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- PDB-1pxe: Solution Structure of a CCHHC Domain of Neural Zinc Finger Factor-1 -

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Basic information

Entry
Database: PDB / ID: 1pxe
TitleSolution Structure of a CCHHC Domain of Neural Zinc Finger Factor-1
Componentsneural zinc finger transcription factor 1
KeywordsMETAL BINDING PROTEIN / CCHHC zinc binding domain / neural zinc finger factor-1 / DNA binding domain
Function / homology
Function and homology information


neuron fate specification / retinoic acid-responsive element binding / neuron fate commitment / cobalt ion binding / neuron development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / chromosome / nervous system development ...neuron fate specification / retinoic acid-responsive element binding / neuron fate commitment / cobalt ion binding / neuron development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / chromosome / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / negative 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-like protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / Torsion angle dynamics Simulated annealing
Model type detailsminimized average
AuthorsBerkovits-Cymet, H.J. / Amann, B.T. / Berg, J.M.
CitationJournal: Biochemistry / Year: 2004
Title: Solution Structure of a CCHHC Domain of Neural Zinc Finger Factor-1 and Its Implications for DNA Binding.
Authors: Berkovits-Cymet, H.J. / Amann, B.T. / Berg, J.M.
History
DepositionJul 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE THE AUTHORS BELIEVE RESIDUE 32 SHOULD BE THR, NOT ASN. THE FIRST 15 RESIDUES had very few ...SEQUENCE THE AUTHORS BELIEVE RESIDUE 32 SHOULD BE THR, NOT ASN. THE FIRST 15 RESIDUES had very few assignments and NOEs and consequently this region is quite unstructured AND HAS BEEN OMITTED FROM THE COORDINATES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: neural zinc finger transcription factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2022
Polymers7,1361
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)21 / 30The submitted conformer models are those with the lowest energies.
RepresentativeModel #1minimized average structure

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Components

#1: Protein neural zinc finger transcription factor 1


Mass: 7136.204 Da / Num. of mol.: 1 / Fragment: zinc binding domain, CCHHC domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: NZF-1 / Plasmid: pNZF-1e / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P70475
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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
111DQF-COSY
1212D TOCSY
1312D NOESY
24215N HSQC
25215N HSQC LongRange
2623D HSQC-TOCSY
2723D HSQC-NOESY
38315N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12.3 mM NZF-1(487-548) 2.3 mM ZnCl2 55 mM deuterated TrisThis sample was initially prepared in 100% D2O. It was then dried down and resuspended in 95% H2O/5% D2O.
22.8 mM NZF-1(487-548), U-15N 2.8 mM ZnCl2 36 mM deuterated Tris98% H2O/2% D2O
31.5 mM NZF-1(487-548), U-15N 1.5 mM CdCl2 (Cd-113) 36 mM deuterated TrisD2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1no salt added 6.95 ambient 293 K
2no salt added 7.02 ambient 303 K
3no salt added 7.00 ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1bcollection
Felix98Accelrysprocessing
In house perl scriptsBerkovits-Cymet, H.J., Amann, B.T.data analysis
CNS1.1Gregory Warren, Michael Nilges, John Kuszewski, Marius Clore and Axel Brungerstructure solution
CNS1.1Warren, Nilges, Kuszewski, Clore, Brungerrefinement
RefinementMethod: Torsion angle dynamics Simulated annealing / Software ordinal: 1
Details: Zinc-ligand bond lengths were constrained as follows: Zn-S(Cys): 2.30 angstroms Zn-N(His): 2.00 angstroms The ligand configuration around the zinc ion was constrained to tetrahedral geometry ...Details: Zinc-ligand bond lengths were constrained as follows: Zn-S(Cys): 2.30 angstroms Zn-N(His): 2.00 angstroms The ligand configuration around the zinc ion was constrained to tetrahedral geometry by the following constraints: assign (resid 20 and name SG) (resid 25 and name SG) 3.76 0.20 0.20 assign (resid 20 and name SG) (resid 44 and name SG) 3.76 0.20 0.20 assign (resid 25 and name SG) (resid 44 and name SG) 3.76 0.20 0.20 assign (resid 20 and name SG) (resid 38 and name NE2) 3.52 0.20 0.20 assign (resid 25 and name SG) (resid 38 and name NE2) 3.52 0.20 0.20 assign (resid 44 and name SG) (resid 38 and name NE2) 3.52 0.20 0.20 Residues 4-63 were included in the structure calculations.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: The submitted conformer models are those with the lowest energies.
Conformers calculated total number: 30 / Conformers submitted total number: 21

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