6AZE

Crystal Structure of the BPTF PHD-bromodomain module bound to H3KC4me3 methyl lysine analog

• PDB DOI: https://doi.org/10.2210/pdb6AZE/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-11 Released: 2018-09-19 
• Deposition Author(s): Chen, Z., Ruthenburg, A.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI), American Cancer Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.213 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Literature

Quantitative and structural assessment of methyllysine analog engagement by cognate binding proteins reveals decrements that can impact qualitative experiment interpretation

Chen, Z., Ruthenburg, A.J., Notti, R.Q., Ueberheide, B., Banaszynski, L.A.

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)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 20.6 kDa 
• Atom Count: 1,517 
• Modelled Residue Count: 173 
• Deposited Residue Count: 173 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleosome-remodeling factor subunit BPTF	A	167	Homo sapiens	Mutation(s): 0  Gene Names: BPTF, FAC1, FALZ
UniProt & NIH Common Fund Data Resources
Find proteins for Q12830 (Homo sapiens) Explore Q12830  Go to UniProtKB:  Q12830
PHAROS:  Q12830 GTEx:  ENSG00000171634

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-ARG-THR-ML3-GLN-THR	B [auth P]	6	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ML3	B [auth P]	L-PEPTIDE LINKING	C8 H19 N2 O2 S		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.213 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.263	α = 90
b = 64.13	β = 90
c = 85.67	γ = 90

Software Package:

Software Name	Purpose
DENZO	data collection
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-09-19 
Deposition Author(s): Chen, Z., Ruthenburg, A.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM115945
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R21HG007426
American Cancer Society	United States	130230- RSG-16-248-01-DMC

Revision History  

• Version 1.0: 2018-09-19
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary