5WXH

Crystal structure of TAF3 PHD finger bound to H3K4me3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • DOI: 10.1073/pnas.1704155114
  • Primary Citation of 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 ...

    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.

    Organizational Affiliation: 

    Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 3A,
B [auth C]		63Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5VWG9
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3K4me3C [auth D],
D [auth P]		7Homo sapiensMutation(s): 0 
Gene Names: 
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 
Entity Groups  
UniProt GroupP68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L		C [auth D],
D [auth P]		L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.244α = 82.96
b = 35.138β = 75.62
c = 38.562γ = 73.49
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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