[English] 日本語
Yorodumi
- EMDB-52216: Structure of Trypanosoma cruzi Prolyl Oligopeptidase in the close... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52216
TitleStructure of Trypanosoma cruzi Prolyl Oligopeptidase in the close state
Map data
Sample
  • Complex: Trypanosoma cruzi Prolyl oligopeptidase
    • Protein or peptide: Prolyl endopeptidase
KeywordsAntigen / Chagas disease / prolyl oligopeptidase / HYDROLASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsBatra S / Ragan TJ / Hesketh E / Campeotto I
Funding support United Kingdom, 2 items
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profound health impact in both endemic and non-endemic areas, no vaccine is available, and the existing therapies are outdated, producing severe side effects.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, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52216.png

Downloads & links

-
Map

FileDownload / File: emd_52216.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 128 pix.
= 167.936 Å		1.31 Å/pix.
x 128 pix.
= 167.936 Å		1.31 Å/pix.
x 128 pix.
= 167.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.312 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0072
Minimum - Maximum-0.0074152164 - 0.028567454
Average (Standard dev.)0.00007349089 (±0.000836964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 167.936 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_52216_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52216_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Trypanosoma cruzi Prolyl oligopeptidase

EntireName: Trypanosoma cruzi Prolyl oligopeptidase
Components
  • Complex: Trypanosoma cruzi Prolyl oligopeptidase
    • Protein or peptide: Prolyl endopeptidase

-
Supramolecule #1: Trypanosoma cruzi Prolyl oligopeptidase

SupramoleculeName: Trypanosoma cruzi Prolyl oligopeptidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Trypanosoma cruzi (eukaryote)

-
Macromolecule #1: Prolyl endopeptidase

MacromoleculeName: Prolyl endopeptidase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
Source (natural)Organism: Trypanosoma cruzi (eukaryote)
Molecular weightTheoretical: 80.362367 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: HHHHHHSSGL VPRGSHMMRS VYPLARRSMA AYTMHNMTVP EPYDYLEDPE NPETKTFVNE QNAFFEEYFA SEAELRKKIF ESISNSQDY PRTSNPSYIN GHYYYYHNSG LQNQSVLMRA MSLTDTAPSI FLDPNSMSSD GTTALKATAW SEDESMLAYS L SDKGSDWQ ...String:
HHHHHHSSGL VPRGSHMMRS VYPLARRSMA AYTMHNMTVP EPYDYLEDPE NPETKTFVNE QNAFFEEYFA SEAELRKKIF ESISNSQDY PRTSNPSYIN GHYYYYHNSG LQNQSVLMRA MSLTDTAPSI FLDPNSMSSD GTTALKATAW SEDESMLAYS L SDKGSDWQ RIHVRRADTV EDTSDVIEWA KFTAIAWWHN LGFFYTRYPA LQGDVDKGAE TDAAQDAFIC FHRIGRPQDE DV VILSVPE HPQWNMGASV SDCHSYVIVV LFDGCEPHNL VWVAELPSVE KGLGSEPLVF KKLVNEFAGR YTYLGNEGST FYF VTTRDA PRKKIVSIDI HTGQETVIVE QQRSVLSQAA LVKKTLLLAY LEDVKDVFYY CRLEDPTLNA IPLPIGTITS FFSD RKKDF VSFKITSFLL PGRSFFLDIN DPQSSLRVFK DDTVEGLLVD DFVTEQTFYN SSDGVRIPMF IVYRKGSVSS ESPLL LYGY GGFNIPLTPA FSSSRMVFLR DLGGVLAVLN IRGGGEYGEE WHDAGRRACK QNCFTDFIEG AKFLHRQGYG SPQTTA IMG GSNGGLLVAA VANQAPELFR CVVCRVGVLD MYKFHKFTIG HAWKSDYGDP EKEEDFRVLQ QYSPLHNIKS GIKYPAI LV VTGDHDDRVV PLHSLKYVAT LQHMNPNEGG PFLARIEVAA GHGAGKPTSK ILREAGDIYT FIAKNINASW KE

UniProtKB: Prolyl endopeptidase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: 20 mM Hepes, 150 mM Nacl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsMonodisperse

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 36.94 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Alpha Fold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.82 Å / Resolution method: OTHER / Details: Dynamight / Number images used: 126459
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Relion Initial Model
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9hjj:
Structure of Trypanosoma cruzi Prolyl Oligopeptidase in the close state

+
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