5Z3O: Snf2-nucleosome complex in ADP state
Structure of Snf2-nucleosome complex in ADP state. Determined by electron microscopy at 3.62 Å resolution. Released 3 Apr 2019.
- Method
- Electron microscopy
- Resolution
- 3.62 Å
- Organisms
- Xenopus laevis, synthetic construct, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 11
- Atoms
- 16,802
- Mol. weight
- 297.5 kDa
- Ligands
- MG, ADP
- Released
- 3 Apr 2019
Explore 5Z3O in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5Z3O contains 70 α-helices and 25 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: 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 | 118-119 | 2 | 2 |
| α-helix | 121-130 | 10 | |
Chain B: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-93 | 11 | |
Chains C and G: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 3 |
| α-helix | 47-72 | 26 | |
| α-helix | 80-89 | 10 | |
| α-helix | 91-97 | 7 | |
Chains D and H: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-45 | 10 | |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 3 |
| α-helix | 88-98 | 11 | |
| α-helix | 103-119 | 17 | |
Chain F: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 5 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 4 |
| α-helix | 83-93 | 11 | |
Chain O: 37 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 672-682 | 11 | |
| α-helix | 684-689 | 6 | |
| α-helix | 746-749 | 4 | |
| α-helix | 757-759 | 3 | |
| α-helix | 769-783 | 15 | |
| β-strand | 788-790 | 3 | 7 |
| α-helix | 798-811 | 14 | |
| β-strand | 819-822 | 4 | 7 |
| α-helix | 825-837 | 13 | |
| β-strand | 844-845 | 2 | 7 |
| α-helix | 850-862 | 13 | |
| β-strand | 868-869 | 2 | 7 |
| α-helix | 874-878 | 5 | |
| α-helix | 880-885 | 6 | |
| β-strand | 890-893 | 4 | 7 |
| α-helix | 896-899 | 4 | |
| α-helix | 905-911 | 7 | |
| β-strand | 918-922 | 5 | 7 |
| α-helix | 936-940 | 5 | |
| α-helix | 943-957 | 15 | |
| α-helix | 969-975 | 7 | |
| α-helix | 977-986 | 10 | |
| α-helix | 996-998 | 3 | |
| β-strand | 1013 | 1 | 8 |
| α-helix | 1021-1030 | 10 | |
| α-helix | 1050-1054 | 5 | |
| α-helix | 1055-1059 | 5 | |
| α-helix | 1069-1072 | 4 | |
| α-helix | 1083-1085 | 3 | |
| α-helix | 1087-1102 | 16 | |
| β-strand | 1106-1110 | 5 | 9 |
| α-helix | 1114-1125 | 12 | |
| β-strand | 1130-1131 | 2 | 9 |
| α-helix | 1140-1149 | 10 | |
| β-strand | 1158-1162 | 5 | 9 |
| β-strand | 1177-1180 | 4 | 9 |
| α-helix | 1188 | 1 | |
| α-helix | 1189-1194 | 6 | |
| α-helix | 1195-1198 | 4 | |
| β-strand | 1207-1210 | 4 | 9 |
| β-strand | 1213 | 1 | 8 |
| α-helix | 1217-1225 | 9 | |
| α-helix | 1228-1232 | 5 | |
| α-helix | 1233-1240 | 8 | |
| α-helix | 1247-1250 | 4 | |
| α-helix | 1252-1262 | 11 | |
| α-helix | 1265-1267 | 3 | |
| α-helix | 1280-1285 | 6 | |
| α-helix | 1291-1306 | 16 | |
| α-helix | 1337-1340 | 4 | |
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
>5Z3O_1 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>5Z3O_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>5Z3O_3 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>5Z3O_4 Histone H2B 1.1 (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK
Sequence of entity 5 (I), FASTA
>5Z3O_5 DNA (167-MER) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGAAGCTTGTCGAGAAGTACGAT
Sequence of entity 6 (J), FASTA
>5Z3O_6 DNA (167-MER) (chains J)
ATCGTACTTCTCGACAAGCTTCAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGAT
Sequence of entity 7 (O), FASTA
>5Z3O_7 Transcription regulatory protein SNF2 (chains O)
AYIKLLDQTKDTRITHLLRQTNAFLDSLTRAVKDQQKYTKEMIDSHIKEASEEVDDLSMV
PKMKDEEYDDDDDNSNVDYYNVAHRIKEDIKKQPSILVGGTLKDYQIKGLQWMVSLFNNH
LNGILADEMGLGKTIQTISLLTYLYEMKNIRGPYLVIVPLSTLSNWSSEFAKWAPTLRTI
SFKGSPNERKAKQAKIRAGEFDVVLTTFEYIIKERALLSKVKWVHMIIDEGHRMKNAQSK
LSLTLNTHYHADYRLILTGTPLQNNLPELWALLNFVLPKIFNSVKSFDEWFNTPFANTGG
QDKIELSEEETLLVIRRLHKVLRPFLLRRLKKDVEKELPDKVEKVVKCKMSALQQIMYQQ
MLKYRRLFIGDQNNKKMVGLRGFNNQIMQLKKICNHPFVFEEVEDQINPTRETNDDIWRV
AGKFELLDRILPKLKATGHRVLIFFQMTQIMDIMEDFLRYINIKYLRLDGHTKSDERSEL
LRLFNAPDSEYLCFILSTRAGGLGLNLQTADTVIIFDTDWNPHQDLQAQDRAHRIGQKNE
VRILRLITTNSVEEVILERAYKKLDIDGKVIQAGKFDNKSTSEEQEALLRSLLDAEEERR
KKRESGVEEEEELKDSEINEILARNDEEMAVLTRMDEDRSKKEEELGVKSRLLEKSELPD
IYSRDIGAELKREESESAAVYNGRGARERKTATYNDNMSEEQWLRQFEVSDDEKNDKQAR
KQRTKKEDKSEAIDG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 1 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 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 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
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