5XMY | pdb_00005xmy

Crystal structure of TAF3 PHD finger bound to H3K4me3Q5ser

• PDB DOI: https://doi.org/10.2210/pdb5XMY/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-05-16 Released: 2018-11-28 
• Deposition Author(s): Zhao, S., Zhang, B., Li, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.221 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of TAF3 PHD finger bound to H3K4me3Q5ser

Zhao, S., Zhang, B., Li, H.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.48 kDa 
• Atom Count: 1,215 
• Modeled Residue Count: 138 
• Deposited Residue Count: 140 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor TFIID subunit 3	A, C	63	Homo sapiens	Mutation(s): 1  Gene Names: TAF3
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VWG9 (Homo sapiens) Explore Q5VWG9  Go to UniProtKB:  Q5VWG9
PHAROS:  Q5VWG9 GTEx:  ENSG00000165632

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone peptide H3(1-15)K4me3Q5ser	B [auth P], D	7	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth C], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	B [auth P], D	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.221 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.982	α = 90
b = 48.096	β = 98.16
c = 52.7	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-28 
Deposition Author(s): Zhao, S., Zhang, B., Li, H.

Revision History  

• Version 1.0: 2018-11-28
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description