9SI3: Chromosomal Passenger Complex

Chromosomal Passenger Complex in complex with H3T3ph Nucleosome. Determined by electron microscopy at 2.83 Å resolution. Released 1 Oct 2025.

Method: Electron microscopy
Resolution: 2.83 Å
Organisms: Homo sapiens, Xenopus laevis, synthetic construct
Chains: 14
Atoms: 14,401
Mol. weight: 384.26 kDa
Released: 1 Oct 2025

Explore 9SI3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9SI3 contains 57 α-helices and 23 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	40-42	3
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	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	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-91	9
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	117-118	2

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	40-42	3
α-helix	45-54	10
α-helix	64-78	15
β-strand	83-84	2	6
α-helix	86-113	28
β-strand	118-119	2	7
α-helix	121-131	11

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	7
α-helix	50-75	26
β-strand	80-81	2	6
α-helix	83-93	11
β-strand	96-98	3	5

Chain G: 7 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	47-72	26
β-strand	77-78	2	9
α-helix	79	1
α-helix	80-89	10
α-helix	93-96	4
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
Borealin	L, O	protein	280	Homo sapiens	Q53HL2 (AlphaFold model)
Histone H3.2	A, E	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
DNA (147-mer)	I	DNA	147	synthetic construct
DNA (147-mer)	J	DNA	147	synthetic construct
Baculoviral IAP repeat-containing protein 5	M	protein	142	Homo sapiens	O15392
Inner centromere protein	N	protein	918	Homo sapiens	Q9NQS7

Sequence of entity 1 (L, O), FASTA

>9SI3_1 Borealin (chains L, O)
MAPRKGSSRVAKTNSLRRRKLASFLKDFDREVEIRIKQIESDRQNLLKEVDNLYNIEILR
LPKALREMNWLDYFALGGNKQALEEAATADLDITEINKLTAEAIQTPLKSAKTRKVIQVD
EMIVEEEEEEENERKNLQTARVKRCPPSKKRTQSIQGKGKGKRSSRANTVTPAVGRLEVS
MVKPTPGLTPRFDSRVFKTPGLRTPAAGERIYNISGNGSPLADSKEIFLTVPVGGGESLR
LLASDLQRHSIAQLDPEALGNIKKLSNRLAQICSSIRTHK

Sequence of entity 2 (A, E), FASTA

>9SI3_2 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 3 (B, F), FASTA

>9SI3_3 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 4 (C, G), FASTA

>9SI3_4 Histone H2A type 1 (chains C, G)
SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK

Sequence of entity 5 (D, H), FASTA

>9SI3_5 Histone H2B type 1-J (chains D, H)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSAK

Sequence of entity 6 (I), FASTA

>9SI3_6 DNA (147-MER) (chains I)
ACAGGATGTATATATGTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG

Sequence of entity 7 (J), FASTA

>9SI3_7 DNA (147-MER) (chains J)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCACATATATACATCCTGT

Sequence of entity 8 (M), FASTA

>9SI3_8 Baculoviral IAP repeat-containing protein 5 (chains M)
MGAPTLPPAWQPFLKDHRISTFKNWPFLEGCACTPERMAEAGFIHCPTENEPDLAQCFFC
FKELEGWEPDDDPIEEHKKHSSGCAFLSVKKQFEELTLGEFLKLDRERAKNKIAKETNNK
KKEFEETAKKVRRAIEQLAAMD

Sequence of entity 9 (N), FASTA

>9SI3_9 Inner centromere protein (chains N)
MGTTAPGPIHLLELCDQKLMEFLCNMDNKDLVWLEEIQEEAERMFTREFSKEPELMPKTP
SQKNRRKKRRISYVQDENRDPIRRRLSRRKSRSSQLSSRRLRSKDSVEKLATVVGENGSV
LRRVTRAAAAAAAATMALAAPSSPTPESPTMLTKKPEDNHTQCQLVPVVEIGISERQNAE
QHVTQLMSTEPLPRTLSPTPASATAPTSQGIPTSDEESTPKKSKARILESITVSSLMATP
QDPKGQGVGTGRSASKLRIAQVSPGPRDSPAFPDSPWRERVLAPILPDNFSTPTGSRTDS
QSVRHSPIAPSSPSPQVLAQKYSLVAKQESVVRRASRRLAKKTAEEPAASGRIICHSYLE
RLLNVEVPQKVGSEQKEPPEEAEPVAAAEPEVPENNGNNSWPHNDTEIANSTPNPKPAAS
SPETPSAGQQEAKTDQADGPREPPQSARRKRSYKQAVSELDEEQHLEDEELQPPRSKTPS
SPCPASKVVRPLRTFLHTVQRNQMLMTPTSAPRSVMKSFIKRNTPLRMDPKCSFVEKERQ
RLENLRRKEEAEQLRRQKVEEDKRRRLEEVKLKREERLRKVLQARERVEQMKEEKKKQIE
QKFAQIDEKTEKAKEERLAEEKAKKKAAAKKMEEVEARRKQEEEARRLRWLQQEEEERRH
QELLQKKKEEEQERLRKAAEAKRLAEQREQERREQERREQERREQERREQERREQERQLA
EQERRREQERLQAERELQEREKALRLQKEQLQRELEEKKKKEEQQRLAERQLQEEQEKKA
KEAAGASKALNVTVDVQSPACTSYQMTPQGHRAPPKINPDNYGMDLNSDDSTDDEAHPRK
PIPTWARGTPLSQAIIHQYYHPPNLLELFGTILPLDLEDIFKKSKPRYHKRTSSAVWNSP
PLQGARVPSSLAYSLKKH

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 Q53HL2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2QFA 1.4 Å, Crystal structure of a Survivin-Borealin-INCENP core complex
6YIF 1.81 Å, Structure of Chromosomal Passenger Complex (CPC) bound to phosphorylated Histone 3…
9D41 1.84 Å, Crystal structure of N-terminal domain of Borealin (20-88) in complex with synthetic…
8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
2RAW 2.4 Å, Crystal structure of the Borealin-Survivin complex
8RUP 2.42 Å, Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome
6YIH 2.55 Å, Structure of Chromosomal Passenger Complex (CPC) bound to phosphorylated Histone 3…
7U5V 2.59 Å, Crystal structure of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor…
9SJ5 2.85 Å, Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class1)
9SI9 2.86 Å, Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class0)
2RAX 3.3 Å, Crystal structure of Borealin (20-78) bound to Survivin (1-120)
6YIE 3.49 Å, Structure of a Borealin-INCENP-Survivin complex

Browse structure collections

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