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- PDB-2mf8: HADDOCK model of MyT1 F4F5 - DNA complex -

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Basic information

Entry
Database: PDB / ID: 2mf8
TitleHADDOCK model of MyT1 F4F5 - DNA complex
Components
  • DNA (5'-D(*AP*CP*CP*GP*AP*AP*AP*GP*TP*TP*CP*AP*C)-3')
  • DNA (5'-D(*GP*TP*GP*AP*AP*CP*TP*TP*TP*CP*GP*GP*T)-3')
  • Myelin transcription factor 1
KeywordsMETAL BINDING PROTEIN/DNA / MyT1 / zinc finger / METAL BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of hormone metabolic process / diaphragm development / endocrine pancreas development / regulation of insulin secretion involved in cellular response to glucose stimulus / intracellular glucose homeostasis / cis-regulatory region sequence-specific DNA binding / post-embryonic development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific ...regulation of hormone metabolic process / diaphragm development / endocrine pancreas development / regulation of insulin secretion involved in cellular response to glucose stimulus / intracellular glucose homeostasis / cis-regulatory region sequence-specific DNA binding / post-embryonic development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Myelin transcription factor 1 / Myelin transcription factor 1 / Zinc finger, C2H2C-type superfamily / Zinc finger, C2HC type / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / Myelin transcription factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsGamsjaeger, R. / O'Connell, M.R. / Cubeddu, L. / Shepherd, N.E. / Lowry, J.A. / Kwan, A.H. / Vandevenne, M. / Swanton, M.K. / Matthews, J.M. / Mackay, J.P.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: A structural analysis of DNA binding by myelin transcription factor 1 double zinc fingers.
Authors: Gamsjaeger, R. / O'Connell, M.R. / Cubeddu, L. / Shepherd, N.E. / Lowry, J.A. / Kwan, A.H. / Vandevenne, M. / Swanton, M.K. / Matthews, J.M. / Mackay, J.P.
History
DepositionOct 8, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jun 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_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_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_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
Revision 1.3May 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: Myelin transcription factor 1
B: DNA (5'-D(*AP*CP*CP*GP*AP*AP*AP*GP*TP*TP*CP*AP*C)-3')
C: DNA (5'-D(*GP*TP*GP*AP*AP*CP*TP*TP*TP*CP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6535
Polymers17,5223
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)1 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Myelin transcription factor 1 / MyT1 / Neural zinc finger factor 2 / NZF-2


Mass: 9579.887 Da / Num. of mol.: 1 / Fragment: UNP residues 792-880
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myt1, Kiaa0835, Nzf2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CFC2
#2: DNA chain DNA (5'-D(*AP*CP*CP*GP*AP*AP*AP*GP*TP*TP*CP*AP*C)-3')


Mass: 3944.601 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*GP*TP*GP*AP*AP*CP*TP*TP*TP*CP*GP*GP*T)-3')


Mass: 3997.607 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Compound detailsFOR DOCKING, THE STARTING DNA STRUCTURE WAS CREATED BY PROGRAM 3DNA AS IDEAL B-FORM DNA.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HN(CA)CO
1712D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.2-1.0 mM [U-13C; U-15N] protein, 0.2-1.0 mM DNA, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMprotein-1[U-13C; U-15N]0.2-1.01
mMDNA-20.2-1.01
Sample conditionsIonic strength: 60 / pH: 7.2 / 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 softwareName: HADDOCK / Developer: Bonvin, A. et al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STARTING STRUCTURE OF THE PROTEIN WAS AN IN SILICO FUSION OF TWO MYT1 F5 ZINC FINGERS FROM PDB ENTRY 2JYD. THE STARTING DNA STRUCTURE WAS CREATED BY PROGRAM 3DNA AS IDEAL B-FORM DNA.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 1

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