7XYF: Fft3-nucleosome complex with Fft3

Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome. Determined by electron microscopy at 3.8 Å resolution. Released 6 Dec 2023.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Drosophila melanogaster, synthetic construct, Schizosaccharomyces pombe 972h-
Chains: 11
Atoms: 17,321
Mol. weight: 255.73 kDa
Released: 6 Dec 2023

Explore 7XYF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XYF contains 75 α-helices and 34 β-strands across 9 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.

Chains A and E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	10
α-helix	88-113	26
β-strand	118-119	2	11
α-helix	121-131	11

Chain B: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45-46	2	11
α-helix	51-75	25
β-strand	80-81	2	10
α-helix	83-92	10

Chain C: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
α-helix	46-72	27
β-strand	77-78	2	1
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-101	2	2
α-helix	113-115	3

Chain D: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	1
α-helix	53-80	28
α-helix	88-98	11
α-helix	101-120	20

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	13
α-helix	50-75	26
β-strand	80-81	2	12
α-helix	84-93	10
β-strand	96-97	2	2

Chain G: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	43	1	3
α-helix	47-72	26
β-strand	77-78	2	4
α-helix	80-89	10
α-helix	92-96	5
α-helix	113-115	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-43	9
β-strand	50-51	2	4
α-helix	53-81	29
β-strand	86	1	3
α-helix	88-98	11
α-helix	101-119	19

Chain K: 37 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	234-247	14
α-helix	250-257	8
α-helix	261-270	10
α-helix	276-280	5
α-helix	284-289	6
α-helix	302-339	38
α-helix	349-351	3
β-strand	354	1	5
α-helix	360-365	6
α-helix	377-378	2
α-helix	386-388	3
α-helix	389-403	15
β-strand	407-410	4	6
α-helix	412-413	2
α-helix	418-431	14
β-strand	438-441	4	6
α-helix	444-446	3
α-helix	448-457	10
β-strand	463-465	3	6
α-helix	470-481	12
β-strand	489-492	4	6
α-helix	494-499	6
α-helix	501-508	8
β-strand	512-518	7	6
α-helix	522-524	3
α-helix	529-536	8
β-strand	539-545	7	6
α-helix	554-564	11
α-helix	577-580	4
α-helix	594-606	13
β-strand	611	1	6
β-strand	612	1	5
β-strand	627-628	2	7
β-strand	632	1	8
α-helix	633-635	3
α-helix	637-643	7
α-helix	645-647	3
α-helix	671-674	4
α-helix	679-688	10
α-helix	692-694	3
α-helix	703-709	7
α-helix	725-728	4
α-helix	734-739	6
α-helix	761-764	4
α-helix	766-770	5
β-strand	780-783	4	7
β-strand	784	1	9
α-helix	787-793	7
β-strand	831-832	2	7
β-strand	835	1	9
β-strand	851-853	3	7
α-helix	865-867	3
β-strand	880-883	4	7
β-strand	885	1	8
α-helix	890-893	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H2A	C, G	protein	106	Drosophila melanogaster	P84051 (AlphaFold model)
Histone H2B	D, H	protein	95	Drosophila melanogaster	P02283 (AlphaFold model)
DNA (167-mer)	J	DNA	146	synthetic construct
DNA (167-mer)	I	DNA	146	synthetic construct
ATP-dependent helicase fft3	K	protein	672	Schizosaccharomyces pombe 972h-	O42861 (AlphaFold model)
Histone H3	A, E	protein	98	Drosophila melanogaster	P02299 (AlphaFold model)
Histone H4	B, F	protein	86	Drosophila melanogaster	P84040

Sequence of entity 1 (C, G), FASTA

>7XYF_1 Histone H2A (chains C, G)
AKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDN
KKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKK

Sequence of entity 2 (D, H), FASTA

>7XYF_2 Histone H2B (chains D, H)
RKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

Sequence of entity 3 (J), FASTA

>7XYF_3 DNA (167-MER) (chains J)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCA

Sequence of entity 4 (I), FASTA

>7XYF_4 DNA (167-MER) (chains I)
TGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCCTGT

Sequence of entity 5 (K), FASTA

>7XYF_5 ATP-dependent helicase fft3 (chains K)
IDTAALKEEVLKYMNRCSTQDLADMTGCTLAEAEFMVAKRPFPDLESALVVKQPRPVIPK
GRRGRREKTPLGPRLVGICMEIMRGYFVVDALIRQCEQLGGKIQRGIEAWGLSNTATSDE
GETSLVNFDQMKSFGTPANSSFITTPPASFSPDIKLQDYQIIGINWLYLLYELKLAGILA
DEMGLGKTCQTIAFFSLLMDKNINGPHLVIAPASTMENWLREFAKFCPKLKIELYYGSQV
EREEIRERINSNKDSYNVMLTTYRLAATSKADRLFLRNQKFNVCVYDEGHYLKNRASERY
RHLMSIPADFRVLLTGTPLQNNLKELISLLAFILPHVFDYGLKSLDVIFTMKKSPESDFE
RALLSEQRVSRAKMMMAPFVLRRKKSQVLDALPKKTRIIEFCEFSEEERRRYDDFASKQS
VNSLLDENVMKTNLDTNANLAKKKSTAGFVLVQLRKLADHPMLFRIHYKDDILRQMAKAI
MNEPQYKKANELYIFEDMQYMSDIELHNLCCKFPSINSFQLKDEPWMDATKVRKLKKLLT
NAVENGDRVVLFSQFTQVLDILQLVMKSLNLKFLRFDGSTQVDFRQDLIDQFYADESINV
FLLSTKAGGFGINLACANMVILYDVSFNPFDDLQAEDRAHRVGQKKEVTVYKFVVKDTIE
EHIQRLANAKIA

Sequence of entity 6 (A, E), FASTA

>7XYF_6 Histone H3 (chains A, E)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASE
AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 7 (B, F), FASTA

>7XYF_7 Histone H4 (chains B, F)
RHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHA
KRKTVTAMDVVYALKRQGRTLYGFGG

Primary citation

Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome (Class I Fft3-nucleosome complex). Nan, Z., Tao, J., Yangao, H. To be published.

Other PDB entries of the same protein (UniProt P84051 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9ZQB 2.1 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1
2NQB 2.3 Å, Drosophila Nucleosome Structure
9ZQC 2.37 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2
2PYO 2.43 Å, Drosophila nucleosome core
8UX1 2.5 Å, Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle
8PP7 2.91 Å, human RYBP-PRC1 bound to mononucleosome
6DZT 2.99 Å, Cryo-EM structure of nucleosome in complex with a single chain antibody fragment
8PP6 3.18 Å, human RYBP-PRC1 bound to H2AK118ub1 nucleosome
9ZQA 3.28 Å, Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 2
9MU4 3.29 Å, Structure of a native Drosophila melanogaster octameric nucleosome
9ZQ9 3.3 Å, Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 1
4X23 3.5 Å, Crystal structure of cenp-C in complex with the nucleosome core particle

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