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- PDB-4xbf: Structure of LSD1:CoREST in complex with ssRNA -

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Basic information

Entry
Database: PDB / ID: 4xbf
TitleStructure of LSD1:CoREST in complex with ssRNA
Components
  • Lysine-specific histone demethylase 1A
  • REST corepressor 1
  • RNA (5'-R(*UP*UP*AP*GP*G)-3')
KeywordsOxidoreductase/Transcription/RNA / LSD1 / lysine specific demethylase / demethylase / demethylation / RNA / CoREST / REST Co-repressor 1 / amine oxidase / coiled-coil / SWIRM / chromatin remodelling enzyme / epigenetics / histone modifying enzyme / non-coding RNA / ncRNA / KDM1A / Oxidoreductase-Transcription-RNA complex
Function / homology
Function and homology information


positive regulation of megakaryocyte differentiation / guanine metabolic process / negative regulation of transcription initiation-coupled chromatin remodeling / protein demethylase activity / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / neuron maturation / muscle cell development ...positive regulation of megakaryocyte differentiation / guanine metabolic process / negative regulation of transcription initiation-coupled chromatin remodeling / protein demethylase activity / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / neuron maturation / muscle cell development / positive regulation of neural precursor cell proliferation / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / MRF binding / regulation of androgen receptor signaling pathway / DNA repair complex / nuclear androgen receptor binding / regulation of double-strand break repair via homologous recombination / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of neuroblast proliferation / DNA repair-dependent chromatin remodeling / positive regulation of stem cell proliferation / histone H3K9 demethylase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / histone methyltransferase complex / histone deacetylase complex / histone demethylase activity / positive regulation of cell size / positive regulation of epithelial to mesenchymal transition / response to fungicide / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription repressor complex / cellular response to cAMP / epigenetic regulation of gene expression / positive regulation of protein ubiquitination / Regulation of PTEN gene transcription / erythrocyte differentiation / HDACs deacetylate histones / promoter-specific chromatin binding / cellular response to gamma radiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / positive regulation of neuron projection development / HDMs demethylate histones / cerebral cortex development / protein modification process / cellular response to UV / p53 binding / transcription corepressor activity / flavin adenine dinucleotide binding / regulation of protein localization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / chromatin organization / transcription regulator complex / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Potential therapeutics for SARS / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / chromosome, telomeric region / oxidoreductase activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1880 / : / Helical region in REST corepressor / : / Histone lysine-specific demethylase / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / ATP synthase, gamma subunit, helix hairpin domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1880 / : / Helical region in REST corepressor / : / Histone lysine-specific demethylase / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / ATP synthase, gamma subunit, helix hairpin domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / : / SANT domain profile. / Amine oxidase / Flavin containing amine oxidoreductase / SANT domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / 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 / RNA / Lysine-specific histone demethylase 1A / REST corepressor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsLuka, Z. / Loukachevitch, L.V. / Martin, W.J. / Wagner, C. / Reiter, N.J.
Funding support United States, 1items
OrganizationGrant numberCountry
American Cancer SocietyIRG-58-009-54 United States
CitationJournal: RNA / Year: 2016
Title: G-quadruplex RNA binding and recognition by the lysine-specific histone demethylase-1 enzyme.
Authors: Hirschi, A. / Martin, W.J. / Luka, Z. / Loukachevitch, L.V. / Reiter, N.J.
History
DepositionDec 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Data collection / Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific histone demethylase 1A
B: REST corepressor 1
D: RNA (5'-R(*UP*UP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,38910
Polymers91,0313
Non-polymers1,3587
Water41423
1
A: Lysine-specific histone demethylase 1A
B: REST corepressor 1
D: RNA (5'-R(*UP*UP*AP*GP*G)-3')
hetero molecules

A: Lysine-specific histone demethylase 1A
B: REST corepressor 1
D: RNA (5'-R(*UP*UP*AP*GP*G)-3')
hetero molecules

A: Lysine-specific histone demethylase 1A
B: REST corepressor 1
D: RNA (5'-R(*UP*UP*AP*GP*G)-3')
hetero molecules

A: Lysine-specific histone demethylase 1A
B: REST corepressor 1
D: RNA (5'-R(*UP*UP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)369,55740
Polymers364,12512
Non-polymers5,43228
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_865-x+3,-y+1,z1
crystal symmetry operation3_855-x+3,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area42310 Å2
ΔGint-539 kcal/mol
Surface area145990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.073, 178.411, 234.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Lysine-specific histone demethylase 1A / BRAF35-HDAC complex protein BHC110 / Flavin-containing amine oxidase domain-containing protein 2


Mass: 74126.781 Da / Num. of mol.: 1 / Fragment: UNP residues 171-836
Source method: isolated from a genetically manipulated source
Details: recombinant plasmid (residues 171-852) / Source: (gene. exp.) Homo sapiens (human) / Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1 / Plasmid: pGEX-6P1
Details (production host): MJ23, N-terminal 6X HIS-tag expression vector
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O60341, Oxidoreductases
#2: Protein REST corepressor 1 / Protein CoREST


Mass: 15317.435 Da / Num. of mol.: 1 / Fragment: UNP residues 308-440
Source method: isolated from a genetically manipulated source
Details: amino acids residues 286-482, gift from Dr. Phillip Cole.
Source: (gene. exp.) Homo sapiens (human) / Gene: RCOR1, KIAA0071, RCOR / Plasmid: Pet28 / Details (production host): MJ65 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE) / References: UniProt: Q9UKL0

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RNA chain , 1 types, 1 molecules D

#3: RNA chain RNA (5'-R(*UP*UP*AP*GP*G)-3')


Mass: 1586.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 30 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity % sol: 80 % / Description: orthorhombic I222 space group
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: The LSD1-CoREST complex 10-12 mg/ml concentration (in 25 mM HEPES-Na, pH 7.4, 100 mM NaCl, 5 mM DTT, 1 mM PMSF) was mixed (1:1) with the reservoir solution [0.60 M Li2SO4, 0.63 M (NH4)2SO4, ...Details: The LSD1-CoREST complex 10-12 mg/ml concentration (in 25 mM HEPES-Na, pH 7.4, 100 mM NaCl, 5 mM DTT, 1 mM PMSF) was mixed (1:1) with the reservoir solution [0.60 M Li2SO4, 0.63 M (NH4)2SO4, 0.25 M NaCl, 100 mM Na-citrate, pH 5.6, 10 mM DTT]
PH range: 5.6-6.4 / Temp details: room temp

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen stream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2014
Details: 12.7 KeV energy range, focused beam size: 50uM x 50uM
RadiationMonochromator: Diamond (C111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.803→49.018 Å / Num. all: 62563 / Num. obs: 62270 / % possible obs: 99.5 % / Redundancy: 14.6 % / Rsym value: 0.037 / Net I/σ(I): 23.8
Reflection shellResolution: 2.803→2.8732 Å / Redundancy: 12.5 % / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
HKL-2000Version v706data reduction
CootVersion 0.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IW5

2iw5


Resolution: 2.803→49.018 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 2000 3.21 %
Rwork0.2011 --
obs0.202 62268 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.8 Å2
Refinement stepCycle: LAST / Resolution: 2.803→49.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6293 86 84 23 6486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036600
X-RAY DIFFRACTIONf_angle_d0.7438974
X-RAY DIFFRACTIONf_dihedral_angle_d14.9662472
X-RAY DIFFRACTIONf_chiral_restr0.0271004
X-RAY DIFFRACTIONf_plane_restr0.0041138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.803-2.87320.32551360.28944073X-RAY DIFFRACTION96
2.8732-2.95090.32611410.27494277X-RAY DIFFRACTION99
2.9509-3.03770.28591410.2754255X-RAY DIFFRACTION100
3.0377-3.13580.30691420.2634279X-RAY DIFFRACTION100
3.1358-3.24780.27321420.25234294X-RAY DIFFRACTION100
3.2478-3.37780.25061430.23964291X-RAY DIFFRACTION100
3.3778-3.53150.22011420.22234284X-RAY DIFFRACTION100
3.5315-3.71760.24561430.21434318X-RAY DIFFRACTION100
3.7176-3.95050.25221420.19524278X-RAY DIFFRACTION100
3.9505-4.25530.24241440.17484330X-RAY DIFFRACTION100
4.2553-4.68320.16331440.15774359X-RAY DIFFRACTION100
4.6832-5.36020.17371430.16534328X-RAY DIFFRACTION100
5.3602-6.75050.23631470.19274398X-RAY DIFFRACTION100
6.7505-49.02530.18291500.17554504X-RAY DIFFRACTION99

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