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- PDB-7zry: Structure of the 2a splicing variant of the full-length human LSD... -

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Basic information

Entry
Database: PDB / ID: 7zry
TitleStructure of the 2a splicing variant of the full-length human LSD1 bound to CoREST (delta305)
Components
  • Isoform of Lysine-specific histone demethylase 1A
  • REST corepressor 1
KeywordsFLAVOPROTEIN / demethylase / histone / splicing / epigenetics
Function / homology
Function and homology information


positive regulation of megakaryocyte differentiation / DNA repair complex / histone deacetylase complex / transcription repressor complex / erythrocyte differentiation / Regulation of PTEN gene transcription / HDACs deacetylate histones / transcription corepressor activity / chromatin organization / Factors involved in megakaryocyte development and platelet production ...positive regulation of megakaryocyte differentiation / DNA repair complex / histone deacetylase complex / transcription repressor complex / erythrocyte differentiation / Regulation of PTEN gene transcription / HDACs deacetylate histones / transcription corepressor activity / chromatin organization / Factors involved in megakaryocyte development and platelet production / transcription regulator complex / Potential therapeutics for SARS / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / enzyme binding / nucleoplasm / nucleus
Similarity search - Function
: / Helical region in REST corepressor / : / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / SANT domain profile. / SANT domain / Myb-like DNA-binding domain ...: / Helical region in REST corepressor / : / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / SANT domain profile. / SANT domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / REST corepressor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCaroli, J. / Mattevi, A.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other governmentOSR-2019-CRG8-4012.2 Saudi Arabia
CitationJournal: Iscience / Year: 2022
Title: Fine-tuned KDM1A alternative splicing regulates human cardiomyogenesis through an enzymatic-independent mechanism.
Authors: Astro, V. / Ramirez-Calderon, G. / Pennucci, R. / Caroli, J. / Saera-Vila, A. / Cardona-Londono, K. / Forastieri, C. / Fiacco, E. / Maksoud, F. / Alowaysi, M. / Sogne, E. / Falqui, A. / ...Authors: Astro, V. / Ramirez-Calderon, G. / Pennucci, R. / Caroli, J. / Saera-Vila, A. / Cardona-Londono, K. / Forastieri, C. / Fiacco, E. / Maksoud, F. / Alowaysi, M. / Sogne, E. / Falqui, A. / Gonzalez, F. / Montserrat, N. / Battaglioli, E. / Mattevi, A. / Adamo, A.
History
DepositionMay 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform of Lysine-specific histone demethylase 1A
B: REST corepressor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,8513
Polymers115,0652
Non-polymers7861
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.755, 179.747, 234.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Isoform of Lysine-specific histone demethylase 1A / BRAF35-HDAC complex protein BHC110 / Flavin-containing amine oxidase domain-containing protein 2 / ...BRAF35-HDAC complex protein BHC110 / Flavin-containing amine oxidase domain-containing protein 2 / [histone H3]-dimethyl-L-lysine(4) FAD-dependent demethylase 1A


Mass: 94820.195 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 (bacteria)
References: [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase
#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 (bacteria) / References: UniProt: Q9UKL0
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 1.0-1.3 M Na/K Tartrate, 0.1 M ADA pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 2.7→49.12 Å / Num. obs: 69570 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Net I/σ(I): 12.8
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 7.2 % / Rmerge(I) obs: 3.105 / Mean I/σ(I) obs: 0.68 / Num. unique obs: 701 / CC1/2: 0.307 / % possible all: 98.9

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V1D

2v1d


Resolution: 2.7→49.12 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 1997 2.89 %
Rwork0.2204 129232 -
obs0.221 69570 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.27 Å2 / Biso mean: 98.4218 Å2 / Biso min: 53.06 Å2
Refinement stepCycle: final / Resolution: 2.7→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6286 0 53 0 6339
Biso mean--73.93 --
Num. residues----798
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.730.45251220.4544224434687
2.73-2.770.45511400.44254683482397
2.77-2.810.50461460.42514756490299
2.81-2.850.5251430.41554816495999
2.85-2.890.39931440.417547674911100
2.89-2.940.40651360.400548084944100
2.94-2.980.50271430.374348364979100
2.98-3.040.32751470.367248014948100
3.04-3.090.42231410.345648534994100
3.09-3.150.36591440.332648174961100
3.15-3.210.31181450.314548044949100
3.21-3.280.34331400.288748004940100
3.28-3.360.29621450.266848074952100
3.36-3.440.32051410.265248715012100
3.44-3.540.29021440.256648464990100
3.54-3.640.29681440.250748084952100
3.64-3.760.24211480.236848234971100
3.76-3.890.23571410.216348394980100
3.89-4.050.20691450.200448054950100
4.05-4.230.21151410.190948434984100
4.23-4.460.18841430.177947994942100
4.46-4.740.17841400.17344768490899
4.74-5.10.19781470.174947964943100
5.1-5.610.23391430.203248154958100
5.61-6.420.2081510.200848675018100
6.42-8.090.20691390.178348264965100
8.09-49.120.15771430.14984754489798

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