[English] 日本語
Yorodumi
- PDB-9hji: Structure of Trypanosoma cruzi Prolyl Oligopeptidase in the close... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hji
TitleStructure of Trypanosoma cruzi Prolyl Oligopeptidase in the close state
ComponentsProlyl endopeptidase
KeywordsHYDROLASE / Antigen / Chagas disease / prolyl oligopeptidase
Function / homology
Function and homology information


oligopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / cytosol
Similarity search - Function
: / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Prolyl endopeptidase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsBatra, S. / Ragan, T.J. / Hesketh, E. / Campeotto, I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust204801/Z/16/Z United Kingdom
Royal SocietyIESR2232167 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM led analysis of open and closed conformations of Chagas vaccine candidate TcPOP.
Authors: Sagar Batra / Francisco Olmo / Timothy J Ragan / Merve Kaplan / Valeria Calvaresi / Asger Meldgaard Frank / Claudia Lancey / Mahya Assadipapari / Cuifeng Ying / Weston B Struwe / Emma L ...Authors: Sagar Batra / Francisco Olmo / Timothy J Ragan / Merve Kaplan / Valeria Calvaresi / Asger Meldgaard Frank / Claudia Lancey / Mahya Assadipapari / Cuifeng Ying / Weston B Struwe / Emma L Hesketh / John M Kelly / Lea Barfod / Ivan Campeotto /
Abstract: Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, remains a significant global public health concern. Despite its profound health impact in both endemic and non-endemic areas, no ...Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, remains a significant global public health concern. Despite its profound health impact in both endemic and non-endemic areas, no vaccine is available, and the existing therapies are outdated, producing severe side effects. The 80 kDa prolyl oligopeptidase of Trypanosoma cruzi (TcPOP) has been identified as a leading candidate for Chagas vaccine development. Here we report the three-dimensional structure of TcPOP in open and closed conformation, at a global resolution of 3.8 and 3.6 Å, respectively, determined using single-particle cryo-electron microscopy. Multiple conformations were observed and further characterized using plasmonic optical tweezers and hydrogen-deuterium exchange mass spectrometry. To assess the immunogenic potential of TcPOP, we immunized female mice and evaluated both polyclonal and monoclonal responses against the TcPOP antigen and its homologues. The anti-TcPOP polyclonal response demonstrates invasion blocking properties via parasite lysis. Polyclonal sera  were cross-reactive with closely-related POPs but not with human homologues. Collectively, our findings provide structural and functional insights necessary to understand the immunogenicity of TcPOP for future Chagas vaccine development.
History
DepositionNov 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prolyl endopeptidase


Theoretical massNumber of molelcules
Total (without water)80,3621
Polymers80,3621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Prolyl endopeptidase


Mass: 80362.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HHHHHHSSGLVPRGSHMMRSVYPLARRSMAAYTMHNMTVPEPYDYLEDPENPETKTFVNEQNAFFEEYFASEAELRK KIFESISNSQDYPRTSNPSYINGHYYYYHNSGLQNQSVLMRAMSLTDTAPSIFLDPNSMS ...Details: HHHHHHSSGLVPRGSHMMRSVYPLARRSMAAYTMHNMTVPEPYDYLEDPENPETKTFVNEQNAFFEEYFASEAELRK KIFESISNSQDYPRTSNPSYINGHYYYYHNSGLQNQSVLMRAMSLTDTAPSIFLDPNSMS SDGTTALKATAWSEDESMLAYSLSDKGSDWQRIHVRRADTVEDTSDVIEWAKFTAIAWWH NLGFFYTRYPALQGDVDKGAETDAAQDAFICFHRIGRPQDEDVVILSVPEHPQWNMGASV SDCHSYVIVVLFDGCEPHNLVWVAELPSVEKGLGSEPLVFKKLVNEFAGRYTYLGNEGST FYFVTTRDAPRKKIVSIDIHTGQETVIVEQQRSVLSQAALVKKTLLLAYLEDVKDVFYYC RLEDPTLNAIPLPIGTITSFFSDRKKDFVSFKITSFLLPGRSFFLDINDPQSSLRVFKDD TVEGLLVDDFVTEQTFYNSSDGVRIPMFIVYRKGSVSSESPLLLYGYGGFNIPLTPAFSS SRMVFLRDLGGVLAVLNIRGGGEYGEEWHDAGRRACKQNCFTDFIEGAKFLHRQGYGSPQ TTAIMGGSNGGLLVAAVANQAPELFRCVVCRVGVLDMYKFHKFTIGHAWKSDYGDPEKEE DFRVLQQYSPLHNIKSGIKYPAILVVTGDHDDRVVPLHSLKYVATLQHMNPNEGGPFLAR IEVAAGHGAGKPTSKILREAGDIYTFIAKNINASWKE
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: TCPO / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q71MD6, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: From bacterial lysate / Type: CELL / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 78.6 MDa / Experimental value: YES
Source (natural)Organism: Trypanosoma cruzi (eukaryote)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4 / Details: 20 mM Hepes, 150 mM NaCl
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodisperse
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 1 sec. / Electron dose: 36.94 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.57 Å / Resolution method: OTHER / Num. of particles: 163153 / Details: Dynamight / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035678
ELECTRON MICROSCOPYf_angle_d0.7517711
ELECTRON MICROSCOPYf_dihedral_angle_d5.369766
ELECTRON MICROSCOPYf_chiral_restr0.049829
ELECTRON MICROSCOPYf_plane_restr0.0051005

+
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