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- PDB-7dyq: Crystal structure of histone lysine demethylase 4D (KDM4D) in com... -

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Basic information

Entry
Database: PDB / ID: 7dyq
TitleCrystal structure of histone lysine demethylase 4D (KDM4D) in complex with the inhibitor 5-hydroxy-2-methylpyrazolo[1,5-a]pyrido[3,2-e]pyrimidine-3-carbonitrile
ComponentsLysine-specific demethylase 4D
KeywordsOXIDOREDUCTASE / KDM4D / inhibitor / complex
Function / homology
Function and homology information


positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation ...positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation / HDMs demethylate histones / chromatin DNA binding / site of double-strand break / regulation of gene expression / blood microparticle / damaged DNA binding / chromatin remodeling / inflammatory response / chromatin / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile.
Similarity search - Domain/homology
: / Chem-HR0 / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsWang, T. / Yang, L.
CitationJournal: To Be Published
Title: Crystal structure of histone lysine demethylase 4D (KDM4D) in complex with the inhibitor 5-hydroxy-2-methylpyrazolo[1,5-a]pyrido[3,2-e]pyrimidine-3-carbonitrile
Authors: Wang, T. / Yang, L.
History
DepositionJan 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Lysine-specific demethylase 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3743
Polymers38,0931
Non-polymers2812
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-14 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.635, 71.635, 151.486
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-528-

HOH

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Components

#1: Protein Lysine-specific demethylase 4D / JmjC domain-containing histone demethylation protein 3D / Jumonji domain-containing protein 2D / ...JmjC domain-containing histone demethylation protein 3D / Jumonji domain-containing protein 2D / [histone H3]-trimethyl-L-lysine(9) demethylase 4D / Histone lysine demethylase 4D


Mass: 38093.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4D, JHDM3D, JMJD2D / Production host: Escherichia coli (E. coli)
References: UniProt: Q6B0I6, [histone H3]-trimethyl-L-lysine9 demethylase
#2: Chemical ChemComp-HR0 / 5-hydroxy-2-methylpyrazolo[1,5-a]pyrido[3,2-e]pyrimidine-3-carbonitrile


Mass: 225.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H7N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium citrate tribasic monohydrate PH 8.3, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jan 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.998→26.023 Å / Num. obs: 27628 / % possible obs: 100 % / Redundancy: 25.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.305 / Num. unique obs: 1343

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D6Q

4d6q


Resolution: 1.998→26.023 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1848 1343 5.01 %
Rwork0.1609 25470 -
obs0.1622 26813 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.19 Å2 / Biso mean: 27.8461 Å2 / Biso min: 3.85 Å2
Refinement stepCycle: final / Resolution: 1.998→26.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 25 302 2987
Biso mean--33.53 34.35 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142767
X-RAY DIFFRACTIONf_angle_d1.3763751
X-RAY DIFFRACTIONf_chiral_restr0.066378
X-RAY DIFFRACTIONf_plane_restr0.008484
X-RAY DIFFRACTIONf_dihedral_angle_d12.2751612
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9982-2.06950.19011410.1509247597
2.0695-2.15240.2031290.1566249097
2.1524-2.25030.20291190.1604252698
2.2503-2.36880.20671360.1609250198
2.3688-2.51710.18911320.1594249997
2.5171-2.71130.17781310.1603254498
2.7113-2.98380.19421110.1611258198
2.9838-3.41470.19031400.1594259299
3.4147-4.29910.16361590.1484259899
4.2991-26.0230.18391450.1777266494

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