7CRR: Native NSD3
Native NSD3 bound to 187-bp nucleosome. Determined by electron microscopy at 3.48 Å resolution. Released 21 Oct 2020.
- Method
- Electron microscopy
- Resolution
- 3.48 Å
- Organisms
- Xenopus laevis, Xenopus tropicalis, synthetic construct
- Chains
- 11
- Atoms
- 14,839
- Mol. weight
- 309.53 kDa
- Ligands
- ZN, SAM
- Released
- 21 Oct 2020
Explore 7CRR in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7CRR contains 44 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 B: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 4 |
| α-helix | 51-61 | 11 | |
| α-helix | 63-74 | 12 | |
| β-strand | 80-81 | 2 | 3 |
| α-helix | 83-91 | 9 | |
| β-strand | 96-98 | 3 | 5 |
Chain C: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-14 | 2 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 6 |
| α-helix | 47-58 | 12 | |
| α-helix | 62-70 | 9 | |
| α-helix | 80-88 | 9 | |
| α-helix | 93-96 | 4 | |
| β-strand | 100-102 | 3 | 7 |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 6 |
| α-helix | 88-96 | 9 | |
| α-helix | 103-119 | 17 | |
Chain E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 48-54 | 7 | |
| α-helix | 64-74 | 11 | |
| β-strand | 83-84 | 2 | 8 |
| α-helix | 90-113 | 24 | |
| 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 | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 9 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 8 |
| α-helix | 85-91 | 7 | |
| β-strand | 96-98 | 3 | 7 |
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 | 47-53 | 7 | |
| α-helix | 55-71 | 17 | |
| β-strand | 77-78 | 2 | 11 |
| α-helix | 80-87 | 8 | |
| α-helix | 93-96 | 4 | |
| β-strand | 100-102 | 3 | 5 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-45 | 8 | |
| β-strand | 50-51 | 2 | 11 |
| α-helix | 56-80 | 25 | |
| β-strand | 85-86 | 2 | 10 |
| α-helix | 90-98 | 9 | |
| α-helix | 103-120 | 18 | |
Chain I: 5 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1070-1072 | 3 | |
| β-strand | 1074-1075 | 2 | 12 |
| β-strand | 1080 | 1 | 1 |
| α-helix | 1115-1118 | 4 | |
| β-strand | 1121 | 1 | 13 |
| β-strand | 1170-1173 | 4 | 14 |
| β-strand | 1177-1179 | 3 | 1 |
| α-helix | 1181-1193 | 13 | |
| β-strand | 1202-1205 | 4 | 1 |
| β-strand | 1208-1211 | 4 | 1 |
| β-strand | 1215-1216 | 2 | 12 |
| α-helix | 1222 | 1 | |
| β-strand | 1223 | 1 | 15 |
| α-helix | 1224 | 1 | |
| β-strand | 1230-1232 | 3 | 14 |
| β-strand | 1235-1237 | 3 | 13 |
| β-strand | 1240-1242 | 3 | 13 |
| β-strand | 1244-1247 | 4 | 14 |
| β-strand | 1258 | 1 | 15 |
| β-strand | 1262 | 1 | 2 |
| β-strand | 1283 | 1 | 16 |
| β-strand | 1286 | 1 | 16 |
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 | synthetic construct | |
| DNA(168-mer) | K | DNA | 187 | synthetic construct | |
| Histone-lysine N-methyltransferase NSD3 | I | protein | 758 | Homo sapiens | Q9BZ95 |
Sequence of entity 1 (E, M), FASTA
>7CRR_1 Histone H3 (chains E, M)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVLKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEASEAYLVGLFEDTNLCGIHAKRVTIL
PKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>7CRR_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>7CRR_3 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK
Sequence of entity 4 (D, H), FASTA
>7CRR_4 Histone H2B (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK
Sequence of entity 5 (A), FASTA
>7CRR_5 DNA (168-MER) (chains A)
ATCGGGTGATGCCCGATCCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAG
ACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGG
GGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTTCCAGTGCCGGTG
TCGCGAT
Sequence of entity 6 (K), FASTA
>7CRR_6 DNA(168-MER) (chains K)
ATCGCGACACCGGCACTGGAACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGA
GTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTA
GAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGGATCGGGCATC
ACCCGAT
Sequence of entity 7 (I), FASTA
>7CRR_7 Histone-lysine N-methyltransferase NSD3 (chains I)
VSDVQSMDSSLSRRGTGMSKKDTVCQICESSGDSLIPCEGECCKHFHLECLGLASLPDSK
FICMECKTGQHPCFSCKVSGKDVKRCSVGACGKFYHEACVRKFPTAIFESKGFRCPQHCC
SACSMEKDIHKASKGRMMRCLRCPVAYHSGDACIAAGSMLVSSYILICSNHSKRSSNSSA
VNVGFCFVCARGLIVQDHSDPMFSSYAYKSHYLLNESNRAELMKLPMIPSSSASKKKCEK
GGRLLCCESCPASFHPECLSIEMPEGCWNCNDCKAGKKLHYKQIVWVKLGNYRWWPAEIC
NPRSVPLNIQGLKHDLGDFPVFFFGSHDYYWVHQGRVFPYVEGDKSFAEGQTSINKTFKK
ALEEAAKRFQELKAQRESKEALEIEKNSRKPPPYKHIKANKVIGKVQIQVADLSEIPRCN
CKPADENPCGLESECLNRMLQYECHPQVCPAGDRCQNQCFTKRLYPDAEIIKTERRGWGL
RTKRSIKKGEFVNEYVGELIDEEECRLRIKRAHENSVTNFYMLTVTKDRIIDAGPKGNYS
RFMNHSCNPNCETQKWTVNGDVRVGLFALCDIPAGMELTFNYNLDCLGNGRTECHCGADN
CSGFLGVRPKSACASTNEEKAKNAKLKQKRRKIKTEPKQMHEDYCFQCGDGGELVMCDKK
DCPKAYHLLCLNLTQPPYGKWECPWHQCDECSSAAVSFCEFCPHSFCKDHEKGALVPSAL
EGRLCCSEHDPMAPVSPEYWSKIKCKWESQDHGEEVKE
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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