[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

TitleAtomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.
Journal, issue, pagesNat Methods, Vol. 14, Issue 4, Page 399-402, Year 2017
Publish dateFeb 13, 2017
AuthorsM Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P Hinck / Guillermo Calero / David Eisenberg / Tamir Gonen /
PubMed AbstractTraditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from ...Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography.
External linksNat Methods / PubMed:28192420 / PubMed Central
MethodsEM (electron crystallography)
Resolution1.1 - 2.9 Å
Structure data

8216

5k7n

EMDB-8216, PDB-5k7n:
MicroED structure of tau VQIVYK peptide at 1.1 A resolution
Method: EM (electron crystallography) / Resolution: 1.1 Å

8217

5k7o

EMDB-8217, PDB-5k7o:
MicroED structure of lysozyme at 1.8 A resolution
Method: EM (electron crystallography) / Resolution: 1.8 Å

8218

5k7p

EMDB-8218, PDB-5k7p:
MicroED structure of xylanase at 2.3 A resolution
Method: EM (electron crystallography) / Resolution: 2.3 Å

8219

5k7q

EMDB-8219, PDB-5k7q:
MicroED structure of thaumatin at 2.5 A resolution
Method: EM (electron crystallography) / Resolution: 2.5 Å

8220

5k7r

EMDB-8220, PDB-5k7r:
MicroED structure of trypsin at 1.7 A resolution
Method: EM (electron crystallography) / Resolution: 1.7 Å

8221

5k7s

EMDB-8221, PDB-5k7s:
MicroED structure of proteinase K at 1.6 A resolution
Method: EM (electron crystallography) / Resolution: 1.6 Å

8222

5k7t

EMDB-8222, PDB-5k7t:
MicroED structure of thermolysin at 2.5 A resolution
Method: EM (electron crystallography) / Resolution: 2.5 Å

8472

5ty4

EMDB-8472, PDB-5ty4:
MicroED structure of a complex between monomeric TGF-b and its receptor, TbRII, at 2.9 A resolution
Method: EM (electron crystallography) / Resolution: 2.9 Å

Chemicals

ChemComp-HOH:
WATER / Water

ChemComp-CL:
Unknown entry / Chloride

ChemComp-NA:
Unknown entry

ChemComp-IOD:
IODIDE ION / Iodide

ChemComp-CA:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM / Dimethyl sulfoxide

ChemComp-IPA:
ISOPROPYL ALCOHOL / alkaloid*YM / Isopropyl alcohol

Source
  • homo sapiens (human)
  • gallus gallus (chicken)
  • Chicken (chicken)
  • Trichoderma reesei (fungus)
  • hypocrea jecorina (fungus)
  • thaumatococcus daniellii (katemfe)
  • Katemfe (katemfe)
  • bos taurus (cattle)
  • Bovine (cattle)
  • engyodontium album (fungus)
  • bacillus thermoproteolyticus (bacteria)
KeywordsPROTEIN FIBRIL / Amyloid / HYDROLASE / PLANT PROTEIN / Sweet protein / TRANSFERASE

+
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://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