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- PDB-5ivf: Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-methyl-1H... -

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Basic information

Entry
Database: PDB / ID: 5ivf
TitleLinked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-methyl-1H-imidazol-4-yl)-2-(4,4,4-trifluorobutoxy)pyrido[3,4-d]pyrimidin-4-ol
ComponentsLysine-specific demethylase 5A
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / demethylase inhibition / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / facultative heterochromatin formation / regulation of DNA-binding transcription factor activity / histone demethylase activity / enzyme inhibitor activity / Chromatin modifications during the maternal to zygotic transition (MZT) / circadian regulation of gene expression / HDMs demethylate histones / protein-DNA complex ...[histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / facultative heterochromatin formation / regulation of DNA-binding transcription factor activity / histone demethylase activity / enzyme inhibitor activity / Chromatin modifications during the maternal to zygotic transition (MZT) / circadian regulation of gene expression / HDMs demethylate histones / protein-DNA complex / chromatin DNA binding / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / : / : / Lysine-specific demethylase-like domain / : / PLU-1-like protein / Lysine-specific demethylase 5, C-terminal helical domain / Zinc finger, C5HC2-type / C5HC2 zinc finger ...: / : / : / : / Lysine-specific demethylase-like domain / : / PLU-1-like protein / Lysine-specific demethylase 5, C-terminal helical domain / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-6EB / : / Lysine-specific demethylase 5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.683 Å
AuthorsHorton, J.R. / Cheng, X.
Citation
Journal: Cell Chem Biol / Year: 2016
Title: Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds.
Authors: Horton, J.R. / Liu, X. / Gale, M. / Wu, L. / Shanks, J.R. / Zhang, X. / Webber, P.J. / Bell, J.S. / Kales, S.C. / Mott, B.T. / Rai, G. / Jansen, D.J. / Henderson, M.J. / Urban, D.J. / Hall, ...Authors: Horton, J.R. / Liu, X. / Gale, M. / Wu, L. / Shanks, J.R. / Zhang, X. / Webber, P.J. / Bell, J.S. / Kales, S.C. / Mott, B.T. / Rai, G. / Jansen, D.J. / Henderson, M.J. / Urban, D.J. / Hall, M.D. / Simeonov, A. / Maloney, D.J. / Johns, M.A. / Fu, H. / Jadhav, A. / Vertino, P.M. / Yan, Q. / Cheng, X.
#1: Journal: J. Biol. Chem. / Year: 2016
Title: Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases.
Authors: Horton, J.R. / Engstrom, A. / Zoeller, E.L. / Liu, X. / Shanks, J.R. / Zhang, X. / Johns, M.A. / Vertino, P.M. / Fu, H. / Cheng, X.
History
DepositionMar 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase 5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3533
Polymers37,9451
Non-polymers4082
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.658, 62.289, 46.498
Angle α, β, γ (deg.)90.00, 91.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-857-

HOH

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Components

#1: Protein Lysine-specific demethylase 5A / Histone demethylase JARID1A / Jumonji/ARID domain-containing protein 1A / Retinoblastoma-binding ...Histone demethylase JARID1A / Jumonji/ARID domain-containing protein 1A / Retinoblastoma-binding protein 2 / RBBP-2


Mass: 37944.836 Da / Num. of mol.: 1
Fragment: Linked KDM5A Jmj Domain, UNP residues 1-87 and 348-588
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM5A, JARID1A, RBBP2, RBP2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): Gold C-PLUS
References: UniProt: P29375, 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
#2: Chemical ChemComp-6EB / 8-(1-methyl-1H-imidazol-4-yl)-2-(4,4,4-trifluorobutoxy)pyrido[3,4-d]pyrimidin-4-ol


Mass: 353.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14F3N5O2
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate
PH range: 8.6-9.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.683→32.972 Å / Num. obs: 36091 / % possible obs: 95.9 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 12.8
Reflection shellResolution: 1.69→2.68 Å / Rmerge(I) obs: 0.893 / % possible all: 67.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E6H

5e6h


Resolution: 1.683→32.972 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.62
RfactorNum. reflection% reflection
Rfree0.2017 1823 5.05 %
Rwork0.1688 --
obs0.1705 36076 95.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.683→32.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 26 172 2611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062541
X-RAY DIFFRACTIONf_angle_d0.763485
X-RAY DIFFRACTIONf_dihedral_angle_d14.0341468
X-RAY DIFFRACTIONf_chiral_restr0.05361
X-RAY DIFFRACTIONf_plane_restr0.006457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6828-1.72830.36421030.30441610X-RAY DIFFRACTION59
1.7283-1.77910.3181230.27482346X-RAY DIFFRACTION85
1.7791-1.83660.29831410.22712629X-RAY DIFFRACTION96
1.8366-1.90220.25121460.21782724X-RAY DIFFRACTION99
1.9022-1.97840.24081320.19292737X-RAY DIFFRACTION100
1.9784-2.06840.19351560.16362751X-RAY DIFFRACTION100
2.0684-2.17740.20921320.16412763X-RAY DIFFRACTION100
2.1774-2.31380.20981500.1652768X-RAY DIFFRACTION100
2.3138-2.49240.21431550.16782754X-RAY DIFFRACTION100
2.4924-2.74310.2071530.16622776X-RAY DIFFRACTION100
2.7431-3.13980.19981410.15652777X-RAY DIFFRACTION100
3.1398-3.95470.17351540.14872765X-RAY DIFFRACTION100
3.9547-32.97830.16111370.15372853X-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)
10.00730.0093-0.00230.01730.00070.0231-0.01330.0269-0.0590.05410.038-0.021-0.05390.051500.0813-0.0095-0.01430.101-0.010.1335-17.852510.97138.1336
2-0.0011-0.0010.0050.00250.0031-0.00470.03060.01540.00920.00030.0322-0.0138-0.0093-0.0352-00.2196-0.0042-0.04520.0905-0.05660.1838-36.431734.992913.8316
30.0024-0.0004-0.00490.0030.0010.0069-0.0565-0.03230.00570.1120.00250.0359-0.018-0.044600.14970.0160.0270.09080.00320.0653-31.563118.921122.433
40.0106-0.0163-0.01020.0276-0.00530.00210.07740.02790.02150.00050.07820.0117-0.10410.10530-0.0718-0.10290.04790.0376-0.01880.0304-13.013821.45754.5134
50.0146-0.0064-0.00080.02830.00160.01160.0191-0.006-0.02740.0218-0.00040.062-0.01680.0561-00.0546-0.0096-0.00740.0481-0.00210.0485-27.984813.57173.0259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 362 )
3X-RAY DIFFRACTION3chain 'A' and (resid 363 through 405 )
4X-RAY DIFFRACTION4chain 'A' and (resid 406 through 485 )
5X-RAY DIFFRACTION5chain 'A' and (resid 486 through 588 )

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