9V33: Calypso/Asx/NCP-ub complex

Calypso/Asx/NCP-ub complex. Determined by electron microscopy at 5.9 Å resolution. Released 18 Mar 2026.

Method: Electron microscopy
Resolution: 5.9 Å
Organisms: Xenopus laevis, Escherichia coli, Drosophila melanogaster
Chains: 15
Atoms: 16,504
Mol. weight: 396.37 kDa
Released: 18 Mar 2026

Explore 9V33 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9V33 contains 66 α-helices and 38 β-strands across 13 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	1
α-helix	86-112	27
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	83-92	10
β-strand	96-98	3	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	17-20	4
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	6

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	27-30	4
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	101-120	20

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-130	10

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	24-28	5
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-93	11
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	47-71	25
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	92-96	5
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	101-121	21

5 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
Histone H3	A, E	protein	136	Xenopus laevis	A0A310TTQ1 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	132	Xenopus laevis	Q6AZJ8 (AlphaFold model)
Histone H2B	D, H	protein	123	Xenopus laevis	A0A8J0U496 (AlphaFold model)
DNA (147-mer)	I	DNA	147	Escherichia coli
DNA (147-mer)	J	DNA	147	Escherichia coli
Ubiquitin carboxyl-terminal hydrolase calypso	K, N	protein	512	Drosophila melanogaster	Q7K5N4
Polycomb group protein Asx	L, O	protein	340	Drosophila melanogaster	Q9V727
Polyubiquitin-B	M	protein	88	Homo sapiens	P0CG47

Sequence of entity 1 (A, E), FASTA

>9V33_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>9V33_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>9V33_3 Histone H2A (chains C, G)
MGMSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEY
LTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLP
KKTESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>9V33_4 Histone H2B (chains D, H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK

Sequence of entity 5 (I), FASTA

>9V33_5 DNA (147-MER) (chains I)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCGATA

Sequence of entity 6 (J), FASTA

>9V33_6 DNA (147-MER) (chains J)
TATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG

Sequence of entity 7 (K, N), FASTA

>9V33_7 Ubiquitin carboxyl-terminal hydrolase calypso (chains K, N)
MWSHPQFEKGGGSGGGSGGGSWSHPQFEKGSSENLYFQGEFMNAAGGGSGAQAAAVAAGN
NSLSHNALLSTASGATTMPMAQLADGWLELESDPGLFTLLLKDFGCHDVQVEEVYDLQKP
IESPYGFIFLFRWIEERRARRKIVETTAEIFVKDEEAISSIFFAQQVVPNSCATHALLSV
LLNCNENNLQLGDTLSRLKTHTKGMSPENKGLAIGNTPELACAHNSHAMPQARRRLERTG
AGVSSCRFTGEAFHFVSFVPINGQLFELDGLKPYPMNHGGWEDSEDWTDKFRRVMAERLG
IATGEQDIRFNLMAVVPDRRIAITHKLKMLRTNQAIVSGTLQKLLKADEQGESGNGDSQR
PDTPTTLLEPSAFTARDLQSLLKNLDTEIAINEQHLADENDRRHMFKVDASRRTHNYDKF
ICTFLSMLAHQGVLGELVSQHLLPSKKVSGQGAANRISKQSTTASAGGSTAAGTASTPKT
QQQQAAAAKNGKSPSKTPGRRRKGRNKCRKRK

Sequence of entity 8 (L, O), FASTA

>9V33_8 Polycomb group protein Asx (chains L, O)
MKTITPDTTTTTSSQHQQLLIPQADQHHQPMLQQQSLLAAPPPTMIMEHVNLVDDDEKDP
LALEQLEVSPSTKHTHSLRRHLPRIIVKPIPPEKKPMAPSEEAAVSTAPAPPTRLICSRR
IQQQQQVKAAAAAAAAAAAAAAAAAAAAQAQATSSYPSAISPGSKAGTSQASTMREVLAS
IPGFSVKPRRRSNKKLTTAAQIEQTKDGKIDLETPDSILASTNLRALLNKQTFSLLPPLY
QYNLIQLLPSVDREASELEQPSSSASGGSPSEAIRLSASCLNNEFFARACLEWRERLSEG
EFTPENQLKLKTEAEREKNKLDPWKLKHFEPFWGEKNSRG

Sequence of entity 9 (M), FASTA

>9V33_9 Polyubiquitin-B (chains M)
GPHHHHHHLGSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK
QLEDGRTLSDYNIQKESTLHLVLRLRGC

Primary citation

Structural basis of nucleosome deubiquitination by the bidentate Calypso/Asx complex. Wang, C., Sun, F., Zhao, H. et al. iScience (2026) 29:114958-114958. DOI 10.1016/j.isci.2026.114958 · PubMed

Other PDB entries of the same protein (UniProt A0A310TTQ1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome
9JNP 2.3 Å, Structure of isw1-nucleosome complex in ATP state
8RUP 2.42 Å, Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome
9JNU 2.5 Å, Structure of isw1-nucleosome complex in ADP state
9N6H 2.54 Å, 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex
9N6I 2.61 Å, 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex
9JNT 2.7 Å, Structure of isw1-nucleosome complex in ADP* state
9LIU 2.7 Å, Structure of isw1-nucleosome double-bound complex in ATP-ATP state
28OE 2.74 Å, Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
9JO5 2.8 Å, Structure of isw1-nucleosome complex in ADP-B state
9V9Q 2.8 Å, Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified…
9C9X 2.83 Å, S.c INO80 in complex with Xenopus 0/80 nucleosome, Nucleosome

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