[English] 日本語
Yorodumi
- EMDB-66758: Plasmodium vivax Perforin-like protein 2 K735C/E771C mutant(PvPLP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66758
TitlePlasmodium vivax Perforin-like protein 2 K735C/E771C mutant(PvPLP2 K735C/E771C) prepore on membrane by cryoET subtomogram averaging
Map dataRefinement map
Sample
  • Complex: Plasmodium vivax Perforin-like Protein 2 K735C/E771C mutant prepore
KeywordsPlasmodium / Perforin-like protein / PvPLP2 / TOXIN
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
Methodsubtomogram averaging / cryo EM / Resolution: 28.27 Å
AuthorsZhang Y / Zhong LJ / Song Y / Gilbert RJC / Ni T / Yu XL
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
Other governmentResearch Grant Council - General Research Fund Hong Kong
CitationJournal: Nat Commun / Year: 2026
Title: Molecular mechanism of pore formation by Plasmodium Perforin-like Protein 2
Authors: Zhang Y / Zhong L / Song Y / Guo M / Ren K / Yang T / Huang Y / Sirotkin I / Yi G / Jiao F / Zhang P / Gilbert RJC / Ni T / Yu X
History
DepositionOct 27, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_66758.png

Downloads & links

-
Map

FileDownload / File: emd_66758.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.28 Å/pix.
x 90 pix.
= 565.56 Å		6.28 Å/pix.
x 90 pix.
= 565.56 Å		6.28 Å/pix.
x 90 pix.
= 565.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.284 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.095
Minimum - Maximum-0.059714 - 0.22131036
Average (Standard dev.)0.00243014 (±0.023574173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions909090
Spacing909090
CellA=B=C: 565.56 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_66758_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map2 from reconstruction

Fileemd_66758_half_map_1.map
Annotationhalf map2 from reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map1 from reconstruction

Fileemd_66758_half_map_2.map
Annotationhalf map1 from reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Plasmodium vivax Perforin-like Protein 2 K735C/E771C mutant prepore

EntireName: Plasmodium vivax Perforin-like Protein 2 K735C/E771C mutant prepore
Components
  • Complex: Plasmodium vivax Perforin-like Protein 2 K735C/E771C mutant prepore

-
Supramolecule #1: Plasmodium vivax Perforin-like Protein 2 K735C/E771C mutant prepore

SupramoleculeName: Plasmodium vivax Perforin-like Protein 2 K735C/E771C mutant prepore
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Plasmodium vivax (malaria parasite P. vivax)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 3.0 e/Å2
Details: The tilt-series were acquired using Thermofisher Krios equipped with a Falcon 4i camera and Selectris energy filter. A dose-symmetric scheme was used, with a tilt range of -60 to 60 at 3 ...Details: The tilt-series were acquired using Thermofisher Krios equipped with a Falcon 4i camera and Selectris energy filter. A dose-symmetric scheme was used, with a tilt range of -60 to 60 at 3 degree increments and an exposure dose of 3 e-/A2 per image. The total dose was 123 e-/A2.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 28.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. v4) / Number subtomograms used: 1496
ExtractionNumber tomograms: 322 / Number images used: 1496 / Software - Name: UCSF ChimeraX (ver. v1.7.1)
CTF correctionSoftware: (Name: emClarity (ver. v1.6.2), RELION (ver. v4)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. v4)
FSC plot (resolution estimation)

+
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