5Z3U: Transcription regulatory protein SNF2

Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state. Determined by electron microscopy at 4.31 Å resolution. Released 22 May 2019.

Method: Electron microscopy
Resolution: 4.31 Å
Organisms: Saccharomyces cerevisiae, Xenopus laevis, synthetic construct
Chains: 11
Atoms: 16,766
Mol. weight: 297.57 kDa
Ligands: ADP, MG, BEF
Released: 22 May 2019

Explore 5Z3U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Z3U contains 74 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	64-76	13
β-strand	83-84	2	6
α-helix	86-113	28
β-strand	118-119	2	7
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45-46	2	7
α-helix	50-76	27
β-strand	80-81	2	6
α-helix	83-93	11
β-strand	97	1	8

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	9
α-helix	47-72	26
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	91-97	7
β-strand	100-101	2	11

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

Element	Residues	Length	Sheet
α-helix	35-43	9
β-strand	50-51	2	10
α-helix	53-80	28
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	102-120	19

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	13
α-helix	50-75	26
β-strand	80-81	2	12
α-helix	83-93	11
β-strand	96-97	2	11

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	14
α-helix	47-72	26
β-strand	77-78	2	15
α-helix	80-89	10
α-helix	91-97	7
β-strand	101	1	8

Chain O: 38 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	675-683	9
α-helix	684-689	6
α-helix	744-747	4
α-helix	758-759	2
α-helix	770-783	14
β-strand	789-790	2	1
α-helix	798-812	15
β-strand	819-823	5	2
α-helix	829-837	9
α-helix	853-860	8
α-helix	861-863	3
β-strand	868-872	5	2
α-helix	875-878	4
α-helix	880-883	4
β-strand	888-890	3	3
β-strand	892-893	2	2
α-helix	896-898	3
α-helix	905-913	9
β-strand	916-918	3	3
β-strand	921-922	2	1
α-helix	934-941	8
α-helix	949-952	4
α-helix	953-956	4
α-helix	968-971	4
α-helix	972-979	8
α-helix	980-987	8
α-helix	996-999	4
β-strand	1013	1	4
α-helix	1017-1025	9
α-helix	1051-1060	10
α-helix	1066-1067	2
α-helix	1068-1072	5
α-helix	1087-1102	16
β-strand	1106-1110	5	5
α-helix	1115-1126	12
β-strand	1130-1132	3	5
α-helix	1141-1150	10
β-strand	1158-1162	5	5
β-strand	1177-1180	4	5
α-helix	1187-1194	8
β-strand	1208-1210	3	5
β-strand	1213	1	4
α-helix	1217-1233	17
α-helix	1236-1239	4
α-helix	1249-1252	4
α-helix	1253-1257	5
α-helix	1258-1268	11
α-helix	1280-1287	8
α-helix	1291-1296	6
α-helix	1298-1300	3
α-helix	1302-1306	5
α-helix	1337-1346	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription regulatory protein SNF2	O	protein	735	Saccharomyces cerevisiae	P22082 (AlphaFold model)
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	Q6AZJ8 (AlphaFold model)
Histone H2B 1.1	D, H	protein	122	Xenopus laevis	P02281
DNA (167-mer)	I	DNA	167	synthetic construct
DNA (167-mer)	J	DNA	167	synthetic construct

Sequence of entity 1 (O), FASTA

>5Z3U_1 Transcription regulatory protein SNF2 (chains O)
AYIKLLDQTKDTRITHLLRQTNAFLDSLTRAVKDQQKYTKEMIDSHIKEASEEVDDLSMV
PKMKDEEYDDDDDNSNVDYYNVAHRIKEDIKKQPSILVGGTLKDYQIKGLQWMVSLFNNH
LNGILADEMGLGKTIQTISLLTYLYEMKNIRGPYLVIVPLSTLSNWSSEFAKWAPTLRTI
SFKGSPNERKAKQAKIRAGEFDVVLTTFEYIIKERALLSKVKWVHMIIDEGHRMKNAQSK
LSLTLNTHYHADYRLILTGTPLQNNLPELWALLNFVLPKIFNSVKSFDEWFNTPFANTGG
QDKIELSEEETLLVIRRLHKVLRPFLLRRLKKDVEKELPDKVEKVVKCKMSALQQIMYQQ
MLKYRRLFIGDQNNKKMVGLRGFNNQIMQLKKICNHPFVFEEVEDQINPTRETNDDIWRV
AGKFELLDRILPKLKATGHRVLIFFQMTQIMDIMEDFLRYINIKYLRLDGHTKSDERSEL
LRLFNAPDSEYLCFILSTRAGGLGLNLQTADTVIIFDTDWNPHQDLQAQDRAHRIGQKNE
VRILRLITTNSVEEVILERAYKKLDIDGKVIQAGKFDNKSTSEEQEALLRSLLDAEEERR
KKRESGVEEEEELKDSEINEILARNDEEMAVLTRMDEDRSKKEEELGVKSRLLEKSELPD
IYSRDIGAELKREESESAAVYNGRGARERKTATYNDNMSEEQWLRQFEVSDDEKNDKQAR
KQRTKKEDKSEAIDG

Sequence of entity 2 (A, E), FASTA

>5Z3U_2 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 3 (B, F), FASTA

>5Z3U_3 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 4 (C, G), FASTA

>5Z3U_4 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 5 (D, H), FASTA

>5Z3U_5 Histone H2B 1.1 (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK

Sequence of entity 6 (I), FASTA

>5Z3U_6 DNA (167-MER) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGAAGCTTGTCGAGAAGTACGAT

Sequence of entity 7 (J), FASTA

>5Z3U_7 DNA (167-MER) (chains J)
ATCGTACTTCTCGACAAGCTTCAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGAT

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	1
BEF	Beryllium trifluoride ion	Be F3	1

Primary citation

Mechanism of DNA translocation underlying chromatin remodelling by Snf2. Li, M., Xia, X., Tian, Y. et al. Nature (2019) 567:409-413. DOI 10.1038/s41586-019-1029-2 · PubMed

Other PDB entries of the same protein (UniProt P22082 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7VRC 2.15 Å, Structure of the Yeast SNF11/SNF2 complex
4I6M 2.8 Å, Structure of Arp7-Arp9-Snf2(HSA)-RTT102 subcomplex of SWI/SNF chromatin remodeler.
7C4J 2.89 Å, Cryo-EM structure of the yeast Swi/Snf complex in a nucleosome free state
6IY2 3.47 Å, Structure of Snf2-MMTV-A nucleosome complex at shl2 in ADP state
7EGM 3.6 Å, The SRM module of SWI/SNF-nucleosome complex
5Z3O 3.62 Å, Structure of Snf2-nucleosome complex in ADP state
6IY3 3.67 Å, Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state
5X0X 3.97 Å, Complex of Snf2-Nucleosome complex with Snf2 bound to position +6 of the nucleosome
9PB3 4.0 Å, ARP of SWI/SNF of PIC-Med-SWI/SNF
5Z3V 4.22 Å, Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state
5Z3L 4.31 Å, Structure of Snf2-nucleosome complex in apo state
5X0Y 4.69 Å, Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome

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