9SI9: Chromosomal Passenger Complex

Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class0). Determined by electron microscopy at 2.86 Å resolution. Released 1 Oct 2025.

Method: Electron microscopy
Resolution: 2.86 Å
Organisms: synthetic construct, Xenopus laevis, Homo sapiens
Chains: 14
Atoms: 14,471
Mol. weight: 384.34 kDa
Released: 1 Oct 2025

Explore 9SI9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9SI9 contains 54 α-helices and 22 β-strands across 12 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	119	1	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	46	1	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	97	1	3

Chain C: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	47-72	26
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	5
α-helix	113-115	3
α-helix	117-119	3

Chain D: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	38-48	11
α-helix	56-83	28
β-strand	88-89	2	4
α-helix	91-101	11
α-helix	105-122	18

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-78	15
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	6
α-helix	121-130	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	6
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-93	11
β-strand	96-98	3	5

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	8
α-helix	47-71	25
β-strand	77-78	2	9
α-helix	80-89	10
α-helix	92-96	5
β-strand	101	1	3
α-helix	113-115	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	9
α-helix	56-83	28
β-strand	88-89	2	8
α-helix	91-101	11
α-helix	105-123	19

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (147-mer)	I	DNA	147	synthetic construct
DNA (147-mer)	J	DNA	147	synthetic construct
Histone H3.2	A	protein	135	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	102	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A type 1	C, G	protein	129	Homo sapiens	P0C0S8 (AlphaFold model)
Histone H2B type 1-J	D, H	protein	125	Homo sapiens	P06899 (AlphaFold model)
Borealin	L, O	protein	280	Homo sapiens	Q53HL2
Baculoviral IAP repeat-containing protein 5	M	protein	142	Homo sapiens	O15392
Inner centromere protein	N	protein	918	Homo sapiens	Q9NQS7
H3.4 histone	E	protein	135	Homo sapiens	S4RAZ3

Sequence of entity 1 (I), FASTA

>9SI9_1 DNA (147-MER) (chains I)
ACAGGATGTATATATGTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG

Sequence of entity 2 (J), FASTA

>9SI9_2 DNA (147-MER) (chains J)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCACATATATACATCCTGT

Sequence of entity 3 (A), FASTA

>9SI9_3 Histone H3.2 (chains A)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 4 (B, F), FASTA

>9SI9_4 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (C, G), FASTA

>9SI9_5 Histone H2A type 1 (chains C, G)
SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK

Sequence of entity 6 (D, H), FASTA

>9SI9_6 Histone H2B type 1-J (chains D, H)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSAK

Sequence of entity 7 (L, O), FASTA

>9SI9_7 Borealin (chains L, O)
MAPRKGSSRVAKTNSLRRRKLASFLKDFDREVEIRIKQIESDRQNLLKEVDNLYNIEILR
LPKALREMNWLDYFALGGNKQALEEAATADLDITEINKLTAEAIQTPLKSAKTRKVIQVD
EMIVEEEEEEENERKNLQTARVKRCPPSKKRTQSIQGKGKGKRSSRANTVTPAVGRLEVS
MVKPTPGLTPRFDSRVFKTPGLRTPAAGERIYNISGNGSPLADSKEIFLTVPVGGGESLR
LLASDLQRHSIAQLDPEALGNIKKLSNRLAQICSSIRTHK

Sequence of entity 8 (M), FASTA

>9SI9_8 Baculoviral IAP repeat-containing protein 5 (chains M)
MGAPTLPPAWQPFLKDHRISTFKNWPFLEGCACTPERMAEAGFIHCPTENEPDLAQCFFC
FKELEGWEPDDDPIEEHKKHSSGCAFLSVKKQFEELTLGEFLKLDRERAKNKIAKETNNK
KKEFEETAKKVRRAIEQLAAMD

Sequence of entity 9 (N), FASTA

>9SI9_9 Inner centromere protein (chains N)
MGTTAPGPIHLLELCDQKLMEFLCNMDNKDLVWLEEIQEEAERMFTREFSKEPELMPKTP
SQKNRRKKRRISYVQDENRDPIRRRLSRRKSRSSQLSSRRLRSKDSVEKLATVVGENGSV
LRRVTRAAAAAAAATMALAAPSSPTPESPTMLTKKPEDNHTQCQLVPVVEIGISERQNAE
QHVTQLMSTEPLPRTLSPTPASATAPTSQGIPTSDEESTPKKSKARILESITVSSLMATP
QDPKGQGVGTGRSASKLRIAQVSPGPRDSPAFPDSPWRERVLAPILPDNFSTPTGSRTDS
QSVRHSPIAPSSPSPQVLAQKYSLVAKQESVVRRASRRLAKKTAEEPAASGRIICHSYLE
RLLNVEVPQKVGSEQKEPPEEAEPVAAAEPEVPENNGNNSWPHNDTEIANSTPNPKPAAS
SPETPSAGQQEAKTDQADGPREPPQSARRKRSYKQAVSELDEEQHLEDEELQPPRSKTPS
SPCPASKVVRPLRTFLHTVQRNQMLMTPTSAPRSVMKSFIKRNTPLRMDPKCSFVEKERQ
RLENLRRKEEAEQLRRQKVEEDKRRRLEEVKLKREERLRKVLQARERVEQMKEEKKKQIE
QKFAQIDEKTEKAKEERLAEEKAKKKAAAKKMEEVEARRKQEEEARRLRWLQQEEEERRH
QELLQKKKEEEQERLRKAAEAKRLAEQREQERREQERREQERREQERREQERREQERQLA
EQERRREQERLQAERELQEREKALRLQKEQLQRELEEKKKKEEQQRLAERQLQEEQEKKA
KEAAGASKALNVTVDVQSPACTSYQMTPQGHRAPPKINPDNYGMDLNSDDSTDDEAHPRK
PIPTWARGTPLSQAIIHQYYHPPNLLELFGTILPLDLEDIFKKSKPRYHKRTSSAVWNSP
PLQGARVPSSLAYSLKKH

Sequence of entity 10 (E), FASTA

>9SI9_10 H3.4 histone (chains E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Primary citation

Nucleosome interaction of the CPC secures centromeric chromatin integrity and chromosome segregation fidelity. Gireesh, A., Abad, M.A., Nozawa, R.S. et al. EMBO J (2025) 44:6556-6597. DOI 10.1038/s44318-025-00594-y · PubMed

Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome

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