9GBF: PHDvC5HCH tandem domain of NSD2

X-RAY structure of PHDvC5HCH tandem domain of NSD2. Determined by X-ray diffraction at 1.76 Å resolution. Released 18 Dec 2024.

Method: X-ray diffraction
Resolution: 1.76 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,444
Mol. weight: 23.8 kDa
Ligands: ZN
Released: 18 Dec 2024

Explore 9GBF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GBF contains 8 α-helices and 17 β-strands across 2 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, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1252-1253	2	1
β-strand	1262-1263	2	1
α-helix	1265-1268	4
α-helix	1281-1283	3
β-strand	1284	1	2
β-strand	1291	1	2
α-helix	1292	1
β-strand	1294-1295	2	3
β-strand	1302-1303	2	3
α-helix	1305-1307	3
β-strand	1314	1	4
β-strand	1322	1	4

Chain B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	1242	1	5
β-strand	1252-1253	2	5
β-strand	1262-1263	2	5
α-helix	1266-1268	3
α-helix	1273-1274	2
α-helix	1281-1283	3
β-strand	1284	1	6
β-strand	1291	1	6
α-helix	1292	1
β-strand	1294-1295	2	7
β-strand	1302-1303	2	7
β-strand	1314-1315	2	8
β-strand	1321-1322	2	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase NSD2	A, B	protein	103	Homo sapiens	O96028 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9GBF_1 Histone-lysine N-methyltransferase NSD2 (chains A, B)
RAKGEGKRQSEDECFRCGDGGQLVLCDRKFCTKAYHLSCLGLGKRPFGKWECPWHHCDVC
GKPSTSFCHLCPNSFCKEHQDGTAFSCTPDGRSYCSEHDLGAA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Water and common crystallization additives (NA, PEG, EPE) are not listed.

Primary citation

The C-terminal PHDVC5HCH tandem domain of NSD2 is a combinatorial reader of unmodified H3K4 and tri-methylated H3K27 that regulates transcription of cell adhesion genes in multiple myeloma. Berardi, A., Kaestner, C.L., Ghitti, M. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkae1121 · PubMed

Other PDB entries of the same protein (UniProt O96028 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9FOC 1.62 Å, Crystal structure of the PWWP1 domain of NSD2 bound by compound 11.
6XCG 1.64 Å, Histone-lysine N-methyltransferase NSD2-PWWP1 with compound UNC6934
9EXY 1.7 Å, Crystal structure of the PWWP1 domain of NSD2 bound by compound 34.
5VC8 1.8 Å, Crystal structure of the WHSC1 PWWP1 domain
9KNB 1.84 Å, NSD2-PWWP1 domain bound with compound 9
9EXX 1.94 Å, Crystal structure of the PWWP1 domain of NSD2 bound by compound 18.
9FOE 1.96 Å, Crystal structure of the PWWP1 domain of NSD2 bound by compound 7.
9KN9 2.0 Å, NSD2-PWWP1 domain bound with compound 1.
9Y60 2.02 Å, Crystal structure of NSD2 PWWP1 domain in complex with (6R)-6-(3,5-dichlorophenyl)morphol…
5LSU 2.14 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
7LMT 2.27 Å, Histone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10241866a
6UE6 2.4 Å, PWWP1 domain of NSD2 in complex with MR837

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