5X0X: Complex of Snf2-Nucleosome complex with Snf2

Complex of Snf2-Nucleosome complex with Snf2 bound to position +6 of the nucleosome. Determined by electron microscopy at 3.97 Å resolution. Released 19 Apr 2017.

Method: Electron microscopy
Resolution: 3.97 Å
Organisms: Xenopus laevis, synthetic construct, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 11
Atoms: 16,748
Mol. weight: 298.45 kDa
Released: 19 Apr 2017

Explore 5X0X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5X0X contains 73 α-helices and 36 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	45-54	10
α-helix	64-78	15
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118	1	2
α-helix	121-131	11

Chains B and F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45	1	2
α-helix	50-76	27
β-strand	80-81	2	1
α-helix	83-93	11
β-strand	96-98	3	3

Chains C and G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
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	92-97	6
β-strand	100-102	3	6
α-helix	113-115	3

Chains D and H: 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	101-120	20

Chain O: 35 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	671-688	18
α-helix	744-748	5
α-helix	769-783	15
β-strand	788	1	11
β-strand	789-790	2	12
α-helix	792-793	2
α-helix	798-810	13
β-strand	819-823	5	11
α-helix	825-837	13
β-strand	844-845	2	11
α-helix	850-862	13
β-strand	868-872	5	11
α-helix	874-878	5
α-helix	880-885	6
β-strand	888-892	5	11
α-helix	896-900	5
α-helix	905-912	8
β-strand	916-920	5	11
α-helix	933-934	2
α-helix	935-939	5
α-helix	940-941	2
α-helix	943-947	5
α-helix	949-957	9
α-helix	968	1
α-helix	969-973	5
α-helix	976-987	12
β-strand	991-992	2	12
β-strand	1009-1011	3	13
β-strand	1014	1	14
α-helix	1015-1016	2
α-helix	1017-1021	5
α-helix	1026-1029	4
α-helix	1049-1060	12
α-helix	1067-1072	6
α-helix	1087-1102	16
α-helix	1104-1105	2
β-strand	1106-1108	3	13
α-helix	1115-1126	12
β-strand	1130-1132	3	13
α-helix	1139-1150	12
β-strand	1158-1160	3	13
α-helix	1163-1166	4
β-strand	1177-1181	5	13
α-helix	1188-1198	11
β-strand	1207-1211	5	13
β-strand	1214	1	14
α-helix	1217-1244	28
α-helix	1248-1268	21
α-helix	1280-1286	7
α-helix	1293-1306	14
α-helix	1337-1348	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.2	A, E	protein	136	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	130	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B 1.1	D, H	protein	125	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

>5X0X_1 Histone H3.2 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>5X0X_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>5X0X_3 Histone H2A (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>5X0X_4 Histone H2B 1.1 (chains D, H)
PEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMS
IMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSAK

Sequence of entity 5 (I), FASTA

>5X0X_5 DNA (167-MER) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGATAGCTTGTCGAGAAGTACGAT

Sequence of entity 6 (J), FASTA

>5X0X_6 DNA (167-MER) (chains J)
ATCGTACTTCTCGACAAGCTATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGAT

Sequence of entity 7 (O), FASTA

>5X0X_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

Browse structure collections

About this viewer

MolViewer shows 5X0X directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.