5WXH | pdb_00005wxh

Crystal structure of TAF3 PHD finger bound to H3K4me3

• PDB DOI: https://doi.org/10.2210/pdb5WXH/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-01-07 Released: 2017-08-16 
• Deposition Author(s): Zhao, S., Huang, J., Li, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.175 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

Kinetic and high-throughput profiling of epigenetic interactions by 3D-carbene chip-based surface plasmon resonance imaging technology

Zhao, S., Yang, M., Zhou, W., Zhang, B., Cheng, Z., Huang, J., Zhang, M., Wang, Z., Wang, R., Chen, Z., Zhu, J., Li, H.

(2017) Proc Natl Acad Sci U S A 114: E7245-E7254

• PubMed: 28808021 
• DOI: https://doi.org/10.1073/pnas.1704155114
• Primary Citation Related Structures: 
  5WXG, 5WXH


• PubMed Abstract: 
  

  Chemical modifications on histones and DNA/RNA constitute a fundamental mechanism for epigenetic regulation. These modifications often function as docking marks to recruit or stabilize cognate "reader" proteins. So far, a platform for quantitative and high-throughput profiling of the epigenetic interactome is urgently needed but still lacking. Here, we report a 3D-carbene chip-based surface plasmon resonance imaging (SPRi) technology for this purpose. The 3D-carbene chip is suitable for immobilizing versatile biomolecules (e.g., peptides, antibody, DNA/RNA) and features low nonspecific binding, random yet function-retaining immobilization, and robustness for reuses. We systematically profiled binding kinetics of 1,000 histone "reader-mark" pairs on a single 3D-carbene chip and validated two recognition events by calorimetric and structural studies. Notably, a discovery on H3K4me3 recognition by the DNA mismatch repair protein MSH6 in Capsella rubella suggests a mechanism of H3K4me3-mediated DNA damage repair in plant.

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Organizational Affiliation: 
• Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.
Chinese Academy of Sciences Center for Excellence in Nanoscience, Chinese Academy of Sciences Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Chinese Academy of Sciences Center for Excellence in Nanoscience, Chinese Academy of Sciences Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China; [e-mail] [e-mail].
Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; [e-mail] [e-mail].

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 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: 1,286 
• Modeled Residue Count: 137 
• 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, B [auth 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 H3K4me3	C [auth D], D [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 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	C [auth D], D [auth P]	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.175 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.244	α = 82.96
b = 35.138	β = 75.62
c = 38.562	γ = 73.49

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Zhao, S., Huang, J., Li, H.

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Data collection, Refinement description
• Version 1.2: 2017-09-13
  Changes: Database references
• Version 1.3: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Structure summary