5XNV

Crystal structure of YEATS2 YEATS bound to H3K27ac peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.696 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer.

Mi, W.Guan, H.Lyu, J.Zhao, D.Xi, Y.Jiang, S.Andrews, F.H.Wang, X.Gagea, M.Wen, H.Tora, L.Dent, S.Y.R.Kutateladze, T.G.Li, W.Li, H.Shi, X.

(2017) Nat Commun 8: 1088-1088

  • DOI: 10.1038/s41467-017-01173-4

  • PubMed Abstract: 
  • Recognition of modified histones by "reader" proteins constitutes a key mechanism regulating diverse chromatin-associated processes important for normal and neoplastic development. We recently identified the YEATS domain as a novel acetyllysine-bindi ...

    Recognition of modified histones by "reader" proteins constitutes a key mechanism regulating diverse chromatin-associated processes important for normal and neoplastic development. We recently identified the YEATS domain as a novel acetyllysine-binding module; however, the functional importance of YEATS domain-containing proteins in human cancer remains largely unknown. Here, we show that the YEATS2 gene is highly amplified in human non-small cell lung cancer (NSCLC) and is required for cancer cell growth and survival. YEATS2 binds to acetylated histone H3 via its YEATS domain. The YEATS2-containing ATAC complex co-localizes with H3K27 acetylation (H3K27ac) on the promoters of actively transcribed genes. Depletion of YEATS2 or disruption of the interaction between its YEATS domain and acetylated histones reduces the ATAC complex-dependent promoter H3K9ac levels and deactivates the expression of essential genes. Taken together, our study identifies YEATS2 as a histone H3K27ac reader that regulates a transcriptional program essential for NSCLC tumorigenesis.


    Organizational Affiliation

    Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. lht@tsinghua.edu.cn.,Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA. xbshi@mdanderson.org.,Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA. xbshi@mdanderson.org.,Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.,Genes and Development and Epigenetics & Molecular Carcinogenesis Graduate Programs, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.,Department of Veterinary Medicine & Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.,MOE 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.,Université de Strasbourg, 67404, Illkirch, France.,MOE 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. lht@tsinghua.edu.cn.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France.,Genes and Development and Epigenetics & Molecular Carcinogenesis Graduate Programs, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA. xbshi@mdanderson.org.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.,Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67404, Illkirch, France.,Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. wl1@bcm.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YEATS domain-containing protein 2
A
133Homo sapiensMutation(s): 0 
Gene Names: YEATS2 (KIAA1197)
Find proteins for Q9ULM3 (Homo sapiens)
Go to Gene View: YEATS2
Go to UniProtKB:  Q9ULM3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ARG-ALY-SER-ALA-PRO-ALA
B
8Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NH4
Query on NH4

Download SDF File 
Download CCD File 
A
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
B
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.696 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.224 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 72.826α = 90.00
b = 72.826β = 90.00
c = 125.232γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data processing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Major State Basic Research Development ProgramChina2015CB910503
National Natural Science Foundation of ChinaChina91519304

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release