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- PDB-5l3g: LSD1-CoREST1 in complex with polymyxin E (colistin) -

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Basic information

Entry
Database: PDB / ID: 5l3g
TitleLSD1-CoREST1 in complex with polymyxin E (colistin)
Components
  • Lysine-specific histone demethylase 1A
  • REST corepressor 1
  • polymyxin E
KeywordsOXIDOREDUCTASE/REPRESSOR / OXIDOREDUCTASE-REPRESSOR complex / LSD1 / KDM1A / CoREST1 / chromatin / epigenetic
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 / histone H4K20 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K4 demethylase activity / telomeric repeat-containing RNA binding ...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 / histone H4K20 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K4 demethylase activity / telomeric repeat-containing RNA binding / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / neuron maturation / muscle cell development / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / MRF binding / regulation of androgen receptor signaling pathway / positive regulation of neural precursor cell proliferation / DNA repair complex / nuclear androgen receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of double-strand break repair via homologous recombination / positive regulation of neuroblast proliferation / DNA repair-dependent chromatin remodeling / positive regulation of stem cell proliferation / histone H3K9 demethylase activity / histone deacetylase complex / negative regulation of DNA damage response, signal transduction by p53 class mediator / histone methyltransferase 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 / epigenetic regulation of gene expression / cellular response to cAMP / positive regulation of protein ubiquitination / Regulation of PTEN gene transcription / erythrocyte differentiation / Negative Regulation of CDH1 Gene Transcription / HDACs deacetylate histones / promoter-specific chromatin binding / positive regulation of neuron projection development / cellular response to gamma radiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / cerebral cortex development / p53 binding / cellular response to UV / 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 / Estrogen-dependent gene expression / DNA-binding transcription factor binding / Potential therapeutics for SARS / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / oxidoreductase activity / chromosome, telomeric region / 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 / 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: 3.1 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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: polymyxin E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5296
Polymers102,6983
Non-polymers8323
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-81 kcal/mol
Surface area38090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.864, 179.490, 236.985
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 / 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 polymyxin E / colistin


Mass: 1173.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paenibacillus polymyxa (bacteria)
#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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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: 6.21 Å3/Da / Density % sol: 80.18 %
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: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→48.784 Å / Num. obs: 46474 / % possible obs: 99.7 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Net I/σ(I): 11.6
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.1 / % possible all: 99.8

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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: 3.1→48.784 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.94
RfactorNum. reflection% reflection
Rfree0.1972 898 1.93 %
Rwork0.1728 --
obs0.1734 46414 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→48.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6293 0 136 0 6429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146561
X-RAY DIFFRACTIONf_angle_d1.658899
X-RAY DIFFRACTIONf_dihedral_angle_d16.2492548
X-RAY DIFFRACTIONf_chiral_restr0.076999
X-RAY DIFFRACTIONf_plane_restr0.0081145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.29420.42721500.35687464X-RAY DIFFRACTION99
3.2942-3.54850.30271380.27137528X-RAY DIFFRACTION99
3.5485-3.90540.24911420.19677577X-RAY DIFFRACTION100
3.9054-4.47020.15611420.14237576X-RAY DIFFRACTION100
4.4702-5.63070.17221600.14187592X-RAY DIFFRACTION100
5.6307-48.79040.16871660.15087779X-RAY DIFFRACTION99
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)
10.7862-0.0137-0.210.6563-0.29961.0538-0.20260.06040.3181-0.0133-0.1617-0.3772-0.22380.56390.00030.7114-0.1598-0.26610.87550.20840.928315.3366-56.4839-17.0469
2-0.2724-0.5310.13280.2940.0392-0.1093-0.0621-0.08280.14410.16090.0318-0.2282-0.2597-0.08870.01641.06150.0979-0.27990.99010.42231.3673-25.3025-14.8761-57.5965
30.6573-0.2753-0.18071.9555-0.11691.2029-0.05890.19870.0851-0.1505-0.3149-0.06870.0796-0.04780.00020.90850.0194-0.0540.92940.15620.88142.8374-62.9334-33.2732
40.00270.00320.00130.00260.00460.0004-0.25070.0122-0.14270.06970.01350.1213-0.0063-0.0554-0.00061.9309-0.3616-0.3211.57190.18031.9435-13.3466-31.278-36.3209
50.011-0.0111-0.00430.01240.00060.00120.1096-0.19820.0322-0.0760.22970.27070.1181-0.0844-01.9776-0.0285-0.56092.24810.28252.0963-26.2173-41.5454-40.5489
60.09810.08690.08650.06890.03720.05890.0539-0.0297-0.1938-0.0354-0.0498-0.38580.0845-0.59220.00011.4373-0.0348-0.27921.40320.35781.4343-28.4803-26.9111-63.01
70.01940.00190.01880.0064-0.00170.0219-0.24890.0129-0.0477-0.1344-0.10280.01870.074-0.106-0.00161.45130.2416-0.19051.39350.29791.4125-29.80062.221-76.9373
80.02550.0046-0.0347-0.0006-0.0040.00580.0213-0.7599-0.09120.2018-0.076-0.0965-0.11730.38380.00081.5653-0.2187-0.47291.5520.05711.8245-33.057826.0236-66.9692
90.03480.00590.01590.0236-0.01090.0153-0.3816-0.5903-0.25830.11080.1232-0.05540.29420.31260.0021.5118-0.0074-0.3071.13190.130.8776-47.08224.5023-65.0266
10-0.00240.0121-0.0330.11690.04210.1681-0.1882-0.5847-0.14671.3535-0.19740.04790.34750.0364-01.65270.0635-0.3251.47760.13481.108-46.856523.7529-57.408
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 317 )
5X-RAY DIFFRACTION5chain 'B' and (resid 318 through 329 )
6X-RAY DIFFRACTION6chain 'B' and (resid 330 through 362 )
7X-RAY DIFFRACTION7chain 'B' and (resid 363 through 370 )
8X-RAY DIFFRACTION8chain 'B' and (resid 371 through 384 )
9X-RAY DIFFRACTION9chain 'B' and (resid 385 through 398 )
10X-RAY DIFFRACTION10chain 'B' and (resid 399 through 440 )

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