[English] 日本語
Yorodumi
- EMDB-54194: ZZ1-SO2H-induced assembly of the YPEL5-CTLH E3 ligase and BRD4(BD... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54194
TitleZZ1-SO2H-induced assembly of the YPEL5-CTLH E3 ligase and BRD4(BD1) neosubstrate
Map data
Sample
  • Complex: ZZ1-SO2H-induced complex of YPEL5-CTLH E3 ligase and the first bromodomain (BD1) of BRD4
KeywordsE3 ubiquitin ligase / CTLH / GID / YPEL5 / Molecular Glue Degrader / Targeted Protein Degradation / LIGASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.77 Å
AuthorsChrustowicz J / Schulman BA
Funding support Germany, European Union, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHU 3196/1-1 Germany
European Research Council (ERC)UPSmeetMet, 101098161European Union
Max Planck Society Germany
CitationJournal: To Be Published
Title: Molecular Glue Prodrug Discovery Enabled by Targeted Degron Display
Authors: Zhuang Z / Woong Sub B / Chrustowicz J / Kozicka Z / Hinshaw SM / Li VL / Donovan KA / Sepic S / You I / Slabicki M / Fischer ES / Ebert BL / Schulman BA / Gray NS
History
DepositionJun 27, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54194.png

Downloads & links

-
Map

FileDownload / File: emd_54194.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.4 Å/pix.
x 128 pix.
= 435.802 Å		3.4 Å/pix.
x 128 pix.
= 435.802 Å		3.4 Å/pix.
x 128 pix.
= 435.802 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.4047 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0534
Minimum - Maximum-0.04178166 - 0.15721674
Average (Standard dev.)0.001955759 (±0.012213161)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 435.8016 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_54194_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_54194_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_54194_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ZZ1-SO2H-induced complex of YPEL5-CTLH E3 ligase and the first br...

EntireName: ZZ1-SO2H-induced complex of YPEL5-CTLH E3 ligase and the first bromodomain (BD1) of BRD4
Components
  • Complex: ZZ1-SO2H-induced complex of YPEL5-CTLH E3 ligase and the first bromodomain (BD1) of BRD4

-
Supramolecule #1: ZZ1-SO2H-induced complex of YPEL5-CTLH E3 ligase and the first br...

SupramoleculeName: ZZ1-SO2H-induced complex of YPEL5-CTLH E3 ligase and the first bromodomain (BD1) of BRD4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: The YPEL5-CTLH complex consists of TWA1, RANBP9, RMND5A, MAEA, WDR26, and YPEL5.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: NITROGEN
DetailsSample mixed with 0.1% beta-OG right before plunging

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 65.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 893388
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

18170

Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 2464
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