), FASTA

>6YIF_3 Inner centromere protein (chains C)
GPIHLLELCDQKLMEFLCNMDNKDLVWLEEIQEEAERMFTREFSKEPELMP

Sequence of entity 4 (D), FASTA

>6YIF_4 Phosphorylated (Thr3) Histone H3 (chains D)
ARTKQTARKSTG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Molecular basis of MKLP2-dependent Aurora B transport from chromatin to the anaphase central spindle. Serena, M., Bastos, R.N., Elliott, P.R. et al. J Cell Biol (2020) 219. DOI 10.1083/jcb.201910059 · PubMed

Other PDB entries of the same protein (UniProt O15392 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2QFA 1.4 Å, Crystal structure of a Survivin-Borealin-INCENP core complex
9TPI 1.8 Å, Survivin 1-122 in complex with a molecular tweezer-Histone-H3-peptide conjugate
9TPH 2.0 Å, Survivin 1-127 in complex with a molecular tweezer-Histone-H3-peptide conjugate
3UEC 2.18 Å, Crystal structure of human Survivin bound to histone H3 phosphorylated on threonine-3.
2RAW 2.4 Å, Crystal structure of the Borealin-Survivin complex
3UIG 2.4 Å, crystal structure of human Survivin in complex with T3 phosphorylated H3(1-15) peptide
3UIH 2.4 Å, crystal structure of human Survivin in complex with Smac/DIABLO(1-15) peptide
8RUP 2.42 Å, Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome
3UEF 2.45 Å, Crystal structure of human Survivin bound to histone H3 (C2 space group).
7LBO 2.5 Å, Crystal structure of human Survivin bound to histone H3 T3phK4me1 peptide
6YIH 2.55 Å, Structure of Chromosomal Passenger Complex (CPC) bound to phosphorylated Histone 3…
1F3H 2.58 Å, X-ray crystal structure of the human anti-apoptotic protein survivin

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