4QBS

Crystal structure of DNMT3a ADD domain E545R mutant bound to H3T3ph peptide

• PDB DOI: https://doi.org/10.2210/pdb4QBS/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-05-08 Released: 2015-05-13 
• Deposition Author(s): Wang, H., Li, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.203 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

Engineering of a histone-recognition domain in a de novo DNA methyltransferase alters the epigenetic landscape of ESCs

Noh, K., Wang, H., Kim, H., Wenderski, W., Fang, F., Li, C., Dewell, S., Wu, X., Ferris, A., Hughes, S.H., Zheng, D., Melnick, A.M., Patel, D.J., Li, H., Allis, C.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.85 kDa 
• Atom Count: 1,287 
• Modelled Residue Count: 145 
• Deposited Residue Count: 145 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 3A	A	138	Homo sapiens	Mutation(s): 1  Gene Names: DNMT3A EC: 2.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6K1 (Homo sapiens) Explore Q9Y6K1  Go to UniProtKB:  Q9Y6K1
PHAROS:  Q9Y6K1 GTEx:  ENSG00000119772

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	B [auth P]	7	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	B [auth P]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.203 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.286	α = 90
b = 57.286	β = 90
c = 71.923	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Wang, H., Li, H.

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release