[English] 日本語
Yorodumi
- PDB-5v2b: Peptide 38148 modified from fragment 41-60 of Plasmodium falcipar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v2b
TitlePeptide 38148 modified from fragment 41-60 of Plasmodium falciparum Thrombospondin-Related Sporozoite Protein (TRSP)
ComponentsThrombospondin-related sporozoite protein
KeywordsCELL INVASION / Modified peptide / Chemically synthesized / Pf-TRSP protein / Alpha-helix residues 8-18
Function / homologyCCN, TSP1 domain / CCN3 Nov like TSP1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / signal transduction / plasma membrane / Thrombospondin-related sporozoite protein
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsBermudez, A. / Patarroyo, M.E.
CitationJournal: To Be Published
Title: Peptide 38148 modified from fragment 41-60 of Plasmodium falciparum Thrombospondin-Related Sporozoite Protein (TRSP)
Authors: Bermudez, A. / Patarroyo, M.E.
History
DepositionMar 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.2May 15, 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: Thrombospondin-related sporozoite protein


Theoretical massNumber of molelcules
Total (without water)2,4321
Polymers2,4321
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2380 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Thrombospondin-related sporozoite protein


Mass: 2431.622 Da / Num. of mol.: 1 / Fragment: UNP residues 41-60 / Mutation: V43T, R53K, L54H / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q8I2A0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D DQF-COSY; 2D 1H-1H TOCSY; 2D 1H-1H NOESY
221anisotropic12D 1H-1H TOCSY
331anisotropic12D 1H-1H TOCSY
441anisotropic12D 1H-1H TOCSY

-
Sample preparation

DetailsType: solution / Contents: 16.6 mg/mL 38148, trifluoroethanol/water
Details: Peptide 38148 modified from fragment 41-60 of Plasmodium falciparum Thrombospondin-Related Sporozoite Protein (TRSP)
Label: 38148 / Solvent system: trifluoroethanol/water
SampleConc.: 16.6 mg/mL / Component: 38148 / Isotopic labeling: natural abundance
Sample conditions

Ionic strength: NULL Not defined / pH: 3.7 / PH err: 0.1 / Pressure: AMBIENT / Temperature err: 0.1

Conditions-IDDetailsLabelTemperature (K)
1TEMPERATURE AMBIENT38148 (295)295 K
2TEMPERATURE 285 K38148 (285)285 K
3TEMPERATURE 305 K38148 (305)305 K
4TEMPERATURE 315 K38148 (315)315 K

-
NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
Insight IIAccelrys Software Inc.refinement
Insight IIAccelrys Software Inc.geometry optimization
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1 / Details: 220 NOEs
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 9

+
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://pdbjlvh1.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