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- PDB-2jyd: Structure of the fifth zinc finger of Myelin Transcription Factor 1 -

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Basic information

Entry
Database: PDB / ID: 2jyd
TitleStructure of the fifth zinc finger of Myelin Transcription Factor 1
ComponentsF5 domain of Myelin transcription factor 1
KeywordsMETAL BINDING PROTEIN / zinc-finger / Myt1 / Alternative splicing / Developmental protein / Differentiation / DNA-binding / Metal-binding / Neurogenesis / Nucleus / Transcription / Transcription regulation
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
Myelin transcription factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, molecular dynamics
AuthorsGamsjaeger, R. / Swanton, M.K. / Kobus, F.J. / Lehtomaki, E. / Lowry, J.A. / Kwan, A.H. / Matthews, J.M. / Mackay, J.P.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural and biophysical analysis of the DNA binding properties of myelin transcription factor 1.
Authors: Gamsjaeger, R. / Swanton, M.K. / Kobus, F.J. / Lehtomaki, E. / Lowry, J.A. / Kwan, A.H. / Matthews, J.M. / Mackay, J.P.
History
DepositionDec 12, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _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 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: F5 domain of Myelin transcription factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7152
Polymers4,6491
Non-polymers651
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 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide F5 domain of Myelin transcription factor 1 / MyT1 / Neural zinc finger factor 2 / NZF-2


Mass: 4649.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CFC2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Sequence detailsSEE REF. 1 IN UNP DATABASE, MYT1_MOUSE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY
1413D HNHA

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Sample preparation

DetailsContents: 1mM [U-13C; U-15N] F5, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: F5 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 10 / pH: 6.5 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger, Adams, Clore, Gros, Nilges and Read / Classification: refinement
RefinementMethod: torsion angle dynamics, simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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