[English] 日本語
Yorodumi
- EMDB-45674: Subtomogram average of a whole Polar Tube cross-section from Ence... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45674
TitleSubtomogram average of a whole Polar Tube cross-section from Encephalitozoon intestinalis microsporidian spores
Map dataThe raw map was filtered by a 50A low-pass filter, then, in Chimera, processed with a Gaussian filter (25 A) and "Hide Dust" function
Sample
  • Cell: Encephalitozoon intestinalis microsporidian spores
KeywordsMicrosporidia / polar tube / subtomogram averaging / outer-filament layer / CELL INVASION
Biological speciesEncephalitozoon intestinalis (fungus)
Methodsubtomogram averaging / cryo EM / Resolution: 70.0 Å
AuthorsUsmani M / Coudray N / Bobe D / Kopylov M / Ekiert DC / Bhabha G
Funding support United States, 8 items
OrganizationGrant numberCountry
American Heart Association915749 United States
Other privateSearle Scholars Program, SSP-2018-2737
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI147131 United States
Other privateHirschl Career Scientist Award
The Pew Charitable TrustsPEW-00033055 United States
Other governmentNIH Common Fund Transformative High Resolution Cryo-Electron Microscopy, U24 GM129539
Simons FoundationSF349247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)9 P41 GM103310 United States
CitationJournal: bioRxiv / Year: 2024
Title: Cryo-ET reveals the architecture of the polar tube invasion apparatus from microsporidian parasites.
Authors: Mahrukh Usmani / Nicolas Coudray / Margot Riggi / Rishwanth Raghu / Harshita Ramchandani / Daija Bobe / Mykhailo Kopylov / Ellen D Zhong / Janet H Iwasa / Damian C Ekiert / Gira Bhabha
Abstract: Microsporidia are divergent fungal pathogens that employ a harpoon-like apparatus called the polar tube (PT) to invade host cells. The PT architecture and its association with neighboring organelles ...Microsporidia are divergent fungal pathogens that employ a harpoon-like apparatus called the polar tube (PT) to invade host cells. The PT architecture and its association with neighboring organelles remain poorly understood. Here, we use cryo-electron tomography to investigate the structural cell biology of the PT in dormant spores from the human-infecting microsporidian species, . Segmentation and subtomogram averaging of the PT reveal at least four layers: two protein-based layers surrounded by a membrane, and filled with a dense core. Regularly spaced protein filaments form the structural skeleton of the PT. Combining cryo-electron tomography with cellular modeling, we propose a model for the 3-dimensional organization of the polaroplast, an organelle that is continuous with the membrane layer that envelops the PT. Our results reveal the ultrastructure of the microsporidian invasion apparatus , laying the foundation for understanding infection mechanisms.
History
DepositionJul 10, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45674.png

Downloads & links

-
Map

FileDownload / File: emd_45674.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe raw map was filtered by a 50A low-pass filter, then, in Chimera, processed with a Gaussian filter (25 A) and "Hide Dust" function
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.31 Å/pix.
x 160 pix.
= 1329.28 Å		8.31 Å/pix.
x 160 pix.
= 1329.28 Å		8.31 Å/pix.
x 160 pix.
= 1329.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.308 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-3.8920908 - 4.2007055
Average (Standard dev.)0.0030308866 (±0.6735272)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-79-79-79
Dimensions160160160
Spacing160160160
CellA=B=C: 1329.2799 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Raw map

Fileemd_45674_additional_1.map
AnnotationRaw map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_45674_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_45674_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Encephalitozoon intestinalis microsporidian spores

EntireName: Encephalitozoon intestinalis microsporidian spores
Components
  • Cell: Encephalitozoon intestinalis microsporidian spores

-
Supramolecule #1: Encephalitozoon intestinalis microsporidian spores

SupramoleculeName: Encephalitozoon intestinalis microsporidian spores / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Encephalitozoon intestinalis (fungus)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7
Component:
ConcentrationFormulaName
200.0 mg/LKClPotassium Chloride
200.0 mg/LKH2PO4Potassium Phosphate monobasic
8000.0 mg/LNaClSodium Chloride
2160.0 mg/LNa2HPO4-7H2)Sodium Phosphate dibasic

Details: Buffer details: DPBS (Gibco 14190144)
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: NITROGEN / Details: Wohlwend Compact 01 HPF.
Details7e7 spores per uL

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 1 / Average exposure time: 0.45 sec. / Average electron dose: 1.67 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 7.0 µm / Nominal magnification: 33000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 70.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 1055
ExtractionNumber tomograms: 1 / Number images used: 1055 / Software - Name: Dynamo
Final 3D classificationSoftware - Name: Dynamo
Final angle assignmentType: OTHER / Software - Name: Dynamo

+
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