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- PDB-6nzl: Solution structure of POS-1, a CCCH-type Tandem Zinc Finger prote... -

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Basic information

Entry
Database: PDB / ID: 6nzl
TitleSolution structure of POS-1, a CCCH-type Tandem Zinc Finger protein from C. elegans
ComponentsCytoplasmic zinc-finger protein
KeywordsRNA BINDING PROTEIN / CCCH-type Tandem Zinc Finger protein
Function / homology
Function and homology information


Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / embryonic pattern specification / embryo development ending in birth or egg hatching / P granule / cell fate specification / poly(U) RNA binding / mRNA 3'-UTR binding / transcription corepressor activity / regulation of translation ...Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / embryonic pattern specification / embryo development ending in birth or egg hatching / P granule / cell fate specification / poly(U) RNA binding / mRNA 3'-UTR binding / transcription corepressor activity / regulation of translation / single-stranded RNA binding / negative regulation of transcription by RNA polymerase II / metal ion binding / cytosol / cytoplasm
Similarity search - Function
RNA-binding protein ZFP36-like / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile.
Similarity search - Domain/homology
RNA-binding protein pos-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsErtekin, A. / Massi, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM117008 United States
CitationJournal: To Be Published
Title: Solution structure of POS-1, a CCCH-type Tandem Zinc Finger protein from C. elegans
Authors: Ertekin, A. / Massi, F.
History
DepositionFeb 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic zinc-finger protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0063
Polymers8,8751
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Cytoplasmic zinc-finger protein / POsterior Segregation


Mass: 8875.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: pos-1, CELE_F52E1.1, F52E1.1 / Plasmid: pet21a / Details (production host): N-terminal (6xHis)-Sumo tag / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G5EF15
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic22D 1H-13C HSQC aliphatic
141isotropic22D 1H-13C HSQC aromatic
151isotropic23D CBCA(CO)NH
161isotropic23D (H)CCH-TOCSY
171isotropic23D HBHA(CO)NH
181isotropic23D (H)CCH-COSY
191isotropic23D (H)CCH-TOCSY
1101isotropic23D HN(CA)CO
1111isotropic23D HNCA
1121isotropic23D HN(CA)CB
1131isotropic23D HNCO
1141isotropic23D HN(CO)CA
1151isotropic13D 1H-15N NOESY
1161isotropic13D 1H-13C NOESY
1171isotropic1(HB)CB(CGCDCE)HE
1181isotropic1(HB)CB(CGCD)HD

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Sample preparation

DetailsType: solution
Contents: 0.4 mM [U-100% 13C; U-100% 15N] POS-1, 50 mM Tris-HCl pH 6.3, 100 mM potassium chloride, 100 uM Zinc Acetate, 1 mM DTT, 10 mM DSS, 92% H2O/8% D2O
Label: 13C15N / Solvent system: 92% H2O/8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMPOS-1[U-100% 13C; U-100% 15N]1
50 mMTris-HCl pH 6.3natural abundance1
100 mMpotassium chloridenatural abundance1
100 uMZinc Acetatenatural abundance1
1 mMDTTnatural abundance1
10 mMDSSnatural abundance1
Sample conditionsIonic strength: 100 mM / Label: sample_1 / pH: 6.3 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Agilent VNMRSVarianAgilent VNMRS8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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