5VC8 | pdb_00005vc8

Crystal structure of the WHSC1 PWWP1 domain

• PDB DOI: https://doi.org/10.2210/pdb5VC8/pdb
• NAKB: 5VC8

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-03-31 Released: 2017-06-28 
• Deposition Author(s): Qin, S., Tempel, W., Dong, A., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.229 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Histone and DNA binding ability studies of the NSD subfamily of PWWP domains.

Zhang, M., Yang, Y., Zhou, M., Dong, A., Yan, X., Loppnau, P., Min, J., Liu, Y.

(2021) Biochem Biophys Res Commun 569: 199-206

• PubMed: 34271259 
• DOI: https://doi.org/10.1016/j.bbrc.2021.07.017
• Primary Citation Related Structures: 
  4RXJ, 5VC8


• PubMed Abstract: 
  

  The NSD proteins, namely NSD1, NSD2 and NSD3, are lysine methyltransferases, which catalyze mono- and di-methylation of histone H3K36. They are multi-domain proteins, including two PWWP domains (PWWP1 and PWWP2) separated by some other domains. These proteins act as potent oncoproteins and are implicated in various cancers. However the biological functions of these PWWP domains are still largely unknown. To better understand the functions of these proteins' PWWP domains, we cloned, expressed and purified all the PWWP domains of these NSD proteins to characterize their interactions with methylated histone peptides and dsDNA by quantitative binding assays and crystallographic analysis. Our studies indicate that all these PWWP domains except NSD1_PWWP1 bind to trimethylated H3K36, H3K79 peptides and dsDNA weakly. Our crystal structures uncover that the NDS3_PWWP2 and NSD2_PWWP1 domains, which hold an extremely long α-helix and α-helix bundle, respectively, need a conformation adjustment to interact with nucleosome.

---

Organizational Affiliation: 
• College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China.
Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China; Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China.
Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China; Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Physiology, University of Toronto, Toronto, Ontario, Canada. Electronic address: [e-mail].
College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.13 kDa 
• Atom Count: 2,860 
• Modeled Residue Count: 291 
• Deposited Residue Count: 321 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase NSD2	A, B	141	Homo sapiens	Mutation(s): 0  Gene Names: NSD2, KIAA1090, MMSET, TRX5, WHSC1 EC: 2.1.1.43 (PDB Primary Data), 2.1.1.357 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O96028 (Homo sapiens) Explore O96028  Go to UniProtKB:  O96028
PHAROS:  O96028 GTEx:  ENSG00000109685

Entity ID: 2
Molecule	Chains	Length	Organism	Image
dodeca-2-deoxy-nucleotide, poorly resolved by electron density	C [auth W], D [auth X], E [auth Y]	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*TP*(DN))-3')	F [auth Z]	3	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.229 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35VC8

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.99	α = 90
b = 82.99	β = 90
c = 115.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
XDS	data reduction
SHELXDE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Qin, S., Tempel, W., Dong, A., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 1.1: 2021-08-04
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary