6NZO: Set2
Set2 bound to nucleosome. Determined by electron microscopy at 3.8 Å resolution. Released 28 Aug 2019.
- Method
- Electron microscopy
- Resolution
- 3.8 Å
- Organisms
- Xenopus laevis, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), synthetic construct
- Chains
- 11
- Atoms
- 13,738
- Mol. weight
- 326.67 kDa
- Ligands
- ZN
- Released
- 28 Aug 2019
Explore 6NZO in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6NZO contains 45 α-helices and 37 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 | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 6 |
| α-helix | 113-115 | 3 | |
Chain D: 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 | 102-119 | 18 | |
Chain E: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 35-36 | 2 | 7 |
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 8 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 9 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 9 |
| α-helix | 50-76 | 27 | |
| β-strand | 80-81 | 2 | 8 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 6 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 10 |
| α-helix | 46-71 | 26 | |
| β-strand | 77-78 | 2 | 11 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 3 |
| α-helix | 113-115 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 11 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 10 |
| α-helix | 88-98 | 11 | |
| α-helix | 101-119 | 19 | |
1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3 | A, E | protein | 136 | Xenopus laevis | P02302 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Xenopus laevis | P62799 (AlphaFold model) |
| Ubiquitin-60S ribosomal protein L40,Histone H2A | C, G | protein | 221 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Xenopus laevis | P06897 (AlphaFold model), P0CH09 (AlphaFold model) |
| Histone H2B 1.1 | D, H | protein | 123 | Xenopus laevis | P02281 |
| DNA (149-mer) | I | DNA | 149 | synthetic construct | |
| DNA (149-mer) | J | DNA | 149 | synthetic construct | |
| Histone-lysine N-methyltransferase | S | protein | 939 | Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) | G0S676 |
Sequence of entity 1 (A, E), FASTA
>6NZO_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVMKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>6NZO_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>6NZO_3 Ubiquitin-60S ribosomal protein L40,Histone H2A (chains C, G)
MDSPDLHHHHHHGTLVPRGSMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGTSSGGSGGSGGSGRSSRAGLQFPVG
RVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVR
NDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>6NZO_4 Histone H2B 1.1 (chains D, H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK
Sequence of entity 5 (I), FASTA
>6NZO_5 DNA (149-MER) (chains I)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGTGC
Sequence of entity 6 (J), FASTA
>6NZO_6 DNA (149-MER) (chains J)
GCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTT
AAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAAT
TGAGCGGCCTCGGCACCGGGATTCTCCAG
Sequence of entity 7 (S), FASTA
>6NZO_7 Histone-lysine N-methyltransferase (chains S)
MEASDRASGPTAGSKSEERTKQNGPRSKKEDASDSSTSTGSKSASRSSSATTMSPDDAKP
ADDSALAQENGVAPKPSRKSSKLPPRNPPQLFNHLPDATEEACRTFQVISDCLYGSRNMG
SSDHDALDCDCAEDWRDGKNHACGEDSDCINRATKIECVIGDCNCGEGCQNQRFQRKQYA
KVSVIKTEKKGYGLRADTDLQPNDFIYEYVGEVINEPTFRSRMLKYDKEGIKHFYFMSLT
KNEFVDATKKGNLGRFCNHSCNPNCYVDKWVVGDKLRMGIFAARYIKAGEELVFNYNVDR
YGADPQPCYCGEPNCVGFIGGKTQTERATKLPLATIEALGIEDGDSWDTTVAKKPRKKKA
SETDEEYVNSLQPKALDEDGVNKVMATLMQCKEKWIAVKLLSRLQATQDDHLRHRVVRMH
GYQILKSTLNAFKHDNNVVLQVLDILYNLPRITKNKISDSNIEAVVQPLASSSDERVAFE
AKRLLEEWDKLETAYRIPRKKDGRVVSAIANSFEEERRSNREEPTKPADPLANVVIPTGP
RSNIPQRNANYYNGVRPRKPPTNLPEGWFVTVDKKTGKYYFYDVNGKVQWQRPTAPAITT
PKPSVKAQQDQKALQDIIDSLTKEPTPRQSAGHTPQRSSTPATEPKKEKWRSLPIEKQMK
IYENTLFPHVKYVMDKFHGKLPREDLKKFARDVNKKLVASDYKHNRVQDPTVPLSSKQAK
KVRKYVYDFFDRALQKYLEYQKRKAQYTSKEGMQSSQTEQNTATPTGTLGKDVDEVMSDV
EAPNSSPQSTSSAGRKRKRDDDQDGDHDMRSPADEDAATSSDPPSVKRIKEDDGTGNDVI
PSPPPPPPPPAEIPMTEEERSMREQEEALMRENEEAQRLEDEAKRKQLELQNGLAAAKNA
GIELGSASFTVSGEPMDVDNDGPPPQEQAQQQKQAVMSH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 3 |
Primary citation
Nucleosome and ubiquitin position Set2 to methylate H3K36. Bilokapic, S., Halic, M. Nat Commun (2019) 10:3795-3795. DOI 10.1038/s41467-019-11726-4 · PubMed
Other PDB entries of the same protein (UniProt P02302 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1M19 2.3 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
- 6YN1 2.35 Å, Crystal structure of histone chaperone APLF acidic domain bound to the histone…
- 1M18 2.45 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
- 1M1A 2.65 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
- 1AOI 2.8 Å, Complex between nucleosome core particle (H3,H4,H2A,H2B) and 146 bp long DNA fragment
- 8TOF 2.8 Å, Rpd3S bound to an H3K36Cme3 modified nucleosome
- 8ETV 3.16 Å, Class2 of the INO80-Hexasome complex
- 8U5H 3.23 Å, Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome
- 6PX1 3.3 Å, Set2 bound to nucleosome
- 8DU4 3.55 Å, Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome
- 7M1X 3.7 Å, Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z
- 6PX3 4.1 Å, Set2 bound to nucleosome
Browse structure collections
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