5Z3L: Snf2-nucleosome complex in apo state

Structure of Snf2-nucleosome complex in apo state. Determined by electron microscopy at 4.31 Å resolution. Released 3 Apr 2019.

Method: Electron microscopy
Resolution: 4.31 Å
Organisms: Xenopus laevis, synthetic construct, Saccharomyces cerevisiae
Chains: 11
Atoms: 16,783
Mol. weight: 297.05 kDa
Released: 3 Apr 2019

Explore 5Z3L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Z3L contains 73 α-helices and 24 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: 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	86-113	28
β-strand	119	1	2
α-helix	121-130	10

Chain B: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	46	1	2
α-helix	49-75	27
β-strand	80-81	2	1
α-helix	83-93	11

Chains C and G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	17-20	4
α-helix	27-36	10
α-helix	47-72	26
α-helix	80-89	10
α-helix	91-97	7

Chains D and H: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	36-45	10
α-helix	53-80	28
α-helix	88-98	11
α-helix	103-119	17

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-78	15
β-strand	83	1	3
α-helix	86-113	28
β-strand	118-119	2	4
α-helix	121-130	10

Chain F: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	45-46	2	4
α-helix	50-75	26
β-strand	80	1	3
α-helix	83-93	11

Chain O: 40 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	675-682	8
α-helix	684-688	5
α-helix	744-749	6
α-helix	758-759	2
α-helix	769-784	16
β-strand	789-790	2	5
α-helix	798-809	12
β-strand	819-821	3	6
α-helix	828-837	10
β-strand	844-845	2	6
α-helix	851-862	12
β-strand	868-869	2	6
α-helix	880-885	6
β-strand	890-892	3	6
α-helix	905-912	8
β-strand	918-920	3	6
β-strand	921-922	2	5
α-helix	936-940	5
α-helix	945-957	13
α-helix	969	1
α-helix	970-975	6
α-helix	976-986	11
α-helix	996-998	3
β-strand	1006	1	7
β-strand	1013	1	8
α-helix	1021-1030	10
α-helix	1051-1057	7
α-helix	1058-1060	3
α-helix	1069-1072	4
α-helix	1083-1085	3
α-helix	1087-1090	4
α-helix	1092-1102	11
β-strand	1106-1110	5	9
α-helix	1114-1126	13
β-strand	1130-1131	2	9
α-helix	1135-1137	3
α-helix	1140-1149	10
β-strand	1158-1162	5	9
β-strand	1177-1180	4	9
α-helix	1188	1
α-helix	1189-1193	5
α-helix	1194-1197	4
β-strand	1206	1	7
β-strand	1207-1210	4	9
β-strand	1213	1	8
α-helix	1217-1222	6
α-helix	1223-1228	6
α-helix	1230-1232	3
α-helix	1233-1242	10
α-helix	1247-1250	4
α-helix	1254-1258	5
α-helix	1262-1268	7
α-helix	1280-1286	7
α-helix	1291-1306	16
α-helix	1339-1343	5
α-helix	1344-1346	3

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	P22082

Sequence of entity 1 (A, E), FASTA

>5Z3L_1 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>5Z3L_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>5Z3L_3 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>5Z3L_4 Histone H2B 1.1 (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK

Sequence of entity 5 (I), FASTA

>5Z3L_5 DNA (167-MER) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGAAGCTTGTCGAGAAGTACGAT

Sequence of entity 6 (J), FASTA

>5Z3L_6 DNA (167-MER) (chains J)
ATCGTACTTCTCGACAAGCTTCAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGAT

Sequence of entity 7 (O), FASTA

>5Z3L_7 Transcription regulatory protein SNF2 (chains O)
AYIKLLDQTKDTRITHLLRQTNAFLDSLTRAVKDQQKYTKEMIDSHIKEASEEVDDLSMV
PKMKDEEYDDDDDNSNVDYYNVAHRIKEDIKKQPSILVGGTLKDYQIKGLQWMVSLFNNH
LNGILADEMGLGKTIQTISLLTYLYEMKNIRGPYLVIVPLSTLSNWSSEFAKWAPTLRTI
SFKGSPNERKAKQAKIRAGEFDVVLTTFEYIIKERALLSKVKWVHMIIDEGHRMKNAQSK
LSLTLNTHYHADYRLILTGTPLQNNLPELWALLNFVLPKIFNSVKSFDEWFNTPFANTGG
QDKIELSEEETLLVIRRLHKVLRPFLLRRLKKDVEKELPDKVEKVVKCKMSALQQIMYQQ
MLKYRRLFIGDQNNKKMVGLRGFNNQIMQLKKICNHPFVFEEVEDQINPTRETNDDIWRV
AGKFELLDRILPKLKATGHRVLIFFQMTQIMDIMEDFLRYINIKYLRLDGHTKSDERSEL
LRLFNAPDSEYLCFILSTRAGGLGLNLQTADTVIIFDTDWNPHQDLQAQDRAHRIGQKNE
VRILRLITTNSVEEVILERAYKKLDIDGKVIQAGKFDNKSTSEEQEALLRSLLDAEEERR
KKRESGVEEEEELKDSEINEILARNDEEMAVLTRMDEDRSKKEEELGVKSRLLEKSELPD
IYSRDIGAELKREESESAAVYNGRGARERKTATYNDNMSEEQWLRQFEVSDDEKNDKQAR
KQRTKKEDKSEAIDG

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 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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