9FH9: CyclinB1 N-terminus

Structure of CyclinB1 N-terminus bound to the NCP. Determined by electron microscopy at 2.5 Å resolution. Released 24 Jul 2024.

Method: Electron microscopy
Resolution: 2.5 Å
Organisms: Homo sapiens, Xenopus laevis
Chains: 12
Atoms: 11,862
Mol. weight: 204.84 kDa
Released: 24 Jul 2024

Explore 9FH9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FH9 contains 37 α-helices and 20 β-strands across 8 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	118-119	2	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	96-98	3	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	47-72	26
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	6

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	102-120	19

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	46-54	9
α-helix	64-76	13
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	82	1
α-helix	83-92	10
β-strand	96-98	3	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	47-72	26
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	93-96	4
β-strand	100-102	3	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	10
α-helix	53-80	28
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	101-120	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G2/mitotic-specific cyclin-B1	K, L	protein	21	Homo sapiens	P14635 (AlphaFold model)
Histone H3.1	A, E	protein	136	Homo sapiens	P68431 (AlphaFold model)
Histone H4	B, F	protein	103	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 3	C, G	protein	130	Homo sapiens	Q7L7L0 (AlphaFold model)
Histone H2B 1.1	D, H	protein	123	Xenopus laevis	P02281
DNA (145-mer)	I	DNA	147	Homo sapiens
DNA (145-mer)	J	DNA	147	Homo sapiens

Sequence of entity 1 (K, L), FASTA

>9FH9_1 G2/mitotic-specific cyclin-B1 (chains K, L)
MALRVTRNSKINAENKAKINM

Sequence of entity 2 (A, E), FASTA

>9FH9_2 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 3 (B, F), FASTA

>9FH9_3 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 4 (C, G), FASTA

>9FH9_4 Histone H2A type 3 (chains C, G)
MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK

Sequence of entity 5 (D, H), FASTA

>9FH9_5 Histone H2B 1.1 (chains D, H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK

Sequence of entity 6 (I), FASTA

>9FH9_6 DNA (145-MER) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT

Sequence of entity 7 (J), FASTA

>9FH9_7 DNA (145-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT

Primary citation

Spatial control of the APC/C ensures the rapid degradation of cyclin B1. Cirillo, L., Young, R., Veerapathiran, S. et al. EMBO J (2024) 43:4324-4355. DOI 10.1038/s44318-024-00194-2 · PubMed

Other PDB entries of the same protein (UniProt P14635 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6GU2 2.0 Å, CDK1/CyclinB/Cks2 in complex with Flavopiridol
5LQF 2.06 Å, CDK1/CyclinB1/CKS2 in complex with NU6102
9Q3N 2.1 Å, Crystal structure of human CDK5-cyclinB1 complex
4Y72 2.3 Å, Human CDK1/CyclinB1/CKS2 With Inhibitor
5HQ0 2.3 Å, Ternary complex of human proteins CDK1, Cyclin B and CKS2, bound to an inhibitor
11GY 2.4 Å, Crystal structure of selective inhibitor 16 bound at the active site of CDK1
9Q3O 2.5 Å, Crystal structure of human CDK5-cyclinB1 complex bound to AMP-PNP
6GU3 2.65 Å, CDK1/CyclinB/Cks2 in complex with AZD5438
4YC3 2.7 Å, CDK1/CyclinB1/CKS2 Apo
6GU4 2.73 Å, CDK1/CyclinB/Cks2 in complex with CGP74514A
2B9R 2.9 Å, Crystal Structure of Human Cyclin B1
2JGZ 2.9 Å, Crystal structure of phospho-CDK2 in complex with Cyclin B

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