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- PDB-8f8y: PHF2 (PHD+JMJ) in Complex with VRK1 N-Terminal Peptide -

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Basic information

Entry
Database: PDB / ID: 8f8y
TitlePHF2 (PHD+JMJ) in Complex with VRK1 N-Terminal Peptide
Components
  • Lysine-specific demethylase PHF2
  • Serine/threonine-protein kinase VRK1 N-terminus peptide
KeywordsOXIDOREDUCTASE/TRANSFERASE / Methyl-lysine binding / aromatic cage / plant homeodomain / PHD / Jumonji domain / plant homeodomain finger 2 / PHF2 / histone H3 lysine 4 tri-methylation / H3K4me3 / PROTEIN BINDING / OXIDOREDUCTASE-TRANSFERASE complex
Function / homology
Function and homology information


histone H4K20 demethylase activity / histone H2AX kinase activity / Cajal body organization / Golgi disassembly / histone H3T3 kinase activity / negative regulation of rDNA heterochromatin formation / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / 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 / mitotic nuclear membrane disassembly ...histone H4K20 demethylase activity / histone H2AX kinase activity / Cajal body organization / Golgi disassembly / histone H3T3 kinase activity / negative regulation of rDNA heterochromatin formation / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / 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 / mitotic nuclear membrane disassembly / protein demethylation / regulation of neuron migration / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / histone H3K9 demethylase activity / Cajal body / nucleosomal DNA binding / methylated histone binding / transcription initiation-coupled chromatin remodeling / liver development / transcription coregulator activity / HDMs demethylate histones / kinetochore / neuron projection development / kinase activity / histone binding / protein autophosphorylation / transcription coactivator activity / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / iron ion binding / protein phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / nucleolus / protein kinase binding / signal transduction / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol
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 ...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 / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Lysine-specific demethylase PHF2 / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 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: Serine/threonine-protein kinase VRK1 N-terminus peptide
F: Serine/threonine-protein kinase VRK1 N-terminus peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,59930
Polymers106,2924
Non-polymers2,30726
Water95553
1
A: Lysine-specific demethylase PHF2
E: Serine/threonine-protein kinase VRK1 N-terminus peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,23714
Polymers53,1462
Non-polymers1,09112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-141 kcal/mol
Surface area20510 Å2
MethodPISA
2
B: Lysine-specific demethylase PHF2
F: Serine/threonine-protein kinase VRK1 N-terminus peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,36116
Polymers53,1462
Non-polymers1,21614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-121 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.406, 84.065, 105.215
Angle α, β, γ (deg.)90.000, 103.990, 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 Serine/threonine-protein kinase VRK1 N-terminus peptide / Vaccinia-related kinase 1


Mass: 1313.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q99986, non-specific serine/threonine protein kinase

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Non-polymers , 4 types, 79 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


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3 Å3/Da / Density % sol: 59.05 % / Description: Conglomerations of small needles
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: Nov 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.06→38.87 Å / Num. obs: 20652 / % possible obs: 86.3 % / Redundancy: 2.6 % / Biso Wilson estimate: 54.17 Å2 / CC1/2: 0.967 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.136 / Net I/σ(I): 4.4
Reflection shellResolution: 3.06→3.16 Å / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1755 / CC1/2: 0.464 / Rpim(I) all: 0.624 / % possible all: 74.3

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Processing

Software
NameVersionClassification
SERGUI1.20.1_4487data collection
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.06→38.87 Å / SU ML: 0.4536 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2576
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.249 1031 5 %
Rwork0.1945 19573 -
obs0.1972 20604 85.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.31 Å2
Refinement stepCycle: LAST / Resolution: 3.06→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6728 0 112 53 6893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00126996
X-RAY DIFFRACTIONf_angle_d0.37259538
X-RAY DIFFRACTIONf_chiral_restr0.03911039
X-RAY DIFFRACTIONf_plane_restr0.00371207
X-RAY DIFFRACTIONf_dihedral_angle_d9.19472422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.220.37991260.30232385X-RAY DIFFRACTION73.53
3.22-3.420.34371370.2582573X-RAY DIFFRACTION79.78
3.42-3.680.32541540.22772950X-RAY DIFFRACTION91.24
3.68-4.050.25061570.18812983X-RAY DIFFRACTION91.84
4.05-4.640.18011560.15452973X-RAY DIFFRACTION90.96
4.64-5.840.24591480.16772811X-RAY DIFFRACTION86.34
5.84-38.870.20051530.17962898X-RAY DIFFRACTION86.85
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)
10.9835832187830.213598560364-0.04525031132021.565106315540.6428468054245.088804664360.01729448093680.03508594553320.114954662680.2080602473320.0891015064888-0.2037821719340.303040408870.46455696975-0.07878392416950.247203415690.09288223883660.04652406010330.2996892326270.005825960445410.46968119074631.82311.395-40.165
20.2366343596670.6365855680230.4710152109521.656175456490.3742156273455.193643037640.00882071977862-0.06258632418740.1245026146760.0683137445152-0.0437948965780.0623761028349-0.33787296901-0.09899885928020.02263287737410.2368229207920.0458030135898-0.01983041364760.235204458483-0.0175865632770.51005089071719.90413.631-51.193
33.251528813511.693221398960.1652553899710.8186878912530.7836040054992.37469262985-0.01477475151820.163855229557-0.1978719618650.0785234864999-0.0728443151799-0.02286533882360.09370743025580.02840032615310.09138072197010.392876036540.049446928794-0.01585436216820.2456940104690.005603242944480.40405359705820.271-0.527-58.443
46.569569761625.0069542557-3.957842262554.3996792681-3.916602250093.761504720190.0321034048901-0.0288720269895-0.1102756710950.2866138269160.08838733969280.149169489682-0.27357109816-0.493299929791-0.09241615077110.409956812461-0.0010228235311-0.05377582962260.321309371077-0.03828040387510.4565211267097.1044.602-65.158
58.84608484106-0.565969385325-3.700255723445.035831610371.706916382255.60789652914-0.07619187899050.828402103387-0.174699992012-0.549361429343-0.222306556049-0.00939671853203-0.430354501373-0.5326640284140.2949261863110.3634101760060.0551258583928-0.09708855707430.4885761659150.0500200744080.3794317783682.02414.437-78.05
67.85784169158-3.46196916402-5.056622006553.48753150781.429923221087.064995546210.610835692830.978139360441-0.485762296080.00363410159829-0.4257817720980.368683208370.257162159543-0.80491716457-0.1612080937540.348775577052-0.0441930607879-0.1118590376230.513015273807-0.05464595724250.57828198374250.43511.75-52.159
70.79552604487-0.138695365188-1.071725003140.1002963101880.2173594919824.87227780632-0.162221283242-0.0358154679522-0.250372840130.0136967767679-0.2788432751120.02076007778781.30255137586-0.5559492486460.4721402441120.664576957369-0.1577152057020.005686251779630.4125220437060.06081350880920.81569001130258.8692.737-37.722
82.48613146909-0.56390720653-0.1045771380662.855774899561.865673680457.39549385370.0386501127345-0.061442857331-0.1995315724090.1513252283780.08983094744620.0696544347531-0.111927039517-0.440550854219-0.1002734056670.222732059951-0.134114731056-0.07380177456010.2697571335180.0991637849860.38091297476159.60419.929-25.967
96.133478157121.16960671761.342461470797.252509388120.05793543755315.266328147390.330485155335-0.0674221790667-0.428979300379-0.288152314025-0.216045303536-0.7771297989920.5839300005160.172817612858-0.1275901895830.1977569383770.03130165219510.00119132382120.319824333464-0.01817573125440.43089055970267.3610.483-39.742
104.553681403311.280635827251.594516162241.388840340222.539435485315.60616540582-0.2728574984250.1960796099950.347374387343-0.2080245763150.02358740244670.292037698712-0.303653277205-0.09006381182020.2949940447160.2566016137920.00402258573985-0.02035512326460.2034354041770.08433026744630.49200735414468.34725.642-26.388
117.23949021169-4.080959123394.24692208875.4871378704-4.561782279133.79923248385-0.182645730649-0.0125293905403-0.5930928107850.1494883373590.135749774270.324933267726-0.134892294260.007043974859360.08342665991340.4102386120240.04530674121960.06849982515730.310823606899-0.003456506281240.25136487542168.0147.71-18.247
122.39997585565-1.23357399940.05571293966230.763321795650.6426876554792.8116218987-0.0986790180285-0.223697601937-0.06267413713720.1575008220420.02979254241260.2645436073490.309886687415-0.5003096669820.03688597395210.318024322814-0.03672388963540.04832773803620.3244729941790.07891166256470.41989857447261.37811.675-19.849
133.91246743696-4.94376392462.022418554066.24403287842-2.491218860721.500279533750.0736213717966-1.08188962860.602272174072-0.421383922421-0.00905148640999-0.7993141894290.237867729329-0.0941913800687-0.0940777736370.414765278481-0.0705348414503-0.02591519104540.4133231119040.0599204381080.45676839630578.3816.748-15.489
147.507123266950.130101415204-2.576960358725.50079746451-1.143154610696.51932805781-0.280307064362-0.05786996544860.2674784139120.3168974362120.0619903882266-0.154047833786-0.491961744501-0.5846995885180.2061475695510.3414481062730.000465093936019-0.1393792705180.353991437042-0.04742822226250.31345663478579.06632.203-6.847
154.85697451621-0.651676000424-3.511831261344.76184581572.06747284887.220828697290.294459943366-0.255610171302-0.0865313057115-0.04630118803380.1499170540320.229799741078-0.2607497269350.54134011503-0.4310277473050.2994276993330.0148103295052-0.1045006569110.253587081114-0.01878965045150.42177175863386.61431.256-7.189
166.00706930953-0.7801921100285.605320877797.84512861224-4.90171830137.47155053504-0.000975657776861-0.760514188301-1.55417526266-0.1478081505430.0983671767113-1.173869369830.681918610644-0.277981304443-0.2530503358740.3305711010450.1058624367590.01924362607690.439213762988-0.04244338427070.44939435281430.88311.086-32.643
178.562290417984.252237022260.6237533495892.656032604921.726001677993.80459951563-0.873574321384-0.554916044233-0.8931428551910.31018612674-0.228442336744-0.4001059193610.949847404004-0.0878931092841.108206302770.447208778219-0.04215175343920.14586748360.2677172141970.02873861171790.66339126850154.2437.174-46.382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:121 )A0 - 121
2X-RAY DIFFRACTION2( CHAIN A AND RESID 122:246 )A122 - 246
3X-RAY DIFFRACTION3( CHAIN A AND RESID 247:338 )A247 - 338
4X-RAY DIFFRACTION4( CHAIN A AND RESID 339:365 )A339 - 365
5X-RAY DIFFRACTION5( CHAIN A AND RESID 366:444 )A366 - 444
6X-RAY DIFFRACTION6( CHAIN B AND RESID 0:50 )B0 - 50
7X-RAY DIFFRACTION7( CHAIN B AND RESID 51:103 )B51 - 103
8X-RAY DIFFRACTION8( CHAIN B AND RESID 104:167 )B104 - 167
9X-RAY DIFFRACTION9( CHAIN B AND RESID 168:200 )B168 - 200
10X-RAY DIFFRACTION10( CHAIN B AND RESID 201:246 )B201 - 246
11X-RAY DIFFRACTION11( CHAIN B AND RESID 247:294 )B247 - 294
12X-RAY DIFFRACTION12( CHAIN B AND RESID 295:338 )B295 - 338
13X-RAY DIFFRACTION13( CHAIN B AND RESID 339:365 )B339 - 365
14X-RAY DIFFRACTION14( CHAIN B AND RESID 366:410 )B366 - 410
15X-RAY DIFFRACTION15( CHAIN B AND RESID 411:449 )B411 - 449
16X-RAY DIFFRACTION16( CHAIN E AND RESID 1:7 )E1 - 7
17X-RAY DIFFRACTION17( CHAIN F AND RESID 1:8 )F1 - 8

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