5C13 | pdb_00005c13

Crystal Structure of TAF3 PHD finger bound to histone H3C4me3 peptide

• PDB DOI: https://doi.org/10.2210/pdb5C13/pdb

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


• Deposited: 2015-06-12 Released: 2015-11-25 
• Deposition Author(s): Li, H., Huang, J.
• Funding Organization(s): ational Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

Crystal Structure of Jarid1a PHD finger bound to histone H3C4me3 peptide

Huang, J., Li, H.

(2015) Nat Commun 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.67 kDa 
• Atom Count: 2,194 
• Modeled Residue Count: 260 
• Deposited Residue Count: 296 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor TFIID subunit 3	A, C, E, G	64	Homo sapiens	Mutation(s): 0  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
H3 peptide	B [auth P], D, F, H	10	synthetic construct	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	I [auth A], J [auth A], K [auth C], L [auth C], M [auth E], N [auth E], O [auth G], P [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4WQ	B [auth P], D, F, H	L-PEPTIDE LINKING	C10 H21 N O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.212	α = 90
b = 50.105	β = 90
c = 85.949	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): Li, H., Huang, J.

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Funding Organization	Location	Grant Number
ational Natural Science Foundation of China	China	31270763

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection, Derived calculations, Experimental preparation
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations