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- PDB-7jm5: Crystal structure of KDM4B in complex with QC6352 -

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Basic information

Entry
Database: PDB / ID: 7jm5
TitleCrystal structure of KDM4B in complex with QC6352
ComponentsLysine-specific demethylase 4B
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / KDM4 / KDM4B / PROTEIN-INHIBITOR COMPLEX / DEMETHYLASE / EPIGENETICS / OXIDOREDUCTASE-INHIBITOR COMPLEX / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex
Function / homology
Function and homology information


histone H3K36 demethylase activity / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / histone demethylase activity / brain development / HDMs demethylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / Estrogen-dependent gene expression ...histone H3K36 demethylase activity / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / histone demethylase activity / brain development / HDMs demethylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / Estrogen-dependent gene expression / chromatin remodeling / chromatin / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
: / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. ...: / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-9DJ / NICKEL (II) ION / Lysine-specific demethylase 4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWhite, S.W. / Yun, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA229739 United States
CitationJournal: Sci Transl Med / Year: 2022
Title: Targeting KDM4 for treating PAX3-FOXO1-driven alveolar rhabdomyosarcoma.
Authors: Singh, S. / Abu-Zaid, A. / Jin, H. / Fang, J. / Wu, Q. / Wang, T. / Feng, H. / Quarni, W. / Shao, Y. / Maxham, L. / Abdolvahabi, A. / Yun, M.K. / Vaithiyalingam, S. / Tan, H. / Bowling, J. / ...Authors: Singh, S. / Abu-Zaid, A. / Jin, H. / Fang, J. / Wu, Q. / Wang, T. / Feng, H. / Quarni, W. / Shao, Y. / Maxham, L. / Abdolvahabi, A. / Yun, M.K. / Vaithiyalingam, S. / Tan, H. / Bowling, J. / Honnell, V. / Young, B. / Guo, Y. / Bajpai, R. / Pruett-Miller, S.M. / Grosveld, G.C. / Hatley, M. / Xu, B. / Fan, Y. / Wu, G. / Chen, E.Y. / Chen, T. / Lewis, P.W. / Rankovic, Z. / Li, Y. / Murphy, A.J. / Easton, J. / Peng, J. / Chen, X. / Wang, R. / White, S.W. / Davidoff, A.M. / Yang, J.
History
DepositionJul 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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 4B
B: Lysine-specific demethylase 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3787
Polymers84,4202
Non-polymers9585
Water55831
1
A: Lysine-specific demethylase 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6563
Polymers42,2101
Non-polymers4462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysine-specific demethylase 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7214
Polymers42,2101
Non-polymers5123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.825, 97.107, 80.068
Angle α, β, γ (deg.)90.000, 106.516, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 42209.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4B, JHDM3B, JMJD2B, KIAA0876 / Production host: Escherichia coli (E. coli)
References: UniProt: O94953, [histone H3]-trimethyl-L-lysine9 demethylase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-9DJ / 3-[({(1R)-6-[methyl(phenyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl}methyl)amino]pyridine-4-carboxylic acid


Mass: 387.474 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: tri-sodium citrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 24351 / % possible obs: 99.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 64.96 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.051 / Net I/σ(I): 16.5
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1435 / CC1/2: 0.867 / Rpim(I) all: 0.34 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXL

4lxl


Resolution: 2.7→41.03 Å / SU ML: 0.3834 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.1037 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2437 1201 4.99 %
Rwork0.1956 22852 -
obs0.198 24053 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.42 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5539 0 61 31 5631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025768
X-RAY DIFFRACTIONf_angle_d0.47577829
X-RAY DIFFRACTIONf_chiral_restr0.0425814
X-RAY DIFFRACTIONf_plane_restr0.004994
X-RAY DIFFRACTIONf_dihedral_angle_d11.40723366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.810.36551280.3312460X-RAY DIFFRACTION96.17
2.81-2.940.31811320.29112511X-RAY DIFFRACTION99.14
2.94-3.090.29941330.26752554X-RAY DIFFRACTION99.89
3.09-3.280.27791340.22772530X-RAY DIFFRACTION99.85
3.28-3.540.24711340.22182545X-RAY DIFFRACTION100
3.54-3.890.26941340.19712547X-RAY DIFFRACTION99.74
3.89-4.460.22231340.16592545X-RAY DIFFRACTION99.85
4.46-5.610.19811350.15522565X-RAY DIFFRACTION99.82
5.61-41.030.22991370.17882595X-RAY DIFFRACTION99.38
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)
11.13685498263-0.3320732736470.5947907309992.89412650213-0.4604580980681.85996087807-0.0514068245227-0.02950711223050.03573400005020.1815468459650.01477745742020.102024884101-0.144841997945-0.07356570551880.03668612334170.604619915718-0.0573913121153-0.0609347735360.485350854882-0.0227514653220.46239233360264.9746916612-3.2885016228425.6252222105
21.84843611844-0.745474311999-1.277709657572.628502238851.029243992273.45132746267-0.0006554848215980.09566461953610.06439998483860.247716054247-0.04314623627380.2334539521090.176910358074-0.3279578511470.03453530308810.519876282001-0.0545766429503-0.0678029616240.5214943347680.007368125244530.5193972770142.0851643813-2.78893435014-10.2598140599
34.26495304649-0.320769751296-1.721570636074.39644605296-0.3355814565518.214531025310.05543689088020.3396219202290.18327653661-0.449505589521-0.07924233442740.218909268539-0.1360108887010.01873269866070.01879992374371.08292593427-0.027629191245-0.2297839206880.8306834310730.2328210248031.1209945306263.7907443026-10.202985755419.8724554267
41.49863019692-0.2608686179261.517556543612.11253414752-2.018628983423.03029909338-0.194375671574-0.2651789296820.131434231530.1395128389420.1952881572090.330881992404-0.09439448462220.0835568621079-0.009089345962911.10169155121-0.109148226245-0.2517146757150.9904278845180.1061147333240.90226269523448.2073321831-8.71056533829-7.89673877968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 362)
2X-RAY DIFFRACTION2(chain 'B' and resid 7 through 362)
3X-RAY DIFFRACTION3(chain 'A' and resid 501)
4X-RAY DIFFRACTION4(chain 'B' and resid 501)

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