› 7crr

Electron Microscopy
3.48Å resolution

Native NSD3 bound to 187-bp nucleosome

Released:
DOI: 10.2210/pdb7crr/pdb
PDB entry 7crr coloured by chain, front view.
PDB entry 7crr coloured by chain, side view.
PDB entry 7crr coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases.
Li W, Tian W, Yuan G, Deng P, Sengupta D, Cheng Z, Cao Y, Ren J, Qin Y, Zhou Y, Jia Y, Gozani O, Patel DJ, Wang Z
Nature 590 498-503 (2021)
PMID: 33361816
Related structures: EMD-30457

Function and Biology Details

Reactions catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(4) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(4)
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(27) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(27)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
PDBe Complex ID:
PDB-CPX-121173 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone H3 Chains: E, M
Molecule details ›
Chains: E, M
Length: 135 amino acids
Theoretical weight: 15.22 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q92133 (Residues: 2-136; Coverage: 99%)
Gene names: H3l, Hist1h3f, h3, h3.2a, h3c8, h3c8.S, h3r, hist1h3g, hist1h3g.L, hist2h3, hist2h3c
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 129 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Sequence domains:
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 122 amino acids
Theoretical weight: 13.52 KDa
Source organism: Xenopus tropicalis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone-lysine N-methyltransferase NSD3 Chain: I
Molecule details ›
Chain: I
Length: 758 amino acids
Theoretical weight: 85.48 KDa
Source organism: Homo sapiens
Expression system: Baculovirus transfer vector pFASTBAC1
UniProt:
  • Canonical: Q9BZ95 (Residues: 680-1437; Coverage: 53%)
Gene names: DC28, NSD3, WHSC1L1
Sequence domains:
DNA (168-MER) Chain: A
Molecule details ›
Chain: A
Length: 187 nucleotides
Theoretical weight: 57.49 KDa
DNA(168-MER) Chain: K
Molecule details ›
Chain: K
Length: 187 nucleotides
Theoretical weight: 57.98 KDa

Ligands and Environments

2 bound ligands:
Ligand SAM 1 x SAM
Ligand ZN 3 x ZN
1 modified residue:
Ligand NLE 6 x NLE

Experiments and Validation Details

Entry percentile scores
Resolution: 3.48Å
Relevant EMDB volumes: EMD-30457
Expression systems:
  • Escherichia coli
  • Baculovirus transfer vector pFASTBAC1

Quick links

Citations

18 review citations

The language of chromatin modification in human cancers.
Zhao et al. (2021)
17 more

4 mentions without citation

Structure, Activity and Function of the NSD3 Protein Lysine Methyltransferase.
Rathert P. (2021)
3 more