[English] 日本語
Yorodumi
- PDB-8i26: NMR structure of Toxoplasma gondii PDCD5 (cis form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8i26
TitleNMR structure of Toxoplasma gondii PDCD5 (cis form)
ComponentsProgrammed cell death 5 protein
KeywordsENDOCYTOSIS / Molten globule / Heparan sulfate/Heparin binding protein / Proline cis form
Function / homologyPDCD5-like / PDCD5-like superfamily / Double-stranded DNA-binding domain / DNA binding / Programmed cell death 5 protein
Function and homology information
Biological speciesToxoplasma gondii GT1 (eukaryote)
MethodSOLUTION NMR / distance geometry
AuthorsLin, M.H. / Hsu, C.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan)110-2113-M-002-023 Taiwan
CitationJournal: To Be Published
Title: Proline isomerization and molten globular property of TgPDCD5 secreted from Toxoplasma gondii confers its regulation of heparin sulfate binding
Authors: Lin, M.H. / Tsun-Ai, Y. / Tsung-Han, W. / Chi-Fon, C. / Hsu, C.H.
History
DepositionJan 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Programmed cell death 5 protein


Theoretical massNumber of molelcules
Total (without water)13,7161
Polymers13,7161
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100000structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Programmed cell death 5 protein /


Mass: 13716.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii GT1 (eukaryote) / Gene: TGGT1_207690 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A125YJ71

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic33D HN(CA)CB
121anisotropic33D CBCA(CO)NH
131anisotropic33D HNCA
141anisotropic33D HNCO
151anisotropic32D 1H-15N HSQC
161anisotropic33D 1H-13C NOESY
171anisotropic33D 1H-15N NOESY

-
Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-100% 13C; U-100% 15N] Protein, 25 mM sodium phosphate, 100 mM sodium chloride, 10 mM sodium azide, 1 mM PMSF, 90% H2O/10% D2O
Details: The purified protein was concentrated to 0.1-0.5 mM in buffer 25 mM sodium phosphate, 100 mM NaCl, 10 mM sodium azide and 1mM PMSF with pH 4.5 for NMR.
Label: 15N_sample, 13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMProtein[U-100% 13C; U-100% 15N]1
25 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
10 mMsodium azidenatural abundance1
1 mMPMSFnatural abundance1
Sample conditionsDetails: The purified protein was concentrated to 0.1-0.5 mM in buffer 25 mM sodium phosphate, 100 mM NaCl, 10 mM sodium azide and 1mM PMSF with pH 4.5 for NMR.
Ionic strength: 125 mM / Label: cis form / pH: 4.5 / Pressure: 1 atm / Temperature: 310 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100000 / 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