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- PDB-5afw: Assembly of methylated LSD1 and CHD1 drives AR-dependent transcri... -

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Basic information

Entry
Database: PDB / ID: 5afw
TitleAssembly of methylated LSD1 and CHD1 drives AR-dependent transcription and translocation
Components
  • CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1
  • LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A
KeywordsHYDROLASE / LSD1K114ME2 / ANDROGEN RECEPTOR / CHD1 / G9A / PROSTATE CANCER / TMPRRS2-ERG
Function / homology
Function and homology information


guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / nucleosome organization / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development ...guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / nucleosome organization / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development / neuron maturation / positive regulation of neural precursor cell proliferation / regulation of androgen receptor signaling pathway / MRF binding / positive regulation by host of viral transcription / DNA repair complex / ATP-dependent chromatin remodeler activity / DNA repair-dependent chromatin remodeling / nuclear androgen receptor binding / regulation of double-strand break repair via homologous recombination / nuclear chromosome / positive regulation of neuroblast proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of stem cell proliferation / negative regulation of DNA binding / histone H3K9 demethylase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of cell size / histone demethylase activity / positive regulation of epithelial to mesenchymal transition / response to fungicide / cellular response to cAMP / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / helicase activity / nuclear receptor coactivator activity / negative regulation of protein binding / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / HDACs deacetylate histones / promoter-specific chromatin binding / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / cellular response to gamma radiation / cerebral cortex development / positive regulation of neuron projection development / regulation of protein localization / cellular response to UV / p53 binding / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / flavin adenine dinucleotide binding / histone binding / DNA-binding transcription factor binding / Estrogen-dependent gene expression / DNA helicase / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / Potential therapeutics for SARS / chromosome, telomeric region / oxidoreductase activity / transcription coactivator activity / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / enzyme binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
CDH1/2, SANT-Helical linker 1 / CDH1/2 SANT-Helical linker 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Histone lysine-specific demethylase / Chromo domain, conserved site / Chromo domain signature. / SWIRM domain / Chromo domain ...CDH1/2, SANT-Helical linker 1 / CDH1/2 SANT-Helical linker 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Histone lysine-specific demethylase / Chromo domain, conserved site / Chromo domain signature. / SWIRM domain / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / SWIRM domain / Chromo and chromo shadow domain profile. / SWIRM domain profile. / : / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Amine oxidase / Flavin containing amine oxidoreductase / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Chromo-like domain superfamily / Helicase conserved C-terminal domain / Homeobox-like domain superfamily / FAD/NAD(P)-binding domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix-like DNA-binding domain superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 1 / Lysine-specific histone demethylase 1A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMetzger, E. / Willmann, D. / McMillan, J. / Petroll, K. / Metzger, P. / Gerhardt, S. / vonMaessenhausen, A. / Schott, A.K. / Espejo, A. / Eberlin, A. ...Metzger, E. / Willmann, D. / McMillan, J. / Petroll, K. / Metzger, P. / Gerhardt, S. / vonMaessenhausen, A. / Schott, A.K. / Espejo, A. / Eberlin, A. / Wohlwend, D. / Schuele, K.M. / Schleicher, M. / Perner, S. / Bedford, M.T. / Dengjel, J. / Flaig, R. / Einsle, O. / Schuele, R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Assembly of Methylated Kdm1A and Chd1 Drives Androgen Receptor-Dependent Transcription and Translocation.
Authors: 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. / ...Authors: 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.
History
DepositionJan 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1
B: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,72614
Polymers22,0612
Non-polymers66512
Water2,144119
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-2.1 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.296, 44.445, 46.194
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2090-

HOH

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Components

#1: Protein CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1 / CHD-1 / ATP-DEPENDENT HELICASE CHD1 / CHROMODOMAIN-HELICASE-D NA-BINDING PROTEIN 1 / CHD1


Mass: 20483.793 Da / Num. of mol.: 1 / Fragment: RESIDUES 270-443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O14646, DNA helicase
#2: Protein/peptide LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A / BRAF35-HDAC COMPLEX PROTEIN BHC110 / FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 2


Mass: 1576.894 Da / Num. of mol.: 1 / Fragment: RESIDUES 108-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60341, Oxidoreductases
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 56 %
Crystal growDetails: 0.1 M HEPES PH 7.5, 0.2 M L-PROLINE, 10% (W/V) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→55.15 Å / Num. obs: 30650 / % possible obs: 98.8 % / Observed criterion σ(I): 0.8 / Redundancy: 4.4 % / Biso Wilson estimate: 35.44 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 16.4
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 4 % / Rmerge(I) obs: 1.41 / Mean I/σ(I) obs: 0.8 / % possible all: 83.9

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B2W

2b2w


Resolution: 1.6→46.19 Å / Cor.coef. Fo:Fc: 0.9503 / Cor.coef. Fo:Fc free: 0.9518 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.089 / SU Rfree Blow DPI: 0.085 / SU Rfree Cruickshank DPI: 0.083
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1520 4.99 %RANDOM
Rwork0.2094 ---
obs0.2103 30488 99.09 %-
Displacement parametersBiso mean: 56.96 Å2
Baniso -1Baniso -2Baniso -3
1-8.9729 Å20 Å20 Å2
2---12.2255 Å20 Å2
3---3.2526 Å2
Refine analyzeLuzzati coordinate error obs: 0.301 Å
Refinement stepCycle: LAST / Resolution: 1.6→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1415 0 39 119 1573
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011481HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.981972HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d533SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes204HARMONIC5
X-RAY DIFFRACTIONt_it1481HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.62
X-RAY DIFFRACTIONt_other_torsion16.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion182SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1687SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.66 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2476 151 5.22 %
Rwork0.2347 2744 -
all0.2353 2895 -
obs--99.09 %
Refinement TLS params.Method: refined / Origin x: 13.733 Å / Origin y: 11.1202 Å / Origin z: 15.0135 Å
111213212223313233
T-0.1828 Å20.0721 Å20.0151 Å2--0.0456 Å20.0259 Å2---0.171 Å2
L4.9342 °22.8072 °2-1.815 °2-2.4106 °2-1.6536 °2--2.5474 °2
S0.0529 Å °0.6028 Å °0.2625 Å °0.1611 Å °0.2647 Å °0.197 Å °-0.207 Å °-0.2264 Å °-0.3175 Å °
Refinement TLS groupSelection details: CHAIN A

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