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- PDB-2m3h: Structure of Dido PHD domain -

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Basic information

Entry
Database: PDB / ID: 2m3h
TitleStructure of Dido PHD domain
ComponentsDeath-inducer obliterator 1
KeywordsAPOPTOSIS / PHD domain
Function / homology
Function and homology information


Meiotic synapsis / apoptotic signaling pathway / spindle / DNA-templated transcription / RNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Death-inducer obliterator 1 / Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 ...Death-inducer obliterator 1 / Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Death-inducer obliterator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsSantiveri, C.M. / Perez-Canadillas, J.M. / Jimenez, M.
CitationJournal: J.Biomol.Nmr / Year: 2013
Title: NMR structure note: PHD domain from death inducer obliterator protein and its interaction with H3K4me3.
Authors: Santiveri, C.M. / Garcia-Mayoral, M.F. / Perez-Canadillas, J.M. / Jimenez, M.A.
History
DepositionJan 19, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Death-inducer obliterator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1793
Polymers7,0481
Non-polymers1312
Water0
1


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

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Components

#1: Protein Death-inducer obliterator 1 / DIO-1 / hDido1 / Death-associated transcription factor 1 / DATF-1


Mass: 7048.042 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIDO1, C20orf158, DATF1, KIAA0333 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BTC0
#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
1112D 1H-1H TOCSY
1212D 1H-1H TOCSY
1312D 1H-1H COSY
1412D 1H-1H TOCSY
1512D 1H-1H NOESY
1622D 1H-15N HSQC
1722D 1H-13C HSQC aliphatic
1823D HNCO
1923D HNCA
11023D HN(CA)CB
11123D CBCA(CO)NH
11223D HBHA(CO)NH
11323D HNHA
11423D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM Dido PHD, 10 uM potassium phosphate, 100 uM TCEP, 90% H2O, 10% D2O, 10 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-99% 13C; U-99% 15N] Dido PHD, 10 uM potassium phosphate, 100 uM TCEP, 0.01% sodium azide, 90% H2O, 10% D2O, 10 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMDido PHD-11
10 uMpotassium phosphate-21
100 uMTCEP-31
90 %H2O-41
10 %D2O-51
10 uMDSS-61
0.4 mMDido PHD-7[U-99% 13C; U-99% 15N]2
10 uMpotassium phosphate-82
100 uMTCEP-92
0.01 %sodium azide-102
90 %H2O-112
10 %D2O-122
10 uMDSS-132
Sample conditionsIonic strength: 10 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdihedral angles
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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