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- PDB-2jx1: Structure of the fifth zinc finger of Myelin Transcription Factor... -

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Basic information

Entry
Database: PDB / ID: 2jx1
TitleStructure of the fifth zinc finger of Myelin Transcription Factor 1 in complex with RARE DNA
Components
  • DNA (5'-D(*DAP*DCP*DCP*DGP*DAP*DAP*DAP*DGP*DTP*DTP*DCP*DAP*DC)-3')
  • DNA (5'-D(*DGP*DTP*DGP*DAP*DAP*DCP*DTP*DTP*DTP*DCP*DGP*DGP*DT)-3')
  • Myelin transcription factor 1
KeywordsTRANSCRIPTION/DNA / protein-DNA complex / TRANSCRIPTION-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 / HADDOCK docking, simulated annealing
AuthorsGamsjaeger, R. / Swanton, M.K. / Kobus, F.J. / Lehtomaki, E. / Lowry, J.A. / Kwan, A.H. / Matthews, J.M. / Mackay, J.P.
CitationJournal: To be Published
Title: Structure of the fifth zinc finger of Myelin Transcription Factor 1 in complex with RARE DNA
Authors: Gamsjaeger, R. / Swanton, M.K. / Kobus, F.J. / Lehtomaki, E. / Lowry, J.A. / Kwan, A.H. / Matthews, J.M. / Mackay, J.P.
History
DepositionNov 1, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: DNA (5'-D(*DAP*DCP*DCP*DGP*DAP*DAP*DAP*DGP*DTP*DTP*DCP*DAP*DC)-3')
C: DNA (5'-D(*DGP*DTP*DGP*DAP*DAP*DCP*DTP*DTP*DTP*DCP*DGP*DGP*DT)-3')
A: Myelin transcription factor 1


Theoretical massNumber of molelcules
Total (without water)11,1063
Polymers11,1063
Non-polymers00
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 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*DAP*DCP*DCP*DGP*DAP*DAP*DAP*DGP*DTP*DTP*DCP*DAP*DC)-3')


Mass: 3944.601 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DGP*DTP*DGP*DAP*DAP*DCP*DTP*DTP*DTP*DCP*DGP*DGP*DT)-3')


Mass: 3997.607 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein/peptide Myelin transcription factor 1 / MyT1 / Neural zinc finger factor 2 / NZF-2


Mass: 3163.508 Da / Num. of mol.: 1 / Fragment: the fifth zinc finger domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8CFC2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D NOESY
2222D TOCSY
1323D 15N-separated NOESY
1423D HNHA
1512D HSQC
1613D HNCA
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D HNCO
11013D (H)CCH-TOCSY
11112D single & double half filtered NOESYs

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Sample preparation

Details
Solution-IDContentsSolvent system
110mM phosphate, 50mM sodium chloride, 1mM DTT, 100% H2O100% H2O
22.5mM MES, 10mM sodium chloride, 1mM DTT, 100% H2O100% H2O
Sample
Conc. (mg/ml)ComponentSolution-ID
10 mMphosphate1
50 mMsodium chloride1
1 mMDTT1
2.5 mMMES2
10 mMsodium chloride2
1 mMDTT2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 7.4 1 atm298 K
210 6.5 1 atm278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR softwareName: CNS / Classification: refinement
RefinementMethod: HADDOCK docking, simulated annealing / Software ordinal: 1 / Details: simulated annealing, water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

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