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- PDB-4xdp: Crystal structure of human KDM4C catalytic domain bound to tris -

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Basic information

Entry
Database: PDB / ID: 4xdp
TitleCrystal structure of human KDM4C catalytic domain bound to tris
ComponentsLysine-specific demethylase 4CKDM4C
KeywordsOXIDOREDUCTASE / LYSINE-SPECIFIC DEMETHYLASE 4C
Function / homology
Function and homology information


H3K9me3 modified histone binding / histone H3K36 demethylase activity / regulation of stem cell differentiation / blastocyst formation / regulation of androgen receptor signaling pathway / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / nuclear androgen receptor binding / stem cell population maintenance / androgen receptor signaling pathway ...H3K9me3 modified histone binding / histone H3K36 demethylase activity / regulation of stem cell differentiation / blastocyst formation / regulation of androgen receptor signaling pathway / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / nuclear androgen receptor binding / stem cell population maintenance / androgen receptor signaling pathway / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / nuclear receptor coactivator activity / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / regulation of gene expression / chromatin remodeling / positive regulation of cell population proliferation / chromatin / enzyme binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / 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. / Small domain found in the jumonji family of transcription factors ...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. / Cupin / 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / TRIETHYLENE GLYCOL / Lysine-specific demethylase 4C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsSwinger, K.K. / Boriack-Sjodin, P.A.
CitationJournal: J Biomol Screen / Year: 2015
Title: A High-Throughput Mass Spectrometry Assay Coupled with Redox Activity Testing Reduces Artifacts and False Positives in Lysine Demethylase Screening.
Authors: Wigle, T.J. / Swinger, K.K. / Campbell, J.E. / Scholle, M.D. / Sherrill, J. / Admirand, E.A. / Boriack-Sjodin, P.A. / Kuntz, K.W. / Chesworth, R. / Moyer, M.P. / Scott, M.P. / Copeland, R.A.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine-specific demethylase 4C
B: Lysine-specific demethylase 4C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,06818
Polymers78,8122
Non-polymers1,25616
Water5,711317
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A: Lysine-specific demethylase 4C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,15411
Polymers39,4061
Non-polymers74810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine-specific demethylase 4C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9157
Polymers39,4061
Non-polymers5096
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.870, 89.750, 98.280
Angle α, β, γ (deg.)90.000, 96.310, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lysine-specific demethylase 4C / KDM4C / Gene amplified in squamous cell carcinoma 1 protein / GASC-1 protein / JmjC domain-containing ...Gene amplified in squamous cell carcinoma 1 protein / GASC-1 protein / JmjC domain-containing histone demethylation protein 3C / Jumonji domain-containing protein 2C


Mass: 39406.035 Da / Num. of mol.: 2 / Fragment: catalytic domain (UNP residues 10-347)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4C, GASC1, JHDM3C, JMJD2C, KIAA0780 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H3R0, 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

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Non-polymers , 8 types, 333 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.8 M Lithium chloride, 0.1 M TRIS pH 8.5, 28 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.07→31.42 Å / Num. obs: 48744 / % possible obs: 98.6 % / Redundancy: 4.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.068 / Net I/σ(I): 11 / Num. measured all: 209621
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.07-2.124.30.6692.31540335580.7330.36697.8
9.26-31.423.90.02735.821605600.9990.01697.3

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→31.42 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 11.105 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2463 5.1 %RANDOM
Rwork0.2066 46275 --
obs0.2084 48738 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.94 Å2 / Biso mean: 27.402 Å2 / Biso min: 9.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20.3 Å2
2---0.36 Å20 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 2.07→31.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5548 0 73 317 5938
Biso mean--32.44 26.27 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195898
X-RAY DIFFRACTIONr_bond_other_d0.0010.025492
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9527951
X-RAY DIFFRACTIONr_angle_other_deg0.7673.00112666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2125696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8323.484287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93151006
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7781535
X-RAY DIFFRACTIONr_chiral_restr0.0810.2802
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216585
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021442
X-RAY DIFFRACTIONr_mcbond_it0.5231.0032741
X-RAY DIFFRACTIONr_mcbond_other0.5221.0012738
X-RAY DIFFRACTIONr_mcangle_it0.9361.4973432
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 159 -
Rwork0.282 3374 -
all-3533 -
obs--97.65 %
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)
10.6411-0.22940.2142.0773-1.02681.3832-0.0216-0.0834-0.01110.03560.02460.0105-0.0039-0.0985-0.0030.129-0.01510.05060.057-0.01210.0211-27.3212.2646.124
20.8434-0.5181-0.9281.81811.18332.45640.0186-0.35780.02070.11010.0567-0.0044-0.0570.501-0.07530.1624-0.05070.01430.2682-0.01990.0038-35.331-7.17494.653
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 347
2X-RAY DIFFRACTION2B10 - 347

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