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- PDB-6pmg: Solution structure of the C-terminal zinc finger of the C. elegan... -

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Basic information

Entry
Database: PDB / ID: 6pmg
TitleSolution structure of the C-terminal zinc finger of the C. elegans protein MEX-5
ComponentsZinc finger protein mex-5
KeywordsRNA BINDING PROTEIN / zinc finger protein / MEX-5 / C. elegans / CCCH zinc finger
Function / homology
Function and homology information


poly-pyrimidine tract binding / multicellular organism development / P granule / mRNA 3'-UTR binding / regulation of protein localization / protein domain specific binding / centrosome / protein kinase binding / DNA binding / metal ion binding ...poly-pyrimidine tract binding / multicellular organism development / P granule / mRNA 3'-UTR binding / regulation of protein localization / protein domain specific binding / centrosome / protein kinase binding / DNA binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
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
Zinc finger protein mex-5
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsMassi, F. / Tavella, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117008 United States
CitationJournal: Biophys.J. / Year: 2020
Title: A Disorder-to-Order Transition Mediates RNA Binding of the Caenorhabditis elegans Protein MEX-5.
Authors: Tavella, D. / Ertekin, A. / Schaal, H. / Ryder, S.P. / Massi, F.
History
DepositionJul 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Zinc finger protein mex-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0972
Polymers4,0321
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10all calculated structures submitted
RepresentativeModel #1target function

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Components

#1: Protein/peptide Zinc finger protein mex-5 /


Mass: 4031.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mex-5, W02A2.7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XUB2
#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-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(CO)CA
161isotropic13D HNCA
171isotropic13D CBCA(CO)NH
181isotropic13D HN(CA)CB
191isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY aromatic
1111isotropic13D 1H-13C NOESY
1121isotropic13D (H)CCH-TOCSY
1131isotropic13D (H)CCH-COSY

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Sample preparation

DetailsType: solution / Contents: 300 nM [U-13C; U-15N] MEX-5, 93% H2O/7% D2O / Label: 13C_sample / Solvent system: 93% H2O/7% D2O
SampleConc.: 300 nM / Component: MEX-5 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 100 mM / Label: condition_1 / pH: 6.2 / Pressure: 1 atm / Temperature: 294 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 20

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