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- PDB-2y48: Crystal structure of LSD1-CoREST in complex with a N-terminal SNA... -

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Basic information

Entry
Database: PDB / ID: 2y48
TitleCrystal structure of LSD1-CoREST in complex with a N-terminal SNAIL peptide
Components
  • LYSINE-SPECIFIC DEMETHYLASE 1A
  • REST COREPRESSOR 1
  • ZINC FINGER PROTEIN SNAI1
KeywordsOXIDOREDUCTASE / FLAVIN / HISTONE / REPRESSOR / TRANSCRIPTION REGULATION / CHROMATIN / NUCLEAR PROTEIN
Function / homology
Function and homology information


negative regulation of cell differentiation involved in embryonic placenta development / cartilage morphogenesis / left/right pattern formation / negative regulation of vitamin D biosynthetic process / Regulation of CDH11 gene transcription / epithelial cell migration / epithelial to mesenchymal transition involved in endocardial cushion formation / trophoblast giant cell differentiation / positive regulation of megakaryocyte differentiation / guanine metabolic process ...negative regulation of cell differentiation involved in embryonic placenta development / cartilage morphogenesis / left/right pattern formation / negative regulation of vitamin D biosynthetic process / Regulation of CDH11 gene transcription / epithelial cell migration / epithelial to mesenchymal transition involved in endocardial cushion formation / trophoblast giant cell differentiation / positive regulation of megakaryocyte differentiation / 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 / Epithelial-Mesenchymal Transition (EMT) during gastrulation / demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / neuron maturation / positive regulation of neural precursor cell proliferation / regulation of androgen receptor signaling pathway / MRF binding / aortic valve morphogenesis / regulation of bicellular tight junction assembly / DNA repair complex / DNA repair-dependent chromatin remodeling / nuclear androgen receptor binding / hair follicle morphogenesis / regulation of double-strand break repair via homologous recombination / positive regulation of neuroblast proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / roof of mouth development / positive regulation of stem cell proliferation / E-box binding / negative regulation of DNA binding / histone H3K9 demethylase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase complex / mesoderm formation / positive regulation of cell size / histone demethylase activity / epithelial to mesenchymal transition / canonical Wnt signaling pathway / pericentric heterochromatin / heterochromatin organization / positive regulation of epithelial to mesenchymal transition / response to fungicide / cellular response to cAMP / Notch signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription repressor complex / erythrocyte differentiation / 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 / RNA polymerase II transcription regulatory region sequence-specific DNA 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 / fibrillar center / kinase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of neuron projection development / osteoblast differentiation / transcription corepressor activity / regulation of protein localization / cellular response to UV / sequence-specific double-stranded DNA binding / p53 binding / chromatin organization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / flavin adenine dinucleotide binding / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / Potential therapeutics for SARS / chromosome, telomeric region / oxidoreductase activity / transcription coactivator activity / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II
Similarity search - Function
C2H2-type zinc finger / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1880 / : / Helical region in REST corepressor / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / Histone lysine-specific demethylase / ATP synthase, gamma subunit, helix hairpin domain ...C2H2-type zinc finger / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1880 / : / Helical region in REST corepressor / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / Histone lysine-specific demethylase / ATP synthase, gamma subunit, helix hairpin domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / SANT domain profile. / SANT domain / Amine oxidase / Flavin containing amine oxidoreductase / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Zinc finger, C2H2 type / SANT/Myb domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / FAD/NAD(P)-binding domain superfamily / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Lysine-specific histone demethylase 1A / Zinc finger protein SNAI1 / REST corepressor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBaron, R. / Binda, C. / Tortorici, M. / McCammon, J.A. / Mattevi, A.
CitationJournal: Structure / Year: 2011
Title: Molecular Mimicry and Ligand Recognition in Binding and Catalysis by the Histone Demethylase Lsd1-Corest Complex.
Authors: Baron, R. / Binda, C. / Tortorici, M. / Mccammon, J.A. / Mattevi, A.
History
DepositionJan 5, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: 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_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_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: LYSINE-SPECIFIC DEMETHYLASE 1A
B: REST COREPRESSOR 1
C: ZINC FINGER PROTEIN SNAI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7034
Polymers103,9173
Non-polymers7861
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-52.3 kcal/mol
Surface area38140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.170, 181.460, 234.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein LYSINE-SPECIFIC DEMETHYLASE 1A / LYSINE-SPECIFIC DEMETHYLASE 1 / BRAF35-HDAC COMPLEX PROTEIN BHC110 / FLAVIN-CONTAINING AMINE ...LYSINE-SPECIFIC DEMETHYLASE 1 / BRAF35-HDAC COMPLEX PROTEIN BHC110 / FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 2


Mass: 81279.438 Da / Num. of mol.: 1 / Fragment: RESIDUES 123-852
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60341, Oxidoreductases
#2: Protein REST COREPRESSOR 1 / COREPRESSOR COREST / PROTEIN COREST


Mass: 20244.824 Da / Num. of mol.: 1 / Fragment: RESIDUES 305-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9UKL0
#3: Protein/peptide ZINC FINGER PROTEIN SNAI1 / TRANSCRIPTION FACTOR SNAIL / PROTEIN SNAIL HOMOLOG 1 / PROTEIN SNA


Mass: 2392.692 Da / Num. of mol.: 1 / Fragment: N-TERMINAL 20 AMINO ACIDS TAIL, RESIUDES 2-21 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O95863
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 7 Å3/Da / Density % sol: 80 % / Description: NONE
Crystal growDetails: 1.2 M SODIUM/POTASSIUM TARTRATE, 100 MM ADA BUFFER PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→70 Å / Num. obs: 50937 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V1D

2v1d


Resolution: 3→71.77 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.871 / SU B: 12.084 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24559 992 1.9 %RANDOM
Rwork0.21227 ---
obs0.21296 49943 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.004 Å2
Baniso -1Baniso -2Baniso -3
1-4.75 Å20 Å20 Å2
2---3.24 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 3→71.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6363 0 53 0 6416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9738885
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3185804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03824.362298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.126151145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.581544
X-RAY DIFFRACTIONr_chiral_restr0.0970.2994
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214924
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7851.54024
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5226502
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.77532527
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2134.52383
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 74 -
Rwork0.338 3666 -
obs--99.87 %

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