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- PDB-3p8d: Crystal structure of the second Tudor domain of human PHF20 (homo... -

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Basic information

Entry
Database: PDB / ID: 3p8d
TitleCrystal structure of the second Tudor domain of human PHF20 (homodimer form)
ComponentsMedulloblastoma antigen MU-MB-50.72
KeywordsPROTEIN BINDING / Tudor domain / LYSINE-METHYLATED P53 BINDING / HISTONE BINDING
Function / homology
Function and homology information


NSL complex / Regulation of TP53 Activity through Association with Co-factors / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / Stabilization of p53 / Regulation of TP53 Degradation / HATs acetylate histones / nuclear membrane / regulation of transcription by RNA polymerase II ...NSL complex / Regulation of TP53 Activity through Association with Co-factors / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / Stabilization of p53 / Regulation of TP53 Degradation / HATs acetylate histones / nuclear membrane / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / zinc ion binding / nucleoplasm
Similarity search - Function
PHD finger protein 20, AT hook / PHD finger protein 20, AT-hook / DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor domain / PHD finger protein 20-like / PhD finger domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 / Zinc finger, PHD-type, conserved site ...PHD finger protein 20, AT hook / PHD finger protein 20, AT-hook / DNA repair protein Crb2, Tudor domain / DNA repair protein Crb2 Tudor domain / PHD finger protein 20-like / PhD finger domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Zinc finger, PHD-type / PHD zinc finger / SH3 type barrels. / Zinc finger, FYVE/PHD-type / Roll / Zinc finger, RING/FYVE/PHD-type / Mainly Beta
Similarity search - Domain/homology
Medulloblastoma antigen MU-MB-50.72 / PHD finger protein 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCui, G. / Lee, J. / Thompson, J.R. / Botuyan, M.V. / Mer, G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: PHF20 is an effector protein of p53 double lysine methylation that stabilizes and activates p53.
Authors: Cui, G. / Park, S. / Badeaux, A.I. / Kim, D. / Lee, J. / Thompson, J.R. / Yan, F. / Kaneko, S. / Yuan, Z. / Botuyan, M.V. / Bedford, M.T. / Cheng, J.Q. / Mer, G.
History
DepositionOct 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 15, 2012Group: Database references
Revision 1.3Sep 26, 2012Group: Database references
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Medulloblastoma antigen MU-MB-50.72
B: Medulloblastoma antigen MU-MB-50.72


Theoretical massNumber of molelcules
Total (without water)15,1792
Polymers15,1792
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-11 kcal/mol
Surface area6800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.548, 48.548, 96.149
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Medulloblastoma antigen MU-MB-50.72 / PHD FINGER PROTEIN 20


Mass: 7589.581 Da / Num. of mol.: 2 / Fragment: UNP residues 84-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PTEV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7Z5E2, UniProt: Q9BVI0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.73 Å3/Da / Density % sol: 67.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12% PEG8000, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.992349 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992349 Å / Relative weight: 1
ReflectionResolution: 2→23.54 Å / Num. obs: 14859 / % possible obs: 99.3 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 31.8
Reflection shellResolution: 2→2.15 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 3.6 / % possible all: 95.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→23.54 Å / SU ML: 0.38 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 753 5.07 %
Rwork0.2284 --
obs0.2301 14859 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.366 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5201 Å2-0 Å20 Å2
2---2.5201 Å2-0 Å2
3---5.0403 Å2
Refinement stepCycle: LAST / Resolution: 2→23.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms856 0 0 147 1003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003912
X-RAY DIFFRACTIONf_angle_d0.6541234
X-RAY DIFFRACTIONf_dihedral_angle_d12.573316
X-RAY DIFFRACTIONf_chiral_restr0.049138
X-RAY DIFFRACTIONf_plane_restr0.002154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.15420.35591580.31462742X-RAY DIFFRACTION97
2.1542-2.37080.37061540.27942851X-RAY DIFFRACTION100
2.3708-2.71350.35931580.29592805X-RAY DIFFRACTION99
2.7135-3.4170.23521480.20192838X-RAY DIFFRACTION99
3.417-23.540.2091350.18472870X-RAY DIFFRACTION99
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)
10.3541-0.33490.08020.2508-0.09080.04451.92910.4283-1.1914-0.9243-0.65270.51493.2373-2.47770.01260.922-0.0131-0.15310.7486-0.16060.6022.5338-2.3582-17.6074
20.5049-0.38220.15380.5343-0.460.31850.2487-0.4236-1.5902-0.1342-0.20650.86850.9293-1.19350.00020.7497-0.14210.00350.4427-0.04910.69054.2324-2.83-8.4939
30.44420.50220.49040.44080.57370.50650.0745-0.9442-0.46681.0122-0.03240.6650.7220.44770.00040.3625-0.03620.04150.3854-0.02640.481814.62177.1522-2.3348
40.2113-0.3628-0.26421.0089-0.0660.7609-0.2917-1.1667-0.81290.2224-0.0267-1.08150.97430.98720.00010.44840.10190.0050.40990.05040.463413.5760.9939-2.6138
50.1674-0.0141-0.21180.3810.22280.2123-0.21580.72930.47710.1134-0.10160.70981.2242-1.31970.00060.5457-0.241-0.10340.69260.14670.4593-0.38742.0191-9.6166
60.38560.05980.3946-0.0790.01910.1882-0.0131-0.8765-0.65660.0676-0.36710.31870.38180.11760.00150.4183-0.0386-0.05550.55440.06860.44141.63447.649-17.7239
70.63460.62170.15610.49780.48020.81620.18180.0725-0.64910.62590.48860.4240.1652-0.8435-0.00340.44-0.0356-0.0530.42320.03440.47363.10082.9747-3.4333
80.4675-0.15-0.10030.53670.35420.19840.32130.5460.16570.2837-0.356-0.165-1.22370.1381-0.00180.38670.080.05730.41730.11060.49773.88217.7661-2.9272
90.6927-0.346-0.20560.1902-0.00740.2449-0.80181.76340.6199-1.69550.66520.11761.8698-0.80970.00060.6337-0.2069-0.0430.6467-0.06550.45259.2045.7745-16.0777
101.4460.17360.5280.46890.65270.8439-0.78730.4502-0.9395-0.38210.9464-1.04842.2226-0.4344-00.82590.0434-0.00440.3387-0.09120.501311.0883-2.1838-10.6369
110.8446-0.7914-0.28940.65960.11820.09850.074-1.72491.92910.28620.2206-2.0912-1.52392.83250.010.7166-0.2687-0.26041.0352-0.20580.661126.794622.53294.3303
120.4422-0.4721-0.60190.83130.12021.08910.473-0.55650.1041-0.1255-0.5803-0.9149-0.24370.75480.00010.3674-0.0934-0.0210.59360.01640.529825.63617.1429-4.0941
130.49160.62550.4810.93490.6090.4958-0.17510.88340.4689-1.14820.0071-1.2780.24031.08570.0030.3710.02510.05440.41730.06610.502919.07499.0862-10.0193
140.52550.3073-0.05550.55-0.74260.92810.1370.10070.5892-0.0476-0.0416-0.3709-0.84861.3945-0.00070.4338-0.11760.01730.5176-0.01420.400923.719119.9945-6.9967
150.0111-0.0076-0.06530.1190.15410.3081-0.27750.50670.1641-1.36310.8250.84660.06760.112-0.00130.6023-0.15860.05890.4693-0.05240.484816.61524.52815.8488
160.65490.56430.33751.14820.07490.5980.27160.02690.22740.64070.03010.2693-0.69110.2640.00060.4678-0.0120.06820.4234-0.08490.31520.548521.0593-5.3199
170.65290.34010.36620.15570.06050.3682-0.24550.0559-0.17650.35990.2253-0.3962-0.5538-0.5713-0.0010.43350.09780.07530.42990.03910.448816.515520.3747-9.2567
180.5892-0.4590.05870.7327-0.39670.31170.777-2.88310.86021.3308-0.78380.3977-2.01391.3281-0.00080.5246-0.1477-0.02430.7309-0.00950.388718.54315.20663.8289
190.8058-0.52671.09191.8620.07911.5575-0.27890.71321.0379-0.01640.3645-1.1178-0.24562.0001-0.00130.2675-0.017-0.07190.9634-0.05160.540826.739713.4994-1.6413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 25:29)
2X-RAY DIFFRACTION2(chain A and resid 30:35)
3X-RAY DIFFRACTION3(chain A and resid 36:40)
4X-RAY DIFFRACTION4(chain A and resid 41:44)
5X-RAY DIFFRACTION5(chain A and resid 45:50)
6X-RAY DIFFRACTION6(chain A and resid 51:56)
7X-RAY DIFFRACTION7(chain A and resid 57:61)
8X-RAY DIFFRACTION8(chain A and resid 62:67)
9X-RAY DIFFRACTION9(chain A and resid 68:71)
10X-RAY DIFFRACTION10(chain A and resid 72:77)
11X-RAY DIFFRACTION11(chain B and resid 25:30)
12X-RAY DIFFRACTION12(chain B and resid 31:36)
13X-RAY DIFFRACTION13(chain B and resid 37:42)
14X-RAY DIFFRACTION14(chain B and resid 43:48)
15X-RAY DIFFRACTION15(chain B and resid 49:54)
16X-RAY DIFFRACTION16(chain B and resid 55:61)
17X-RAY DIFFRACTION17(chain B and resid 62:67)
18X-RAY DIFFRACTION18(chain B and resid 68:71)
19X-RAY DIFFRACTION19(chain B and resid 72:77)

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