[English] 日本語
Yorodumi
- PDB-7qdw: Solution structure of the complex between plasmodial ZNHIT3 and N... -

+
Open data


ID or keywords:

Loading...

-
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
Similarity search - Function
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 / FMR1-interacting protein 1 conserved 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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

-
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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more