5AFW

Assembly of methylated LSD1 and CHD1 drives AR-dependent transcription and translocation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Assembly of Methylated Kdm1A and Chd1 Drives Androgen Receptor-Dependent Transcription and Translocation.

Metzger, E.Willmann, D.Mcmillan, J.Forne, I.Metzger, P.Gerhardt, S.Petroll, K.Von Maessenhausen, A.Urban, S.Schott, A.Espejo, A.Eberlin, A.Wohlwend, D.Schule, K.M.Schleicher, M.Perner, S.Bedford, M.T.Jung, M.Dengjel, J.Flaig, R.Imhof, A.Einsle, O.Schule, R.

(2016) Nat.Struct.Mol.Biol. 23: 132

  • DOI: 10.1038/nsmb.3153

  • PubMed Abstract: 
  • Prostate cancer evolution is driven by a combination of epigenetic and genetic alterations such as coordinated chromosomal rearrangements, termed chromoplexy. TMPRSS2-ERG gene fusions found in human prostate tumors are a hallmark of chromoplexy. TMPR ...

    Prostate cancer evolution is driven by a combination of epigenetic and genetic alterations such as coordinated chromosomal rearrangements, termed chromoplexy. TMPRSS2-ERG gene fusions found in human prostate tumors are a hallmark of chromoplexy. TMPRSS2-ERG fusions have been linked to androgen signaling and depend on androgen receptor (AR)-coupled gene transcription. Here, we show that dimethylation of KDM1A at K114 (to form K114me2) by the histone methyltransferase EHMT2 is a key event controlling androgen-dependent gene transcription and TMPRSS2-ERG fusion. We identified CHD1 as a KDM1A K114me2 reader and characterized the KDM1A K114me2-CHD1 recognition mode by solving the cocrystal structure. Genome-wide analyses revealed chromatin colocalization of KDM1A K114me2, CHD1 and AR in prostate tumor cells. Together, our data link the assembly of methylated KDM1A and CHD1 with AR-dependent transcription and genomic translocations, thereby providing mechanistic insight into the formation of TMPRSS2-ERG gene fusions during prostate-tumor evolution.


    Organizational Affiliation

    Centre of Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Germany.,Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.,Diamond Light Source, Didcot, UK.,Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.,Deutsches Konsortium für Translationale Krebsforschung, Freiburg, Germany.,Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Freiburg, Germany.,Pathology Network of the University Hospital of Luebeck and Leibniz Research Center Borstel, Luebeck and Borstel, Germany.,Department of Carcinogenesis, University of Texas, Smithville, Texas, USA.,Department of New Therapeutic Concept Discovery, Boehringer Ingelheim, Vienna, Austria.,Center for Biological Systems Analysis, Freiburg, Germany.,Adolf-Butenandt Institut, University of Munich, München, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1
A
174Homo sapiensMutation(s): 0 
Gene Names: CHD1
EC: 3.6.4.12
Find proteins for O14646 (Homo sapiens)
Go to Gene View: CHD1
Go to UniProtKB:  O14646
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A
B
12Homo sapiensMutation(s): 0 
Gene Names: KDM1A (AOF2, KDM1, KIAA0601, LSD1)
EC: 1.-.-.-
Find proteins for O60341 (Homo sapiens)
Go to Gene View: KDM1A
Go to UniProtKB:  O60341
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
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
B
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 110.296α = 90.00
b = 44.445β = 90.00
c = 46.194γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
BUSTERrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-01-20
    Type: Database references
  • Version 1.2: 2016-03-02
    Type: Database references