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- PDB-9azi: NMR solution structure of cell-permeant miniature protein ZF5.3 -

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Basic information

Entry
Database: PDB / ID: 9azi
TitleNMR solution structure of cell-permeant miniature protein ZF5.3
ComponentsDesigned Zinc finger protein 5.3
KeywordsDE NOVO PROTEIN / mini-protein / cell-permeant / zinc finger / endosomal escape
Function / homology
Function and homology information


mRNA 3'-end processing by stem-loop binding and cleavage / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Generic Transcription Pathway / RNA Polymerase II Transcription Termination / Cajal body / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleoplasm ...mRNA 3'-end processing by stem-loop binding and cleavage / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Generic Transcription Pathway / RNA Polymerase II Transcription Termination / Cajal body / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
Krueppel-associated box (KRAB) profile. / KRAB box / krueppel associated box / Krueppel-associated box / KRAB domain superfamily / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger protein 473
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsGiudice, J.A. / Kelly, M. / Schepartz, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2203903 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134963 United States
CitationJournal: To be published
Title: Structural and mechanistic basis for efficient endosomal escape by designed mini-proteins
Authors: Giudice, J.A. / Brauer, D. / Vazquez Maldonado, A. / Zoltek, M. / Schepartz, A.
History
DepositionMar 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Designed Zinc finger protein 5.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,2692
Polymers3,2041
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Designed Zinc finger protein 5.3 / Zinc finger protein 100 homolog / Zfp-100


Mass: 3203.776 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNF473, KIAA1141, ZFP100 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q8WTR7
#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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-13C NOESY
161isotropic23D 1H-15N NOESY
121isotropic22D 1H-13C HSQC
131isotropic22D 1H-13C HSQC aromatic
141isotropic22D 1H-15N HSQC
151isotropic23D (H)CCH-TOCSY
171isotropic21D 1H
181isotropic21D 1H

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Sample preparation

DetailsType: solution
Contents: 800 uM [U-13C; U-15N] ZF5.3, 20 mM TRIS, 100 mM sodium chloride, 2 mM TCEP, 1.6 mM ZnCl2, 90% H2O/10% D2O
Label: 13C-15N / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
800 uMZF5.3[U-13C; U-15N]1
20 mMTRISnatural abundance1
100 mMsodium chloridenatural abundance1
2 mMTCEPnatural abundance1
1.6 mMZnCl2natural abundance1
Sample conditionsIonic strength: 150 mM / Label: 1 / pH: 5.5 / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE NEOBrukerAVANCE NEO60015mm TCI Cryoprobe
Bruker AVANCE NEOBrukerAVANCE NEO80025mm TCI Cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis Assign3.2.0Laue E.D.chemical shift assignment
TopSpin4.3.0Bruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIH3.5Schwieters, Kuszewski, Tjandra and Clorerefinement
ARTINAKlukowski, P., Riek, R. and Guntert, P.peak picking
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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