5X0Y: Complex of Snf2-Nucleosome complex with Snf2

Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome. Determined by electron microscopy at 4.69 Å resolution. Released 19 Apr 2017.

Method: Electron microscopy
Resolution: 4.69 Å
Organisms: Xenopus laevis, synthetic construct, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 11
Atoms: 16,798
Mol. weight: 297.02 kDa
Released: 19 Apr 2017

Explore 5X0Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5X0Y contains 75 α-helices and 38 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.

Chain A: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-55	11
α-helix	64-75	12
β-strand	84	1	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	31-41	11
β-strand	45-46	2	2
α-helix	50-76	27
β-strand	81	1	1
α-helix	83-92	10
β-strand	97	1	3

Chain C: 7 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	46-73	28
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-97	7
β-strand	100-101	2	6
α-helix	102	1
α-helix	113-115	3

Chains D and H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-43	9
β-strand	50-51	2	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	102-119	18

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-55	11
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45-46	2	8
α-helix	50-76	27
β-strand	80-81	2	7
α-helix	83-93	11
β-strand	96-97	2	6

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	9
α-helix	46-73	28
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	91-97	7
β-strand	101	1	3
α-helix	102	1
α-helix	113-115	3

Chain O: 36 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	671-677	7
α-helix	678-682	5
α-helix	683-688	6
α-helix	744-748	5
α-helix	770-783	14
β-strand	788-790	3	11
α-helix	792-793	2
α-helix	798-811	14
β-strand	819-822	4	11
α-helix	825-837	13
α-helix	850-862	13
β-strand	868-871	4	11
α-helix	873-885	13
β-strand	888-893	6	11
α-helix	896-900	5
α-helix	906-913	8
β-strand	916-922	7	11
α-helix	933-941	9
α-helix	943-957	15
α-helix	974-976	3
α-helix	977-981	5
α-helix	982-987	6
α-helix	988-990	3
β-strand	991-992	2	11
α-helix	996-999	4
β-strand	1007-1008	2	12
β-strand	1011	1	13
β-strand	1015	1	14
α-helix	1018-1022	5
α-helix	1023-1031	9
α-helix	1050	1
α-helix	1051-1058	8
α-helix	1059-1060	2
α-helix	1067-1072	6
α-helix	1082-1085	4
β-strand	1086	1	14
α-helix	1087-1102	16
β-strand	1106-1108	3	15
α-helix	1114-1126	13
β-strand	1130-1132	3	15
α-helix	1139-1149	11
β-strand	1158-1160	3	15
α-helix	1164-1167	4
β-strand	1177-1178	2	15
β-strand	1180	1	16
α-helix	1187-1195	9
β-strand	1207-1208	2	12
β-strand	1210	1	16
β-strand	1211	1	13
α-helix	1217-1242	26
α-helix	1247-1266	20
α-helix	1280-1286	7
α-helix	1291-1306	16
α-helix	1337-1347	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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	C, G	protein	129	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B 1.1	D, H	protein	122	Xenopus laevis	P02281 (AlphaFold model)
DNA (167-mer)	I	DNA	167	synthetic construct
DNA (167-mer)	J	DNA	167	synthetic construct
Transcription regulatory protein SNF2	O	protein	735	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P22082

Sequence of entity 1 (A, E), FASTA

>5X0Y_1 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>5X0Y_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>5X0Y_3 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>5X0Y_4 Histone H2B 1.1 (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK

Sequence of entity 5 (I), FASTA

>5X0Y_5 DNA (167-MER) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGATAGCTTGTCGAGAAGTACGAT

Sequence of entity 6 (J), FASTA

>5X0Y_6 DNA (167-MER) (chains J)
ATCGTACTTCTCGACAAGCTATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGAT

Sequence of entity 7 (O), FASTA

>5X0Y_7 Transcription regulatory protein SNF2 (chains O)
AYIKLLDQTKDTRITHLLRQTNAFLDSLTRAVKDQQKYTKEMIDSHIKEASEEVDDLSMV
PKMKDEEYDDDDDNSNVDYYNVAHRIKEDIKKQPSILVGGTLKDYQIKGLQWMVSLFNNH
LNGILADEMGLGKTIQTISLLTYLYEMKNIRGPYLVIVPLSTLSNWSSEFAKWAPTLRTI
SFKGSPNERKAKQAKIRAGEFDVVLTTFEYIIKERALLSKVKWVHMIIDEGHRMKNAQSK
LSLTLNTHYHADYRLILTGTPLQNNLPELWALLNFVLPKIFNSVKSFDEWFNTPFANTGG
QDKIELSEEETLLVIRRLHKVLRPFLLRRLKKDVEKELPDKVEKVVKCKMSALQQIMYQQ
MLKYRRLFIGDQNNKKMVGLRGFNNQIMQLKKICNHPFVFEEVEDQINPTRETNDDIWRV
AGKFELLDRILPKLKATGHRVLIFFQMTQIMDIMEDFLRYINIKYLRLDGHTKSDERSEL
LRLFNAPDSEYLCFILSTRAGGLGLNLQTADTVIIFDTDWNPHQDLQAQDRAHRIGQKNE
VRILRLITTNSVEEVILERAYKKLDIDGKVIQAGKFDNKSTSEEQEALLRSLLDAEEERR
KKRESGVEEEEELKDSEINEILARNDEEMAVLTRMDEDRSKKEEELGVKSRLLEKSELPD
IYSRDIGAELKREESESAAVYNGRGARERKTATYNDNMSEEQWLRQFEVSDDEKNDKQAR
KQRTKKEDKSEAIDG

Primary citation

Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure. Liu, X., Li, M., Xia, X. et al. Nature (2017) 544:440-445. DOI 10.1038/nature22036 · 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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