[English] 日本語
Yorodumi
- PDB-3pus: PHF2 Jumonji-NOG-Ni(II) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pus
TitlePHF2 Jumonji-NOG-Ni(II)
ComponentsPHD finger protein 2
KeywordsPROTEIN BINDING / alpha-ketoglutarate-Fe2+ dependent dioxygenases
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 / transcription coactivator activity / iron ion binding / nucleolus / 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 / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / N-OXALYLGLYCINE / OXYGEN MOLECULE / Lysine-specific demethylase PHF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsHorton, J.R. / Upadhyay, A.K. / Hashimoto, H. / Zhang, X. / Cheng, X.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural basis for human PHF2 Jumonji domain interaction with metal ions.
Authors: Horton, J.R. / Upadhyay, A.K. / Hashimoto, H. / Zhang, X. / Cheng, X.
History
DepositionDec 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Sep 6, 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_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_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHD finger protein 2
B: PHD finger protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,81423
Polymers89,4302
Non-polymers1,38321
Water4,792266
1
A: PHD finger protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2679
Polymers44,7151
Non-polymers5528
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHD finger protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,54714
Polymers44,7151
Non-polymers83213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.353, 96.979, 66.194
Angle α, β, γ (deg.)90.00, 89.78, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein PHD finger protein 2 / / GRC5


Mass: 44715.215 Da / Num. of mol.: 2 / Fragment: Jumonji domain (unp residues 60-451)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF2, KIAA0662 / Plasmid: pXC870 / Production host: Escherichia coli (E. coli) / References: UniProt: O75151

-
Non-polymers , 6 types, 287 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#6: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growMethod: vapor diffusion / pH: 6
Details: 18-30% polyethylene glycol 3350 and 100 mM NaCitrate, pH 5.2-6.0, VAPOR DIFFUSION

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.08→33.53 Å / Num. obs: 48987 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 29.63 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.3
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4931 / % possible all: 99.9

-
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
Starting model: PDB ENTRY 3KV4
Resolution: 2.08→33.53 Å / SU ML: 0.31 / σ(F): 0.02 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 1815 3.94 %
Rwork0.1751 --
obs0.1774 46042 92.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.885 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.5599 Å20 Å21.5799 Å2
2--16.6243 Å20 Å2
3----7.0644 Å2
Refinement stepCycle: LAST / Resolution: 2.08→33.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5670 0 82 266 6018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075912
X-RAY DIFFRACTIONf_angle_d0.9758020
X-RAY DIFFRACTIONf_dihedral_angle_d13.5432104
X-RAY DIFFRACTIONf_chiral_restr0.064876
X-RAY DIFFRACTIONf_plane_restr0.0051029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0798-2.15410.28981580.23283652X-RAY DIFFRACTION77
2.1541-2.24040.29691540.21454103X-RAY DIFFRACTION86
2.2404-2.34230.23551770.20854218X-RAY DIFFRACTION89
2.3423-2.46570.28831870.19014343X-RAY DIFFRACTION92
2.4657-2.62020.23611800.17594499X-RAY DIFFRACTION94
2.6202-2.82240.24431930.17754596X-RAY DIFFRACTION97
2.8224-3.10620.26481860.1784692X-RAY DIFFRACTION98
3.1062-3.55530.20071880.1724717X-RAY DIFFRACTION99
3.5553-4.47760.20341980.154739X-RAY DIFFRACTION99
4.4776-33.53540.20811940.16284668X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.8915-0.2576-0.15441.5609-0.55551.5866-0.1811-0.13-0.07180.10190.15910.07280.0581-0.2329-0.00510.2489-0.01370.0240.399-0.00770.1885-17.1137-7.210114.1727
20.9586-0.17480.35390.7512-0.2880.7927-0.03760.0078-0.0433-0.05820.07670.0135-0.02810.0114-0.03680.1744-0.01220.01120.2087-0.00310.1829-12.9169-5.34824.5956
31.8089-0.82821.31941.3834-0.74140.98240.16760.3750.1101-0.1685-0.2199-0.04140.010.21850.07860.2175-0.0170.01960.33280.04970.2291-14.97117.007-16.1616
40.56730.08960.4311.2602-0.15631.3965-0.12620.3622-0.0398-0.2010.11220.08110.0202-0.2975-0.00310.0941-0.0034-0.00360.36320.00950.100714.5173-5.316233.8591
50.97230.5982-0.42881.1523-0.09910.50110.00970.18210.07610.05960.00230.056-0.0211-0.1628-0.01190.1020.01840.00030.2363-0.00420.129722.56890.329541.4073
61.38870.7269-0.62431.2677-0.46570.48050.287-0.4838-0.18010.0732-0.3468-0.02570.02750.02630.07320.2433-0.07220.00780.50810.08680.231718.9363-16.498562.1155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 80:200)
2X-RAY DIFFRACTION2(chain A and resid 201:356)
3X-RAY DIFFRACTION3(chain A and resid 357:444)
4X-RAY DIFFRACTION4(chain B and resid 83:245)
5X-RAY DIFFRACTION5(chain B and resid 246:362)
6X-RAY DIFFRACTION6(chain B and resid 363:444)

+
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