[English] 日本語
Yorodumi
- EMDB-67291: Sampling-mismatch-corrected ptychographic SPA reconstruction of t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-67291
TitleSampling-mismatch-corrected ptychographic SPA reconstruction of the Thermoplasma acidophilum 20S proteasome
Map dataDensity map of T. Acidophilum 20S proteasome reconstructed from the sampling-mismatch corrected micrographs using THUNDER software package in ptychographic SPA.
Sample
  • Complex: T. Acidophilum 20S proteasome
KeywordsProteasome / Protein degradation / Archaeal complex / D7 symmetry / HYDROLASE
Biological speciesThermoplasma acidophilum (acidophilic)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsLi T / Li S / Yan Z / Li X
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32430056 China
Ministry of Science and Technology (MoST, China)2024YFA1307302 China
CitationJournal: To Be Published
Title: Sampling Mismatch and Correction for Ptychographic Single-Particle Analysis
Authors: Li T / Li S / Yan Z / Shen Y / Li X
History
DepositionNov 26, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_67291.png

Downloads & links

-
Map

FileDownload / File: emd_67291.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map of T. Acidophilum 20S proteasome reconstructed from the sampling-mismatch corrected micrographs using THUNDER software package in ptychographic SPA.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 256 pix.
= 359.091 Å		1.4 Å/pix.
x 256 pix.
= 359.091 Å		1.4 Å/pix.
x 256 pix.
= 359.091 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4027 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0471
Minimum - Maximum-0.14458026 - 0.18503156
Average (Standard dev.)-0.00006309839 (±0.0076020416)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 359.0912 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Density map of T. Acidophilum 20S proteasome reconstructed...

Fileemd_67291_additional_1.map
AnnotationDensity map of T. Acidophilum 20S proteasome reconstructed from the sampling-mismatch corrected micrographs using RELION software package in ptychographic SPA.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Density map of T. Acidophilum 20S proteasome reconstructed...

Fileemd_67291_additional_2.map
AnnotationDensity map of T. Acidophilum 20S proteasome reconstructed from the sampling-mismatch corrected micrographs using cryoSPARC software package in ptychographic SPA.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 of T. Acidophilum 20S proteasome...

Fileemd_67291_half_map_1.map
AnnotationHalf map 2 of T. Acidophilum 20S proteasome reconstructed from the sampling-mismatch corrected micrographs using THUNDER software package in ptychographic SPA.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1 of T. Acidophilum 20S proteasome...

Fileemd_67291_half_map_2.map
AnnotationHalf map 1 of T. Acidophilum 20S proteasome reconstructed from the sampling-mismatch corrected micrographs using THUNDER software package in ptychographic SPA.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : T. Acidophilum 20S proteasome

EntireName: T. Acidophilum 20S proteasome
Components
  • Complex: T. Acidophilum 20S proteasome

-
Supramolecule #1: T. Acidophilum 20S proteasome

SupramoleculeName: T. Acidophilum 20S proteasome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Thermoplasma acidophilum (acidophilic)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS TITAN THEMIS
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 128 pixel / Digitization - Dimensions - Height: 128 pixel / Average electron dose: 63.0 e/Å2
Details: An Electron Microscope Pixel Array Detector G1 (EMPAD G1, 128 by 128 pixels, Thermo Fisher Company) was used.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: 4D-STEM / Nominal defocus max: 1.971 µm / Nominal defocus min: 1.0090000000000001 µm

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 105665
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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