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- PDB-2jw6: Solution structure of the DEAF1 MYND domain -

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Basic information

Entry
Database: PDB / ID: 2jw6
TitleSolution structure of the DEAF1 MYND domain
ComponentsDeformed epidermal autoregulatory factor 1 homolog
KeywordsTRANSCRIPTION / zinc binding domain / Disease mutation / DNA-binding / Metal-binding / Nucleus / Phosphorylation / Secreted / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


regulation of mammary gland epithelial cell proliferation / embryonic skeletal system development / germ cell development / anatomical structure morphogenesis / neural tube closure / RNA polymerase II transcription regulatory region sequence-specific DNA binding / fibrillar center / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific ...regulation of mammary gland epithelial cell proliferation / embryonic skeletal system development / germ cell development / anatomical structure morphogenesis / neural tube closure / RNA polymerase II transcription regulatory region sequence-specific DNA binding / fibrillar center / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / extracellular region / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Helix Hairpins - #2220 / SAND domain / SAND domain / SAND domain profile. / SAND domain / MYND finger / SAND-like domain superfamily / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. ...Helix Hairpins - #2220 / SAND domain / SAND domain / SAND domain profile. / SAND domain / MYND finger / SAND-like domain superfamily / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Deformed epidermal autoregulatory factor 1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsSpadaccini, R. / Perrin, H. / Bottomley, M. / Ansieu, S. / Sattler, M.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Retraction notice to "Structure and functional analysis of the MYND domain" [J. Mol. Biol. (2006) 358, 498-508].
Authors: Spadaccini, R. / Perrin, H. / Bottomley, M.J. / Ansieau, S. / Sattler, M.
#1: Journal: J.Mol.Biol. / Year: 2006
Title: Structure and functional analysis of the MYND domain.
Authors: Spadaccini, R. / Perrin, H. / Bottomley, M.J. / Ansieau, S. / Sattler, M.
History
DepositionOct 8, 2007Deposition site: BMRB / Processing site: RCSB
SupersessionDec 25, 2007ID: 2FV6
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 10, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_atom_id / _struct_conn.ptnr1_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deformed epidermal autoregulatory factor 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0093
Polymers5,8791
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Deformed epidermal autoregulatory factor 1 homolog / Nuclear DEAF-1- related transcriptional regulator / NUDR / Suppressin / Zinc finger MYND domain- ...Nuclear DEAF-1- related transcriptional regulator / NUDR / Suppressin / Zinc finger MYND domain-containing protein 5


Mass: 5878.600 Da / Num. of mol.: 1 / Fragment: mynd domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pet24d / Production host: Escherichia coli (E. coli) / References: UniProt: O75398
#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 1H-13C NOESY
1213D HNCA
1313D 1H-15N NOESY

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Sample preparation

DetailsContents: 0,4 mM [U-100% 13C; U-100% 15N] mynd, 4 mM DTT, 20 mM sodium phosphate, 100 mM sodium chloride, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMmynd[U-100% 13C; U-100% 15N]1
4 mMDTT1
20 mMsodium phosphate1
100 mMsodium chloride1
Sample conditionsIonic strength: 20mM phosphate, 100mM NaCl / pH: 6.8 / Pressure: ambient atm / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX9001
Bruker DRXBrukerDRX8002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: molecular dynamics The NMR ensemble has been refined in a shell of water molecules. refinement details can be found in the jrnl citation above and linge et al. structures were calculated ...Details: molecular dynamics The NMR ensemble has been refined in a shell of water molecules. refinement details can be found in the jrnl citation above and linge et al. structures were calculated with aria 1.2 in combination with cns.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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