[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleAn Algorithm for Enhancing the Image Contrast of Electron Tomography.
Journal, issue, pagesSci Rep, Vol. 8, Issue 1, Page 16711, Year 2018
Publish dateNov 12, 2018
AuthorsHao Wu / Xiaobo Zhai / Dongsheng Lei / Jianfang Liu / Yadong Yu / Rongfang Bie / Gang Ren /
PubMed AbstractThree-dimensional (3D) reconstruction of a single protein molecule is essential for understanding the relationship between the structural dynamics and functions of the protein. Electron tomography ...Three-dimensional (3D) reconstruction of a single protein molecule is essential for understanding the relationship between the structural dynamics and functions of the protein. Electron tomography (ET) provides a tool for imaging an individual particle of protein from a series of tilted angles. Individual-particle electron tomography (IPET) provides an approach for reconstructing a 3D density map from a single targeted protein particle (without averaging from different particles of this type of protein), in which the target particle was imaged from a series of tilting angles. However, owing to radiation damage limitations, low-dose images (high noise, and low image contrast) are often challenging to be aligned for 3D reconstruction at intermediate resolution (1-3 nm). Here, we propose a computational method to enhance the image contrast, without increasing any experimental dose, for IPET 3D reconstruction. Using an edge-preserving smoothing-based multi-scale image decomposition algorithm, this method can detect the object against a high-noise background and enhance the object image contrast without increasing the noise level or significantly decreasing the image resolution. The method was validated by using both negative staining (NS) ET and cryo-ET images. The successful 3D reconstruction of a small molecule (<100 kDa) indicated that this method can be used as a supporting tool to current ET 3D reconstruction methods for studying protein dynamics via structure determination from each individual particle of the same type of protein.
External linksSci Rep / PubMed:30420636 / PubMed Central
MethodsEM (tomography)
Resolution17.0 - 97.7 Å
Structure data

EMDB-9262:
Single-Molecule 3D Image of Double Complexes of DNA-Nanogold Conjugates (No. 01)
Method: EM (tomography) / Resolution: 17.6 Å

EMDB-9263:
Single-Molecule 3D Image of Double Complexes of DNA-Nanogold Conjugates (No. 02)
Method: EM (tomography) / Resolution: 17.0 Å

EMDB-9266:
Single-Molecule 3D Image of DNA Origami Bennett Linkage by Image Contrast Enhancement and Individual Particle Electron Tomography (No. 01)
Method: EM (tomography) / Resolution: 97.7 Å

EMDB-9267:
Single-Molecule 3D Image of DNA Origami Bennett Linkage by Image Contrast Enhancement and Individual Particle Electron Tomography (No. 02)
Method: EM (tomography) / Resolution: 97.4 Å

EMDB-9268:
Single-Molecule 3D Image of Low-Density Lipoprotein in Complex with Cholesteryl Ester Transfer Protein (No. 01)
Method: EM (tomography) / Resolution: 71.0 Å

EMDB-9269:
Single-Molecule 3D Image of Low-Density Lipoprotein in Complex with Cholesteryl Ester Transfer Protein (No. 02)
Method: EM (tomography) / Resolution: 71.0 Å

EMDB-9270:
Single-Molecule 3D Image of Cholesteryl Ester Transfer Protein by Individual-Particle Electron Tomography (No. 01)
Method: EM (tomography) / Resolution: 95.5 Å

EMDB-9271:
Single-Molecule 3D Image of Cholesteryl Ester Transfer Protein by Individual-Particle Electron Tomography (No. 02)
Method: EM (tomography) / Resolution: 95.5 Å

Source
  • synthetic construct (others)
  • Enterobacteria phage M13 (virus)
  • Homo sapiens (human)

+
About Yorodumi Papers

-
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://pdbjlvh1.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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more