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- PDB-4a24: Structural and functional analysis of the DEAF-1 and BS69 MYND domains -

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Basic information

Entry
Database: PDB / ID: 4a24
TitleStructural and functional analysis of the DEAF-1 and BS69 MYND domains
ComponentsDEFORMED EPIDERMAL AUTOREGULATORY FACTOR 1 HOMOLOG
KeywordsTRANSCRIPTION / ZINC-BINDING / TRANSCRIPTIONAL REGULATION / PROTEIN BINDING
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
AuthorsKateb, F. / Perrin, H. / Tripsianes, K. / Zou, P. / Spadaccini, R. / Bottomley, M. / Bepperling, A. / Ansieau, S. / Sattler, M.
CitationJournal: Plos One / Year: 2013
Title: Structural and Functional Analysis of the Deaf-1 and Bs69 Mynd Domains.
Authors: Kateb, F. / Perrin, H. / Tripsianes, K. / Zou, P. / Spadaccini, R. / Bottomley, M. / Franzmann, T.M. / Buchner, J. / Ansieau, S. / Sattler, M.
History
DepositionSep 22, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Data collection / Category: pdbx_nmr_spectrometer
Item: _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 2.0Jun 14, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _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_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

Downloads & links

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Assembly

Deposited unit
A: DEFORMED EPIDERMAL AUTOREGULATORY FACTOR 1 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,4083
Polymers5,2771
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein/peptide DEFORMED EPIDERMAL AUTOREGULATORY FACTOR 1 HOMOLOG / DEAF-1 MYND / NUCLEAR DEAF-1-RELATED TRANSCRIPTIONAL REGULATOR SUPPRESSIN / ZINC FINGER MYND DOMAIN- ...DEAF-1 MYND / NUCLEAR DEAF-1-RELATED TRANSCRIPTIONAL REGULATOR SUPPRESSIN / ZINC FINGER MYND DOMAIN-CONTAINING PROTEIN 5


Mass: 5276.947 Da / Num. of mol.: 1 / Fragment: RESIDUES 501-544
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETMTHX-MYND / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75398
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTHE FIRST THREE RESIDUES, GAM, RESULT FROM THE TEV CLEAVAGE SITE TO REMOVE THE N-TERMINAL TAG

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2213D 1H-15N NOESY
3313D 1H-13C NOESY (ALIPHATIC CARBONS)
4413D 1H- 13C NOESY (AROMATIC CARBONS)
NMR detailsText: THE CHEMICAL SHIFTS OF THE DEAF-1 MYND DOMAIN WERE ASSIGNED USING STANDARD HETERONUCLEAR EXPERIMENTS ACQUIRED AT 295 K ON A 1 MM UNIFORMLY 15N,13C LABELED SAMPLE. EXPERIMENTS WERE CARRIED OUT ...Text: THE CHEMICAL SHIFTS OF THE DEAF-1 MYND DOMAIN WERE ASSIGNED USING STANDARD HETERONUCLEAR EXPERIMENTS ACQUIRED AT 295 K ON A 1 MM UNIFORMLY 15N,13C LABELED SAMPLE. EXPERIMENTS WERE CARRIED OUT ON BRUKER SPECTROMETERS OPERATING AT A PROTON FREQUENCY BETWEEN 500 AND 900 MHZ. ALL SPECTRA WERE PROCESSED USING THE PACKAGE NMRPIPE- NMRDRAW

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM6.5 1.0 atm295.0 K
2100 mM6.5 1.0 atm295.0 K
3100 mM6.5 1.0 atm295.0 K
4100 mM6.5 1.0 atm295.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE9002
Bruker AVANCEBrukerAVANCE9003
Bruker AVANCEBrukerAVANCE9004

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Processing

NMR software
NameDeveloperClassification
CNS-ARIANILGESrefinement
NMRPipestructure solution
TALOSstructure solution
Sparkystructure solution
CYANAstructure solution
ARIA-CNSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: DISTANCE RESTRAINTS DERIVED FROM THE CYANA CALCULATIONS, TORSION ANGLE RESTRAINTS DERIVED FROM TALOS BASED ON SECONDARY CHEMICAL SHIFTS, AND RDC RESTRAINTS WERE APPLIED FOR A WATER ...Details: DISTANCE RESTRAINTS DERIVED FROM THE CYANA CALCULATIONS, TORSION ANGLE RESTRAINTS DERIVED FROM TALOS BASED ON SECONDARY CHEMICAL SHIFTS, AND RDC RESTRAINTS WERE APPLIED FOR A WATER REFINEMENT CALCULATION USING A SIMULATED ANNEALING PROTOCOL IN CNS. THE ZINC COORDINATION GEOMETRY WAS DEFINED AND MAINTAINED BY DISTANCE AND ANGLE CONSTRAINTS. .
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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