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- PDB-7qdw: Solution structure of the complex between plasmodial ZNHIT3 and N... -

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Basic information

Entry
Database: PDB / ID: 7qdw
TitleSolution structure of the complex between plasmodial ZNHIT3 and NUFIP1 proteins
Components
  • NUFIP1 domain-containing protein
  • Zinc finger protein, putative
KeywordsSIGNALING PROTEIN / PAC-HIT FOLD / JAW HELICES
Function / homology
Function and homology information


snoRNA localization / pre-snoRNP complex / box C/D snoRNP assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nucleus / metal ion binding
Similarity search - Function
Zinc finger HIT domain-containing protein 3 / FMR1-interacting protein 1, conserved domain / FMR1-interacting protein 1 (NUFIP1) / Zinc finger HIT-type profile. / Zinc finger, HIT-type
Similarity search - Domain/homology
Zinc finger protein, putative / NUFIP1 domain-containing protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodSOLUTION NMR / molecular dynamics
AuthorsChagot, M.E. / Quinternet, M.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-11-BSV8-01503 France
French National Research AgencyANR-16-CE11-0032-02] France
CitationJournal: Biochemistry / Year: 2022
Title: Structural Analysis of the Plasmodial Proteins ZNHIT3 and NUFIP1 Provides Insights into the Selectivity of a Conserved Interaction.
Authors: Chagot, M.E. / Boutilliat, A. / Kriznik, A. / Quinternet, M.
History
DepositionNov 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4Jun 19, 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

Downloads & links

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Assembly

Deposited unit
A: Zinc finger protein, putative
B: NUFIP1 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)11,6862
Polymers11,6862
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2250 Å2
ΔGint-20 kcal/mol
Surface area6750 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest restraint energy
RepresentativeModel #1structure with the lowest restraint energy

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Components

#1: Protein Zinc finger protein, putative


Mass: 8578.843 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0916900 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8I2Y4
#2: Protein/peptide NUFIP1 domain-containing protein


Mass: 3107.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_1473900 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IK99

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D HN(CA)CO
181isotropic13D HBHA(CO)NH
171isotropic13D C(CO)NH
161isotropic13D H(CCO)NH
1101isotropic13D (H)CCH-COSY
191isotropic13D (H)CCH-TOCSY
1111isotropic13D HNHA
1121isotropic13D HNCO ECOSY
1151isotropic12D 1H-1H NOESY
1141isotropic13D 1H-13C NOESY aliphatic
1131isotropic13D 1H-13C NOESY aromatic
1161isotropic13D 1H-15N NOESY
1171isotropic12D 1H-13C HSQC aliphatic
1181isotropic12D 1H-13C HSQC aromatic
1191isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 0.7 mM [U-100% 13C; U-100% 15N] pfZNHIT3, 0.7 mM [U-100% 13C; U-100% 15N] pfNUFIP1, 150 mM sodium chloride, 10 mM sodium phosphate, 95% H2O/5% D2O
Label: cplx / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMpfZNHIT3[U-100% 13C; U-100% 15N]1
0.7 mMpfNUFIP1[U-100% 13C; U-100% 15N]1
150 mMsodium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 6.4 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.6.2Bruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
TopSpin3.6.2Bruker Biospinprocessing
CARAKeller and Wuthrichpeak picking
TALOS-NYang Shen, and Ad Baxstructure calculation
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 7
NMR representativeSelection criteria: structure with the lowest restraint energy
NMR ensembleConformer selection criteria: structures with the lowest restraint energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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