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- PDB-1wep: Solution structure of PHD domain in PHF8 -

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Basic information

Entry
Database: PDB / ID: 1wep
TitleSolution structure of PHD domain in PHF8
ComponentsPHF8
KeywordsDNA BINDING PROTEIN / structural genomics / PHD domain / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


histone H3K36me/H3K36me2 demethylase activity / HDMs demethylate histones / histone H3K9me/H3K9me2 demethylase activity / histone H3K27me2/H3K27me3 demethylase activity / negative regulation of rDNA heterochromatin formation / histone H4K20 demethylase activity / histone H3K36 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / 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 H3K4me3 reader activity ...histone H3K36me/H3K36me2 demethylase activity / HDMs demethylate histones / histone H3K9me/H3K9me2 demethylase activity / histone H3K27me2/H3K27me3 demethylase activity / negative regulation of rDNA heterochromatin formation / histone H4K20 demethylase activity / histone H3K36 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / 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 H3K4me3 reader activity / histone H3K9 demethylase activity / positive regulation of transcription by RNA polymerase I / histone demethylase activity / transcription coregulator activity / G1/S transition of mitotic cell cycle / brain development / nuclear membrane / chromatin remodeling / iron ion binding / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Jumonji, helical domain / Jumonji helical domain / : / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 ...Jumonji, helical domain / Jumonji helical domain / : / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone lysine demethylase PHF8
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHe, F. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of PHD domain in protein AA017385
Authors: He, F. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Muto, Y. / Yokoyama, S.
History
DepositionMay 25, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX AUTHOR DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHF8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7213
Polymers8,5911
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein PHF8


Mass: 8590.635 Da / Num. of mol.: 1 / Fragment: PHD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell free protein synthesis / Gene: RIKEN cDNA 4921501E09 / Plasmid: P030408-65 / References: UniProt: Q80TJ7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 0.8mM U-15, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 0.1mM ZnCl2; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio,F.processing
NMRView5.0.4Johnson,B.A.data analysis
KUJIRA0.863Cobayashi,N.data analysis
CYANA2.0.17Guentert,P.structure solution
CYANA2.0.17Guentert,P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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