7CRO: NSD2 bearing E1099K/T1150A dual mutation
NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP. Determined by electron microscopy at 3.75 Å resolution. Released 21 Oct 2020.
- Method
- Electron microscopy
- Resolution
- 3.75 Å
- Organisms
- Xenopus laevis, Xenopus tropicalis, Homo sapiens
- Chains
- 11
- Atoms
- 14,797
- Mol. weight
- 303.73 kDa
- Ligands
- ZN, SAM
- Released
- 21 Oct 2020
Explore 7CRO in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7CRO contains 45 α-helices and 32 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 B: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-41 | 11 | |
| α-helix | 50-61 | 12 | |
| α-helix | 63-75 | 13 | |
| β-strand | 80-81 | 2 | 2 |
| α-helix | 85-91 | 7 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 47-70 | 24 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-87 | 8 | |
| α-helix | 93-96 | 4 | |
| β-strand | 101-102 | 2 | 6 |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-42 | 8 | |
| β-strand | 50-51 | 2 | 5 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 88-96 | 9 | |
| α-helix | 103-119 | 17 | |
Chain E: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-74 | 11 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 90-113 | 24 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 54-74 | 21 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 85-92 | 8 | |
| β-strand | 97-98 | 2 | 6 |
Chain G: 8 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 47-55 | 9 | |
| α-helix | 57-68 | 12 | |
| α-helix | 71-73 | 3 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-87 | 8 | |
| α-helix | 93-96 | 4 | |
| β-strand | 100-102 | 3 | 3 |
| α-helix | 117-118 | 2 | |
Chain H: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-30 | 3 | |
| α-helix | 38-43 | 6 | |
| β-strand | 50-51 | 2 | 10 |
| α-helix | 57-80 | 24 | |
| β-strand | 85-86 | 2 | 9 |
| α-helix | 91-98 | 8 | |
| α-helix | 103-105 | 3 | |
| α-helix | 107-120 | 14 | |
Chain I: 4 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 998-999 | 2 | 1 |
| α-helix | 1013-1015 | 3 | |
| β-strand | 1039 | 1 | 11 |
| α-helix | 1066-1068 | 3 | |
| β-strand | 1078 | 1 | 12 |
| β-strand | 1088-1091 | 4 | 13 |
| β-strand | 1095-1096 | 2 | 1 |
| α-helix | 1099-1109 | 11 | |
| α-helix | 1110-1112 | 3 | |
| β-strand | 1119-1123 | 5 | 1 |
| β-strand | 1126-1129 | 4 | 1 |
| β-strand | 1148-1150 | 3 | 13 |
| β-strand | 1153-1155 | 3 | 11 |
| β-strand | 1158-1160 | 3 | 11 |
| β-strand | 1162-1165 | 4 | 13 |
| β-strand | 1174 | 1 | 12 |
| β-strand | 1180-1181 | 2 | 1 |
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 | E, M | protein | 135 | Xenopus laevis | Q92133 (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 | D, H | protein | 122 | Xenopus tropicalis | P02281 (AlphaFold model) |
| DNA (168-mer) | A | DNA | 187 | Xenopus laevis | |
| DNA (168-mer) | K | DNA | 187 | Xenopus laevis | |
| Histone-lysine N-methyltransferase NSD2 | I | protein | 705 | Homo sapiens | O96028 |
Sequence of entity 1 (E, M), FASTA
>7CRO_1 Histone H3 (chains E, M)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVLKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEASEAYLVGLFEDTNLCGIHAKRVTIL
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>7CRO_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>7CRO_3 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>7CRO_4 Histone H2B (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK
Sequence of entity 5 (A), FASTA
>7CRO_5 DNA (168-MER) (chains A)
ATCGGGTGATGCCCGATCCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAG
ACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGG
GGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTTCCAGTGCCGGTG
TCGCGAT
Sequence of entity 6 (K), FASTA
>7CRO_6 DNA (168-MER) (chains K)
ATCGCGACACCGGCACTGGAACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGGATCGGGCATC
ACCCGAT
Sequence of entity 7 (I), FASTA
>7CRO_7 Histone-lysine N-methyltransferase NSD2 (chains I)
GVTAKKEYVCQLCEKPGSLLLCEGPCCGAFHLACLGLSRRPEGRFTCSECASGIHSCFVC
KESKTDVKRCVVTQCGKFYHEACVKKYPLTVFESRGFRCPLHSCVSCHASNPSNPRPSKG
KMMRCVRCPVAYHSGDACLAAGCSVIASNSIICTAHFTARKGKRHHAHVNVSWCFVCSKG
GSLLCCESCPAAFHPDCLNIEMPDGSWFCNDCRAGKKLHFQDIIWVKLGNYRWWPAEVCH
PKNVPPNIQKMKHEIGEFPVFFFGSKDYYWTHQARVFPYMEGDRGSRYQGVRGIGRVFKN
ALQEAEARFREIKLQREARETQESERKPPPYKHIKVNKPYGKVQIYTADISEIPKCNCKP
TDENPCGFDSECLNRMLMFECHPQVCPAGEFCQNQCFTKRQYPETKIIKTDGKGWGLVAK
RDIRKGEFVNEYVGELIDKEECMARIKHAHENDITHFYMLTIDKDRIIDAGPKGNYSRFM
NHSCQPNCEALKWTVNGDTRVGLFAVCDIPAGTELTFNYNLDCLGNEKTVCRCGASNCSG
FLGDRPKTSTTLSSEEKGKKTKKKTRRRRAKGEGKRQSEDECFRCGDGGQLVLCDRKFCT
KAYHLSCLGLGKRPFGKWECPWHHCDVCGKPSTSFCHLCPNSFCKEHQDGTAFSCTPDGR
SYCCEHDLGAASVRSTKTEKPPPEPGKPKGKRRRRRGWRRVTEGK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 3 |
| SAM | S-adenosylmethionine | C15 H22 N6 O5 S | 1 |
Primary citation
Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases. Li, W., Tian, W., Yuan, G. et al. Nature (2021) 590:498-503. DOI 10.1038/s41586-020-03069-8 · PubMed
Other PDB entries of the same protein (UniProt Q92133 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3MEA 1.26 Å, Crystal structure of the SGF29 in complex with H3K4me3
- 3MEU 1.28 Å, Crystal structure of SGF29 in complex with H3R2me2sK4me3
- 3ME9 1.37 Å, Crystal structure of SGF29 in complex with H3K4me3 peptide
- 3H91 1.5 Å, Crystal structure of the complex of human chromobox homolog 2 (CBX2) and H3K27 peptide
- 3O7A 1.67 Å, Crystal structure of PHF13 in complex with H3K4me3
- 3MEV 1.83 Å, Crystal structure of SGF29 in complex with R2AK4me3
- 3GL6 1.9 Å, Crystal structure of JARID1A-PHD3 complexed with H3(1-9)K4me3 peptide
- 4HSU 1.99 Å, Crystal structure of LSD2-NPAC with H3(1-26)in space group P21
- 3MET 2.0 Å, Crystal structure of SGF29 in complex with H3K4me2
- 7CRQ 3.15 Å, NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)
- 7CRP 3.2 Å, NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode)
- 7UNK 3.45 Å, Structure of Importin-4 bound to the H3-H4-ASF1 histone-histone chaperone complex
Browse structure collections
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