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- PDB-9p3z: Solution structure of the novel zinc finger from ZC4H2 -

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Basic information

Entry
Database: PDB / ID: 9p3z
TitleSolution structure of the novel zinc finger from ZC4H2
ComponentsZinc finger C4H2 domain-containing protein
KeywordsMETAL BINDING PROTEIN / HCA127 KIAA1166 ZARD C4 zinc finger
Function / homology
Function and homology information


noradrenergic neuron development / regulation of transcription regulatory region DNA binding / spinal cord motor neuron differentiation / neuromuscular junction development / protein monoubiquitination / positive regulation of DNA-binding transcription factor activity / positive regulation of neuron differentiation / nervous system development / postsynaptic membrane / neuronal cell body ...noradrenergic neuron development / regulation of transcription regulatory region DNA binding / spinal cord motor neuron differentiation / neuromuscular junction development / protein monoubiquitination / positive regulation of DNA-binding transcription factor activity / positive regulation of neuron differentiation / nervous system development / postsynaptic membrane / neuronal cell body / protein-containing complex / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Zinc finger C4H2 domain-containing protein / Zinc finger C4H2-type / Zinc finger-containing protein / Zinc finger C4H2-type profile.
Similarity search - Domain/homology
Zinc finger C4H2 domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsAlexandrescu, A.T. / Rua, A.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biomolecules / Year: 2025
Title: Zinc-Induced Folding and Solution Structure of the Eponymous Novel Zinc Finger from the ZC4H2 Protein
Authors: Harris, R.E. / Rua, A.J. / Alexandrescu, A.T.
History
DepositionJun 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger C4H2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,0972
Polymers3,0321
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Zinc finger C4H2 domain-containing protein / Hepatocellular carcinoma-associated antigen 127


Mass: 3031.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized by Biomatik / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NQZ6
#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 TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
242isotropic22D 1H-1H TOCSY
252isotropic22D 1H-1H NOESY
262isotropic22D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.6 mM ZC4H2-ZL, 1.6 mM zinc, 90 M H2O, 10 % [U-2H] D2O, 90% H2O/10% D2OSample used for experiments in H2Osample_190% H2O/10% D2O
solution20.9 mM ZC4H2-ZL, 0.9 mM zinc, 100 M [U-2H] D2O, 100% D2OSample used for experiments in D2Osample_2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.6 mMZC4H2-ZLnatural abundance1
1.6 mMzincnatural abundance1
90 MH2Onatural abundance1
10 %D2O[U-2H]1
0.9 mMZC4H2-ZLnatural abundance2
0.9 mMzincnatural abundance2
100 MD2O[U-2H]2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1No added buffers or salts except Zn2+ (listed ionic strength as 0)0 mMsample_conditions_161 atm283 K
2No added buffers or salts except Zn2+ (listed ionic strength as 0)0 mMsample_conditions_25.91 atm283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO8001
Bruker AVANCE NEOBrukerAVANCE NEO6002

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.5.2CCPNchemical shift assignment
DISNMR6.3.0Mestrelabprocessing
TopSpin4.1Bruker Biospincollection
X-PLOR NIH3.8Schwieters, Kuszewski, Tjandra and Clorestructure calculation
ARIALinge, O'Donoghue and Nilgesrefinement
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 5 / Details: water refinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 300 / Conformers submitted total number: 20

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