[English] 日本語
Yorodumi
- PDB-9cq0: Event-based electron counting microED structure of thiostrepton f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9cq0
TitleEvent-based electron counting microED structure of thiostrepton from a single crystal
ComponentsThiostrepton
KeywordsANTIBIOTIC / Cyclic / macrocycle
Function / homologyTHIOSTREPTON
Function and homology information
Biological speciesStreptomyces azureus (bacteria)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / Resolution: 1.5 Å
AuthorsVlahakis, N.W. / Qu, S. / Richards, L.S. / deMoraes, L.S. / Nelson, H.M. / Rodriguez, J.A.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Department of Energy (DOE, United States) United States
National Science Foundation (NSF, United States) United States
CitationJournal: Acta Crystallogr C Struct Chem / Year: 2025
Title: Fast event-based electron counting for small-molecule structure determination by MicroED.
Authors: Niko Vlahakis / Songrong Qu / Logan S Richards / Lygia Silva de Moraes / Duilio Cascio / Hosea M Nelson / Jose A Rodriguez /
Abstract: Electron counting helped realize the resolution revolution in single-particle cryoEM and is now accelerating the determination of MicroED structures. Its advantages are best demonstrated by new ...Electron counting helped realize the resolution revolution in single-particle cryoEM and is now accelerating the determination of MicroED structures. Its advantages are best demonstrated by new direct electron detectors capable of fast (kilohertz) event-based electron counting (EBEC). This strategy minimizes the inaccuracies introduced by coincidence loss (CL) and promises rapid determination of accurate structures. We used the Direct Electron Apollo camera to leverage EBEC technology for MicroED data collection. Given its ability to count single electrons, the Apollo collects high-quality MicroED data from organic small-molecule crystals illuminated with incident electron beam flux densities as low as 0.01-0.045 e/Å/s. Under even the lowest flux density (0.01 e/Å/s) condition, fast EBEC data produced ab initio structures of a salen ligand (268 Da) and biotin (244 Da). Each structure was determined from a 100° wedge of data collected from a single crystal in as few as 50 s, with a delivered fluence of only ∼0.5 e/Å. Fast EBEC data collected with a fluence of 2.25 or 3.33 e/Å also facilitated a 1.5 Å structure of thiostrepton (1665 Da). While refinement of these structures appeared unaffected by CL, a CL adjustment applied to EBEC data further improved the distribution of intensities measured from the salen ligand and biotin crystals. However, CL adjustment only marginally improved the refinement of their corresponding structures, signaling the already high counting accuracy of detectors with counting rates in the kilohertz range. Overall, by delivering low-dose structure-worthy data, fast EBEC collection strategies open new possibilities for high-throughput MicroED.
History
DepositionJul 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thiostrepton


Theoretical massNumber of molelcules
Total (without water)1,8061
Polymers1,8061
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint1 kcal/mol
Surface area1650 Å2
Unit cell
Length a, b, c (Å)26.470, 26.470, 27.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

-
Components

#1: Protein/peptide Thiostrepton


Type: Thiopeptide / Class: Antibiotic / Mass: 1805.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Thiostrepton is a hetrocyclic thiopeptide belonging to the thiocillin family, consisting of four thiazole, one thiozoline and one piperideine rings. A modified quinoline linked to main-chain ...Details: Thiostrepton is a hetrocyclic thiopeptide belonging to the thiocillin family, consisting of four thiazole, one thiozoline and one piperideine rings. A modified quinoline linked to main-chain residue 1 and side-chain of residue 12. Post translational maturation of thiazole and oxazole containing antibiotics involves the enzymic condensation of a Cys or Ser with the alpha-carbonyl of the preceding amino acid to form a thioether or ether bond, then dehydration to form a double bond with the alpha-amino nitrogen. Thiazoline or oxazoline ring are dehydrogenated to form thiazole or oxazole rings. the pyridinyl involves the cross-linking of a Ser and a Cys-Ser pair usually separated by 7 or 8 residues along the peptide chain. The Ser residues are dehydrated to didehydroalanines, then bonded between their beta carbons. The alpha carbonyl of the Cys condenses with alpha carbon of the first Ser to form a pyridinyl ring. The ring may be mutiply dehydrogenated to form a pyridine ring with loss of the amino nitrogen of the first Ser. The amidation of Ser-17 probably does not occur by the same mechanism, oxidative cleavage of glycine, as in eukaryotes.
Source: (natural) Streptomyces azureus (bacteria) / References: THIOSTREPTON
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYLIC ...THIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYLIC CORE, CONSISTING OF A NITROGEN CONTAINING, SIX-MEMBERED RING CENTRAL TO DEHYDROAMINO ACIDS AND A SUBSET OF FIVE MEMBER RING STRUCTURES INCLUDING THIAZOLES, THIAZOLINES AND OXAZOLES. HERE, THIOSTREPTON IS REPRESENTED BY THE SEQUENCE (SEQRES)
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

-
Sample preparation

ComponentName: Microcrystal of thiostrepton / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 1.81 kDa/nm / Experimental value: NO
Source (natural)Organism: Streptomyces azureus (bacteria)
EM crystal formationAtmosphere: Standard temperature and pressure
Details: Thiostrepton (30 mg) was dissolved in 1.95 mL 24:1 Chloroform:Isoamyl Alcohol. 390 uL of Ethanol and 195 uL of 100% Glycerol were each mixed into the solution, and tetragonal crystals of ...Details: Thiostrepton (30 mg) was dissolved in 1.95 mL 24:1 Chloroform:Isoamyl Alcohol. 390 uL of Ethanol and 195 uL of 100% Glycerol were each mixed into the solution, and tetragonal crystals of various sizes (including microcrystals) formed after approximately 2 days of slow evaporation of the solvent under ambient conditions.
Temperature: 293 K / Time: 2 DAY
Buffer solutionpH: 7 / Details: 24:1 chloroform/isoamyl alcohol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO

-
Data collection

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Temperature (max): 100 K / Temperature (min): 100 K
Image recordingAverage exposure time: 3.33 sec. / Electron dose: 0.0333 e/Å2 / Film or detector model: DIRECT ELECTRON APOLLO (4k x 4k) / Num. of diffraction images: 100 / Num. of grids imaged: 1
Image scansWidth: 4096 / Height: 4096
EM diffraction shellResolution: 1.5→1.6 Å / Fourier space coverage: 98.6 % / Multiplicity: 7.4 / Num. of structure factors: 289 / Phase residual: 38 °
EM diffraction statsFourier space coverage: 99.3 % / High resolution: 1.5 Å / Num. of intensities measured: 12605 / Num. of structure factors: 1738
Phase error rejection criteria: Phases were determined by molecular replacement and cross-validated by free R-value during refinement
Rmerge: 20.4

-
Processing

EM software
IDNameVersionCategory
8PHENIX(1.20.1_4487: ???)model refinement
9MOLREPmolecular replacement
Image processingDetails: Images were gain corrected and binned at 4k x 4k pixels. A pedestal of 1 pixel value was applied to each pixel during conversion to SMV file format.
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 26.47 Å / B: 26.47 Å / C: 27.29 Å / Space group name: P4(3)2(1)2 / Space group num: 96
CTF correctionType: NONE
3D reconstructionResolution: 1.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 13.09
Atomic model buildingPDB-ID: 1E9W

1e9w


Accession code: 1E9W / Source name: PDB / Type: experimental model
RefinementResolution: 1.5→18.72 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 174 10.01 %
Rwork0.2013 --
obs0.2026 1738 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.015113
ELECTRON CRYSTALLOGRAPHYf_angle_d4.4153
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d22.85227
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.05715
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.04920
LS refinement shellResolution: 1.5→18.72 Å
RfactorNum. reflection% reflection
Rfree0.2167 174 -
Rwork0.2013 1564 -
obs--100 %

+
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