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- PDB-5l3f: LSD1-CoREST1 in complex with polymyxin B -

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Basic information

Entry
Database: PDB / ID: 5l3f
TitleLSD1-CoREST1 in complex with polymyxin B
Components
  • Lysine-specific histone demethylase 1A
  • Polmyxin B
  • REST corepressor 1RCOR1
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE-REPRESSOR Complex / LSD1 / KDM1A / CoREST1 / chromatin / epigenetic
Function / homology
Function and homology information


positive regulation of megakaryocyte differentiation / guanine metabolic process / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / protein demethylation / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / regulation of DNA methylation-dependent heterochromatin formation / muscle cell development / histone H3K4 demethylase activity ...positive regulation of megakaryocyte differentiation / guanine metabolic process / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / protein demethylation / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / regulation of DNA methylation-dependent heterochromatin formation / muscle cell development / histone H3K4 demethylase activity / positive regulation of neural precursor cell proliferation / neuron maturation / MRF binding / regulation of androgen receptor signaling pathway / DNA repair complex / DNA repair-dependent chromatin remodeling / nuclear androgen receptor binding / 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 / 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 / histone deacetylase complex / positive regulation of cell size / histone demethylase activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to fungicide / cellular response to cAMP / transcription repressor complex / erythrocyte differentiation / nuclear receptor coactivator activity / negative regulation of protein binding / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / promoter-specific chromatin binding / HDACs deacetylate histones / cellular response to gamma radiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / positive regulation of neuron projection development / cerebral cortex development / transcription corepressor activity / cellular response to UV / regulation of protein localization / p53 binding / flavin adenine dinucleotide binding / chromatin organization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / chromosome, telomeric region / transcription coactivator activity / oxidoreductase activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / enzyme binding / 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 / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / Histone lysine-specific demethylase / SWIRM domain / SWIRM domain ...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 / SWIRM domain / SWIRM domain / SWIRM domain profile. / ATP synthase, gamma subunit, helix hairpin domain / 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 / 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 / Lysine-specific histone demethylase 1A / REST corepressor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Paenibacillus polymyxa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSperanzini, V. / Rotili, D. / Ciossani, G. / Pilotto, S. / Forgione, M. / Lucidi, A. / Forneris, F. / Velankar, S. / Mai, A. / Mattevi, A.
Funding support Italy, United States, 11items
OrganizationGrant numberCountry
AIRCIG-15208 Italy
MIURProgetto Bandiera Epigenomica - EPIGEN Italy
RF-2010-2318330 Italy
Sapienza Award Project 2014 Italy
IIT-Sapienza Project Italy
AIRC-Fondazione CariploTRIDEO Id. 17515 Italy
MIURPRIN 2012CTAYSY Italy
EUFP7 Projects BLUEPRINT/282510
A-PARADDISE/602080
Giovanni Armenise-Harvard foundationCareer development award 2013 United States
MIURProgramma Giovani Ricercatori Rita Levi-Montalcini 2013 Italy
CitationJournal: Sci Adv / Year: 2016
Title: Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features.
Authors: Speranzini, V. / Rotili, D. / Ciossani, G. / Pilotto, S. / Marrocco, B. / Forgione, M. / Lucidi, A. / Forneris, F. / Mehdipour, P. / Velankar, S. / Mai, A. / Mattevi, A.
History
DepositionApr 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
C: Polmyxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5314
Polymers102,7463
Non-polymers7861
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-56 kcal/mol
Surface area37720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.204, 178.998, 235.777
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 histone demethylase 1A / BRAF35-HDAC complex protein BHC110 / Flavin-containing amine oxidase domain-containing protein 2


Mass: 81279.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RP plus / References: UniProt: O60341, Oxidoreductases
#2: Protein REST corepressor 1 / RCOR1 / Protein CoREST


Mass: 20244.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RCOR1, KIAA0071, RCOR / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9UKL0
#3: Protein/peptide Polmyxin B


Mass: 1221.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paenibacillus polymyxa (bacteria)
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 6.12 Å3/Da / Density % sol: 79.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.3 M Na/K Tartrate 100 mM ADA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.5→49.61 Å / Num. obs: 32150 / % possible obs: 99.9 % / Redundancy: 4.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.161 / Net I/σ(I): 7.7
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v1d

2v1d


Resolution: 3.5→49.227 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.74
RfactorNum. reflection% reflection
Rfree0.2097 637 1.98 %
Rwork0.1863 --
obs0.1868 32130 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→49.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6293 0 138 0 6431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136566
X-RAY DIFFRACTIONf_angle_d1.2448905
X-RAY DIFFRACTIONf_dihedral_angle_d15.8762550
X-RAY DIFFRACTIONf_chiral_restr0.056998
X-RAY DIFFRACTIONf_plane_restr0.0051146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.77020.31681230.3116226X-RAY DIFFRACTION100
3.7702-4.14940.28871090.23586236X-RAY DIFFRACTION100
4.1494-4.74940.20211270.16176247X-RAY DIFFRACTION100
4.7494-5.98210.2011350.17556319X-RAY DIFFRACTION100
5.9821-49.23190.17751430.15766465X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.38030.2725-0.51350.987-0.39031.083-0.04820.00460.31970.0333-0.1037-0.4104-0.14130.5259-0.00020.9218-0.0854-0.22331.0370.12641.139815.3259-56.2275-16.9013
2-0.0254-1.18270.56980.6165-0.2446-0.30260.0041-0.10860.12140.05570.0238-0.1342-0.2296-0.10660.00011.39260.1297-0.28191.3520.38621.6735-25.2093-14.8207-57.3859
30.8512-0.08910.08511.9326-0.15261.4943-0.09850.35560.1117-0.3238-0.2273-0.09070.14650.0267-0.00040.99060.0255-0.02051.13420.11381.04422.8199-62.7888-33.0494
40.0172-0.00610.00650.0301-0.0177-0.00130.14220.0076-0.1460.31150.21220.6077-0.3883-0.25940.00041.994-0.2895-0.26782.33990.28672.1885-19.9535-36.4734-38.2005
50.21210.1170.10340.12760.01040.0614-0.0665-0.2271-0.63820.1410.0774-0.180.2164-0.4642-0.00041.77070.021-0.34121.64340.46081.8973-28.3735-26.9258-62.7824
60.0086-0.00210.00930.0435-0.00940.0122-0.28110.0949-0.2069-0.1592-0.1191-0.12410.0481-0.0441-0.0011.43930.1858-0.28571.940.52111.8104-29.70232.2187-76.822
70.0136-0.00040.0054-0.00240.01430.00110.1159-0.7892-0.07150.3061-0.2244-0.2778-0.16020.20770.00051.7975-0.2665-0.36241.8493-0.04791.7903-32.817525.9858-66.9311
80.02830.0084-0.06190.21810.09590.2472-0.176-0.9236-0.32561.1428-0.2118-0.52450.20020.6564-0.00081.89540.0252-0.31591.71630.12221.3847-46.615423.85-59.1447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 171 through 371 )
2X-RAY DIFFRACTION2chain 'A' and (resid 372 through 513 )
3X-RAY DIFFRACTION3chain 'A' and (resid 514 through 836 )
4X-RAY DIFFRACTION4chain 'B' and (resid 308 through 329 )
5X-RAY DIFFRACTION5chain 'B' and (resid 330 through 362 )
6X-RAY DIFFRACTION6chain 'B' and (resid 363 through 370 )
7X-RAY DIFFRACTION7chain 'B' and (resid 371 through 384 )
8X-RAY DIFFRACTION8chain 'B' and (resid 385 through 440 )

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