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- PDB-8sxm: NMR structure of the ZNF750 zinc finger domain, Z* -

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Basic information

Entry
Database: PDB / ID: 8sxm
TitleNMR structure of the ZNF750 zinc finger domain, Z*
ComponentsZinc finger protein 750
KeywordsMETAL BINDING PROTEIN / degenerate zinc finger / ZNF750 / ZN750 / nuclear transcription factor / protein structure evolution / somatic cancer mutations / psoriasis / skin differentiation / DNA-binding motif / CCHC zinc finger / antiparallel bba motif / protein folding / protein structure prediction / seborrhea-like dermatosis with non-arthritic psoriasiform elements / SLDP
Function / homology
Function and homology information


membrane biogenesis / positive regulation of ceramide biosynthetic process / Generic Transcription Pathway / negative regulation of epithelial to mesenchymal transition / epidermis development / establishment of skin barrier / promoter-specific chromatin binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation ...membrane biogenesis / positive regulation of ceramide biosynthetic process / Generic Transcription Pathway / negative regulation of epithelial to mesenchymal transition / epidermis development / establishment of skin barrier / promoter-specific chromatin binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / metal ion binding / nucleus
Similarity search - Function
Zinc finger protein 750-like, zinc finger / Zinc finger protein 750 / Zinc-finger
Similarity search - Domain/homology
Zinc finger protein 750
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsRua, A.J. / Alexandrescu, A.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Struct Biol X / Year: 2023
Title: NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750.
Authors: Rua, A.J. / Whitehead 3rd, R.D. / Alexandrescu, A.T.
History
DepositionMay 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 1, 2024Group: Database references / Category: citation / citation_author / database_2
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Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger protein 750
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,3802
Polymers3,3151
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, Actually the experiments to show ZN2+ binding included an NMR titration to demonstrate folding in the presence of Zn2+, a CD titration used to determine the Kd for ...Evidence: NMR Distance Restraints, Actually the experiments to show ZN2+ binding included an NMR titration to demonstrate folding in the presence of Zn2+, a CD titration used to determine the Kd for Zn2+, and mutagenesis to rule out alternative Zn2+ ligands in the polypeptide sequence. None of these were options in the pull-down menus above.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Zinc finger protein 750


Mass: 3314.924 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q32MQ0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
181isotropic12D 1H-15N sofastHMQC
252isotropic12D 1H-13C HSQC
262isotropic12D 1H-1H NOESY
292isotropic12D DQF-COSY
2102isotropic12D ECOSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.9 mM Z*, 2.9 mM ZnSO4, 10 mM NaPO4, 90% H2O/10% D2OZ* H2O90% H2O/10% D2O
solution23.8 mM Z*, 4.8 mM ZnSO4, 20 mM NaPO4, 100% D2OZ* D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.9 mMZ*natural abundance1
2.9 mMZnSO4natural abundance1
3.8 mMZ*natural abundance2
4.8 mMZnSO4natural abundance2
10 mMNaPO4natural abundance1
20 mMNaPO4natural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
110 mMZ* H2O5.91 atm288 K
220 mMZ* D2O5.91 atm288 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz / Details: TCI cryogenic probe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
CcpNmr Analysis2.5.2Vranken, W. F., Boucher, W., Stevens, T. J., Fogh, R. H., Pajon, A., Llinas, M., Ulrich, E. L., Markley, J. L., Ionides, J., and Laue, E. D. (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59, 687-696peak picking
CcpNmr Analysis2.5.2Vranken, W. F., Boucher, W., Stevens, T. J., Fogh, R. H., Pajon, A., Llinas, M., Ulrich, E. L., Markley, J. L., Ionides, J., and Laue, E. D. (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59, 687-696chemical shift assignment
X-PLOR NIHSchwieters, C. D., Kuszewski, J. J., Tjandra, N., and Clore, G. M. (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160, 65-73structure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
Details: Structures are based on 330 NOE restraints, 12 (x2) hydrogen bonds, 4 restraints to the zinc ion, and 60 dihedral angles.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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