[English] 日本語
Yorodumi
- PDB-3p8d: Crystal structure of the second Tudor domain of human PHF20 (homo... -

+
Open data


ID or keywords:

Loading...

-
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 / chromatin organization / HATs acetylate histones ...: / 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 / chromatin organization / HATs acetylate histones / nuclear membrane / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
PHD finger protein 20 / 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 ...PHD finger protein 20 / 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 C2H2 type domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Zinc finger, RING/FYVE/PHD-type / Roll / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more