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- PDB-5e6h: A Linked Jumonji Domain of the KDM5A Lysine Demethylase -

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Basic information

Entry
Database: PDB / ID: 5e6h
TitleA Linked Jumonji Domain of the KDM5A Lysine Demethylase
ComponentsLysine-specific demethylase 5A
KeywordsOXIDOREDUCTASE / JUMANJI DOMAIN / JARID5A / KDM5A
Function / homology
Function and homology information


facultative heterochromatin formation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / regulation of DNA-binding transcription factor activity / enzyme inhibitor activity / histone demethylase activity / Chromatin modifications during the maternal to zygotic transition (MZT) / circadian regulation of gene expression / HDMs demethylate histones / chromatin DNA binding ...facultative heterochromatin formation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / regulation of DNA-binding transcription factor activity / enzyme inhibitor activity / histone demethylase activity / Chromatin modifications during the maternal to zygotic transition (MZT) / circadian regulation of gene expression / HDMs demethylate histones / chromatin DNA binding / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / regulation of DNA-templated transcription / chromatin / nucleolus / positive regulation of DNA-templated transcription / 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
2-OXOGLUTARIC ACID / : / Lysine-specific demethylase 5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.238 Å
AuthorsHorton, J.R. / Cheng, X.
CitationJournal: 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
DepositionOct 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Feb 17, 2016Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,3305
Polymers37,9451
Non-polymers3854
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.365, 61.591, 46.583
Angle α, β, γ (deg.)90.00, 92.55, 90.00
Int Tables number5
Space group name H-MC121
DetailsMonomer according to Gel Filtration

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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
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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 Matthews: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.5 M Ammonium sulfate 100mM Tris-HCl, pH 8.5 12% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.238→32.6 Å / Num. obs: 15751 / % possible obs: 99.5 % / Redundancy: 11.7 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.241 / Net I/σ(I): 13.3
Reflection shellResolution: 2.238→2.32 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 3.7 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MANUFACTURED MODEL

Resolution: 2.238→32.596 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 741 4.71 %RANDOM
Rwork0.1791 ---
obs0.1809 15746 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.238→32.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 23 100 2529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042511
X-RAY DIFFRACTIONf_angle_d0.683405
X-RAY DIFFRACTIONf_dihedral_angle_d14.472915
X-RAY DIFFRACTIONf_chiral_restr0.045346
X-RAY DIFFRACTIONf_plane_restr0.005446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2385-2.41130.24071550.21262906X-RAY DIFFRACTION97
2.4113-2.65380.27391530.20342968X-RAY DIFFRACTION100
2.6538-3.03760.21931340.18473025X-RAY DIFFRACTION100
3.0376-3.82610.20191550.16783032X-RAY DIFFRACTION100
3.8261-32.59930.20571440.1673074X-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)
11.28950.2986-0.56080.54370.10471.42620.0639-0.0473-0.0650.06040.05-0.0937-0.01280.23560.18890.1244-0.0071-0.03890.1409-0.00680.2092-14.18238.31757.837
20.8939-0.3992-0.24221.23480.611.25860.1221-0.12060.1870.0163-0.06380.0477-0.3907-0.1756-0.17010.18370.0090.02520.134-0.00060.1189-30.483223.295217.5969
30.6464-0.2637-0.17190.3587-0.020.22290.01790.09460.13010.04290.0171-0.0494-0.160.3667-0.17180.1674-0.08640.02610.3525-0.01150.2383-3.111620.50574.6294
40.78170.1139-0.0411.32530.20321.0040.00010.0872-0.0113-0.1033-0.00670.1195-0.0613-0.113-0.11320.0865-0.0006-0.01060.07950.00970.0725-27.537915.00513.1788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((chain A and resid 12:69) and not occupancy = 0)
2X-RAY DIFFRACTION2((chain A and resid 70:418) and not occupancy = 0)
3X-RAY DIFFRACTION3((chain A and resid 419:454) and not occupancy = 0)
4X-RAY DIFFRACTION4((chain A and resid 455:588) and not occupancy = 0)

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