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- PDB-3k3o: Crystal structure of the catalytic core domain of human PHF8 comp... -

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Basic information

Entry
Database: PDB / ID: 3k3o
TitleCrystal structure of the catalytic core domain of human PHF8 complexed with alpha-ketoglutarate
ComponentsPHD finger protein 8PHF8
KeywordsOXIDOREDUCTASE / PHF8 (PHD finger protein 8) / histone demethylase / chromatin modification / methylated H3K9 / Mental retardation / Metal-binding / Phosphoprotein / Zinc-finger
Function / homology
Function and homology information


histone H4K20 demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / negative regulation of rDNA heterochromatin formation / histone H3K36 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / positive regulation of transcription by RNA polymerase I ...histone H4K20 demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K27me2/H3K27me3 demethylase activity / negative regulation of rDNA heterochromatin formation / histone H3K36 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / positive regulation of transcription by RNA polymerase I / histone H3K9 demethylase activity / histone demethylase activity / methylated histone binding / Condensation of Prophase Chromosomes / transcription coregulator activity / brain development / G1/S transition of mitotic cell cycle / HDMs demethylate histones / nuclear membrane / iron ion binding / chromatin binding / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1360 / Jumonji, helical domain / Jumonji helical domain / 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 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1360 / Jumonji, helical domain / Jumonji helical domain / 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. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Histone lysine demethylase PHF8 / Histone lysine demethylase PHF8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYu, L. / Wang, Y. / Huang, S. / Wang, J. / Deng, Z. / Wu, W. / Gong, W. / Chen, Z.
CitationJournal: Cell Res. / Year: 2010
Title: Structural insights into a novel histone demethylase PHF8
Authors: Yu, L. / Wang, Y. / Huang, S. / Wang, J. / Deng, Z. / Zhang, Q. / Wu, W. / Zhang, X. / Liu, Z. / Gong, W. / Chen, Z.
History
DepositionOct 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 1, 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4813
Polymers43,2791
Non-polymers2022
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.092, 52.532, 134.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PHD finger protein 8 / PHF8 / PHF8


Mass: 43279.344 Da / Num. of mol.: 1 / Fragment: residues in UNP 86-447
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF8 / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) cells
References: UniProt: Q5JPR9, UniProt: Q9UPP1*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation ...References: UniProt: Q5JPR9, UniProt: Q9UPP1*PLUS, 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-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-FE2 / FE (II) ION


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.: 109 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 200mM KCl, 100mM Mes, pH 6.5, 20% PEG5K, 5mM H3K9me2, 1.7mM KG, 1mM DTT, 1mM Fe2+, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 22413 / Num. obs: 19197 / % possible obs: 85.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.05 / Rsym value: 0.044 / Net I/σ(I): 48.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 3.2 / Num. unique all: 825 / Rsym value: 0.469 / % possible all: 4.3

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YU2

2yu2


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.474 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.311 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 934 4.9 %RANDOM
Rwork0.22 ---
obs0.22 18163 85.74 %-
all-19097 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.25 Å2 / Biso mean: 31.619 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å20 Å2
2---1.57 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 11 109 2784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222745
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.9453739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4235347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37123.604111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24215400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6651511
X-RAY DIFFRACTIONr_chiral_restr0.0730.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212082
X-RAY DIFFRACTIONr_mcbond_it0.3781.51744
X-RAY DIFFRACTIONr_mcangle_it0.70922789
X-RAY DIFFRACTIONr_scbond_it1.131001
X-RAY DIFFRACTIONr_scangle_it1.714.5950
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 63 -
Rwork0.293 1148 -
all-1211 -
obs--77.04 %
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)
12.3104-3.5659-5.84925.60149.113314.8855-0.3324-0.2157-0.00830.61110.5529-0.31170.96510.7467-0.22050.85350.0181-0.28610.8465-0.32121.3595-7.565-19.898-7.142
24.13-3.48052.3329.6843-1.12345.1508-0.0128-0.0232-0.62270.5556-0.12171.19880.2707-0.37110.13460.1569-0.16520.06920.2145-0.02940.2326-29.807-11.48-16.437
33.4933-1.41252.81847.1446-1.05356.24580.129-0.0422-0.573-0.0913-0.05610.80390.494-0.468-0.07290.14-0.107-0.01660.2117-0.05290.2016-25.988-10.73-21.011
45.0596-3.4671.51556.3368-2.35835.69890.18540.80850.4072-0.4591-0.389-0.984-0.00370.65170.20360.22130.03520.17410.3817-0.03640.2426-3.585-6.485-30.86
56.5198-6.00970.536910.00971.30734.77110.23150.42490.224-0.2361-0.0803-0.58880.17350.3689-0.15120.08210.02040.12150.2606-0.04850.23360.827-9.831-27.27
66.39360.276-1.77372.36330.5393.54270.23960.97270.3479-0.7875-0.0514-0.0769-0.3261-0.0615-0.18820.3060.01120.05920.40110.01080.1028-16.145-1.17-34.357
72.29471.23310.714110.8332-3.47822.9084-0.09130.52880.0964-0.7734-0.02070.1718-0.1233-0.16970.1120.18570.1252-0.04710.3127-0.01690.0445-25.0258.025-25.811
82.1725-1.1704-0.58545.3-0.31552.35360.03990.21510.3333-0.0356-0.0482-0.7346-0.04350.04730.00820.0577-0.01640.00960.1549-0.01420.1305-11.81-0.622-20.441
92.4028-0.5143-0.00415.41251.37817.3734-0.1454-0.1559-0.20460.62010.1067-0.2960.2065-0.00750.03870.1716-0.0166-0.02960.0885-0.00590.0455-14.734-8.476-11.061
1014.75061.3074-0.67357.38913.40012.9435-0.2189-0.36620.08720.11070.2882-0.7120.26790.3586-0.06930.24930.0873-0.0970.1245-0.02380.2065-2.461-2.255-1.955
111.7684-0.19291.01892.29882.230710.3635-0.0942-0.2129-0.45680.62650.0046-0.24250.74210.10550.08970.31840.0251-0.06830.07050.0750.219-12.819-13.606-7.439
121.8351-1.50730.27994.6454-0.30492.2952-0.02880.1949-0.08470.06050.0117-0.19960.2427-0.00520.01710.0969-0.0367-0.00450.1148-0.04030.0316-16.65-7.265-18.593
1310.3023-0.07372.38915.3542-2.60497.03290.1217-0.1981-0.02780.4677-0.0696-0.32940.3014-0.1549-0.05210.1085-0.0104-0.05190.02630.00040.0355-20.4746.677-8.4
147.2717-3.07758.11221.3324-3.31513.45860.02590.69140.46170.018-0.2775-0.31540.05031.53520.25160.3481-0.0491-0.09470.36660.05790.5317-11.0019.184-12.381
159.70280.6098-2.35443.82080.74642.4987-0.13780.77280.1028-0.05990.01530.1926-0.1798-0.52230.12260.10750.0461-0.00760.20.00540.0212-30.66215.543-16.759
1611.152-2.68723.705510.6026-2.48444.9381-0.1290.0071-0.02290.4365-0.01641.0507-0.1037-0.74750.14550.0293-0.02930.0870.4316-0.1360.3868-42.7689.056-13.809
177.62155.5717-0.29349.89421.85684.0753-0.0362-0.0480.21880.6319-0.07630.3195-0.0915-0.39650.11240.12280.04410.02010.0875-0.00620.0176-27.21214.957-7.371
184.9409-4.2966-1.595911.11912.511413.6559-0.1437-0.0645-0.08540.4632-0.05450.0596-0.07720.2590.19820.1116-0.0093-0.02620.0131-0.00750.0419-15.25124.554-5.676
195.6476-0.1816-0.79814.17611.01854.3407-0.05350.61080.80630.01870.10510.0312-0.5324-0.278-0.05160.2240.0590.0280.10190.09610.139-24.22123.521-14.149
2011.26674.7691-6.38362.0259-2.91299.9767-0.01340.47140.589-0.0050.21730.2413-0.0312-0.7823-0.20390.23540.06890.1320.16460.00660.1785-43.25616.212-4.439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A91 - 96
2X-RAY DIFFRACTION2A97 - 118
3X-RAY DIFFRACTION3A119 - 135
4X-RAY DIFFRACTION4A136 - 173
5X-RAY DIFFRACTION5A174 - 194
6X-RAY DIFFRACTION6A195 - 208
7X-RAY DIFFRACTION7A209 - 223
8X-RAY DIFFRACTION8A224 - 256
9X-RAY DIFFRACTION9A257 - 280
10X-RAY DIFFRACTION10A281 - 290
11X-RAY DIFFRACTION11A291 - 307
12X-RAY DIFFRACTION12A308 - 338
13X-RAY DIFFRACTION13A339 - 349
14X-RAY DIFFRACTION14A350 - 363
15X-RAY DIFFRACTION15A364 - 383
16X-RAY DIFFRACTION16A384 - 392
17X-RAY DIFFRACTION17A393 - 408
18X-RAY DIFFRACTION18A409 - 415
19X-RAY DIFFRACTION19A416 - 434
20X-RAY DIFFRACTION20A435 - 445

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