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- PDB-8f8z: PHF2 (PHD+JMJ) in Complex with H3 Histone N-Terminal Peptide -

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Basic information

Entry
Database: PDB / ID: 8f8z
TitlePHF2 (PHD+JMJ) in Complex with H3 Histone N-Terminal Peptide
Components
  • H3 N-Terminal Peptide
  • Lysine-specific demethylase PHF2
KeywordsOXIDOREDUCTASE/TRANSFERASE / Methyl-lysine binding / aromatic cage / plant homeodomain (PHD) / Jumonji domain / plant homeodomain finger 2 (PHF2) / histone H3 lysine 4 tri-methylation (H3K4me3) / OXIDOREDUCTASE-TRANSFERASE complex
Function / homology
Function and homology information


histone H4K20 demethylase activity / negative regulation of rDNA heterochromatin formation / protein demethylation / 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 / histone H3K9 demethylase activity / transcription initiation-coupled chromatin remodeling / methylated histone binding / liver development / transcription coregulator activity / HDMs demethylate histones ...histone H4K20 demethylase activity / negative regulation of rDNA heterochromatin formation / protein demethylation / 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 / histone H3K9 demethylase activity / transcription initiation-coupled chromatin remodeling / methylated histone binding / liver development / transcription coregulator activity / HDMs demethylate histones / kinetochore / structural constituent of chromatin / nucleosome / transcription coactivator activity / iron ion binding / nucleolus / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Jumonji, helical domain / Jumonji helical domain / 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. ...Jumonji, helical domain / Jumonji helical domain / 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 / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Lysine-specific demethylase PHF2 / Gene for histone H3 (germline gene)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsHorton, J.R. / Cheng, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134744 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR160029 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: A complete methyl-lysine binding aromatic cage constructed by two domains of PHF2.
Authors: Horton, J.R. / Zhou, J. / Chen, Q. / Zhang, X. / Bedford, M.T. / Cheng, X.
History
DepositionNov 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase PHF2
B: Lysine-specific demethylase PHF2
E: H3 N-Terminal Peptide
F: H3 N-Terminal Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,04428
Polymers108,9294
Non-polymers2,11524
Water86548
1
A: Lysine-specific demethylase PHF2
E: H3 N-Terminal Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,36412
Polymers54,4642
Non-polymers89910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-115 kcal/mol
Surface area20220 Å2
MethodPISA
2
B: Lysine-specific demethylase PHF2
F: H3 N-Terminal Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,68016
Polymers54,4642
Non-polymers1,21614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-123 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.854, 83.756, 104.128
Angle α, β, γ (deg.)90.000, 103.670, 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

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Protein / Protein/peptide , 2 types, 4 molecules ABEF

#1: Protein Lysine-specific demethylase PHF2 / GRC5 / PHD finger protein 2


Mass: 51832.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF2, CENP-35, KIAA0662 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold Plus
References: UniProt: O75151, 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: Protein/peptide H3 N-Terminal Peptide / Gene for histone H3 (germline gene)


Mass: 2632.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: V9H1G0

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Non-polymers , 4 types, 72 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 2.5M Ammonium Sulfate 90mM Bis-Tris Propane, pH 6.3 4% Pentaerythritol ethoxylate (3/4 EO/OH)

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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: Oct 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→54.5 Å / Num. obs: 36233 / % possible obs: 98.6 % / Redundancy: 7.8 % / Biso Wilson estimate: 66.17 Å2 / CC1/2: 0.929 / Net I/σ(I): 3.4
Reflection shellResolution: 3.3→3.4 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3642 / CC1/2: 0.434 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUIdata collection
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→54.5 Å / SU ML: 0.4838 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6858
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.256 1809 5.02 %
Rwork0.2133 34237 -
obs0.2154 36046 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.85 Å2
Refinement stepCycle: LAST / Resolution: 3.3→54.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6711 0 102 48 6861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026968
X-RAY DIFFRACTIONf_angle_d0.42159502
X-RAY DIFFRACTIONf_chiral_restr0.03931041
X-RAY DIFFRACTIONf_plane_restr0.00371204
X-RAY DIFFRACTIONf_dihedral_angle_d9.76672407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.390.37161420.31282633X-RAY DIFFRACTION97.78
3.39-3.490.34581430.30012654X-RAY DIFFRACTION98.69
3.49-3.60.35171380.28652636X-RAY DIFFRACTION99.11
3.6-3.730.29171340.26072636X-RAY DIFFRACTION98.96
3.73-3.880.29861380.24152627X-RAY DIFFRACTION99.21
3.88-4.060.27431360.22482613X-RAY DIFFRACTION98.78
4.06-4.270.22421400.21282629X-RAY DIFFRACTION98.75
4.27-4.540.19631370.18182582X-RAY DIFFRACTION97.04
4.54-4.890.22861370.16912659X-RAY DIFFRACTION99.11
4.89-5.380.25611420.19122655X-RAY DIFFRACTION99.79
5.38-6.160.22941440.20532673X-RAY DIFFRACTION99.79
6.16-7.750.24181390.19932617X-RAY DIFFRACTION99.1
7.76-54.50.20751390.15972623X-RAY DIFFRACTION97.98
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)
14.04782789627-2.21927395287-2.412611500842.779245129091.895883512646.59229636419-0.0541623793975-0.1945056300880.2929822878320.3166078661720.269707254987-0.683235065780.2083720865760.390467094688-0.2073080937130.4446973951830.0277873053872-0.00955221511860.400104102089-0.07456085023540.56609430754132.892683766217.5195593881-27.6734231838
26.602065729080.715650837947-1.689638518865.03499498306-4.656799306169.14509314079-0.137357448465-0.0444774935353-0.0256705202874-0.4125420536710.426690974769-0.07233472688471.193877322520.492689439407-0.3403774242320.5766688137250.1627996540910.03852728416840.542581779641-0.1293624280690.44347580921728.02295739940.886958098136-65.1383448926
31.539357302570.4578324224020.361848982780.628197375199-0.0598896732268.80083992466-0.0761881242168-0.1836048711090.0926215538988-0.09162509854470.143291867043-0.116052122682-0.456059769793-0.040834283145-0.08178441958580.364021513415-0.0139469171098-0.006737758506440.278355377918-0.02571498115850.53501598324919.498114285514.095446051-49.9283688878
43.070876631971.561317661960.6552788183370.9338260052770.7817822905161.905410586420.110709529683-0.0193013456167-0.1923272395170.147944996737-0.0906013321328-0.04277855094380.215552615393-0.122613691316-0.04009740442220.4660795791920.00704870964663-0.02161743264950.303953184815-0.03229409210090.44257141818619.8548303932-0.547742159836-57.8115221019
56.956823372324.45590305926-0.06272238781516.50294140565-0.2831713264360.872641757680.0587847852406-0.08755723777020.3334935789940.737609358243-0.08615005391920.4647265649840.57478856771-0.1604971437990.07771283276410.520770301571-0.0613560318691-0.002183022237180.381125566318-0.06401257273690.4878125609316.873762801764.64708851927-64.441619747
68.376985325040.264294609526-2.230522548678.164421147-2.001556822969.3369654604-0.07325203455780.6585376881090.33590069506-0.629837598037-0.217765881948-0.1791840796850.0427523404805-0.08749680370520.2719369815860.4354832300920.09506882074-0.06832470455050.6034906809950.07353669193350.4143411184611.9854130963914.2859101084-77.5193244334
71.367120395660.179706261741.019460585150.6907797420360.8033950265783.535867110280.04502931193830.11608963906-0.1013036984760.0880610828315-0.02026216548270.1807883665670.270293429164-0.311838951829-0.03121030357120.382535024489-0.04552026973690.02249415190440.3796941071680.01038807646220.47033181988559.74389051915.6402580397-35.5036497769
83.57663725987-2.074399191290.9343414880233.63278789923-1.213496102692.42159734738-0.0821511699948-0.346153836654-0.1393773288790.16734435380.116054253087-0.06839681804260.210636472599-0.138588181152-0.03886109663150.402298278377-0.001022845375130.008963445854610.4112013584050.08145210801050.37555688543767.352099834411.3039325849-17.9424999788
92.781056057111.61820638652-1.882262811762.56796788885-0.2572089786546.02489120280.00310554809560.04732374728580.2165252200830.19746874304-0.03778211940340.169852306921-0.785654951883-0.4446957633780.07803429838130.4973102941450.0486457085539-0.02692298757410.370988379039-0.09307619128340.41301989734481.801886674931.708868684-6.94201405745
104.99630866757-6.60057275777-0.3043443815899.42287877408-2.039029094098.481462763281.30290309557-0.557284387959-0.795932769532-0.635932539889-0.0508211986259-0.2336385966231.136328973940.630128405433-1.205088063630.45745041239-0.0201450939087-0.1022784358270.705348045945-0.1046337355880.66067590258531.040757129511.0407613858-32.4380797774
113.875698387862.92045714817-2.864567032222.18369694012-2.034254693392.287280603250.26743940079-0.632558056375-1.869588639230.234222453271-0.636049944457-0.07069820033841.16601330401-1.056883673510.5140155406990.686600807072-0.2724491927920.04389161671710.632837102848-0.05768660630150.80784129768253.30685944826.95124995911-45.5627517085
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 86 )AA0 - 861 - 67
22chain 'A' and (resid 87 through 126 )AA87 - 12668 - 107
33chain 'A' and (resid 127 through 246 )AA127 - 246108 - 227
44chain 'A' and (resid 247 through 338 )AA247 - 338228 - 319
55chain 'A' and (resid 339 through 365 )AA339 - 365320 - 346
66chain 'A' and (resid 366 through 444 )AA366 - 444347 - 425
77chain 'B' and (resid 0 through 246 )BL0 - 2461 - 230
88chain 'B' and (resid 247 through 365 )BL247 - 365231 - 349
99chain 'B' and (resid 366 through 449 )BL366 - 449350 - 433
1010chain 'E' and (resid 1 through 7 )EZ1 - 71 - 7
1111chain 'F' and (resid 1 through 8 )FAA1 - 81 - 8

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