[English] 日本語
Yorodumi
- EMDB-53836: Cryo-EM structure of the E3 ligase HECTD3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53836
TitleCryo-EM structure of the E3 ligase HECTD3
Map dataMain map after non-uniform refinement
Sample
  • Complex: HECTD3 ligase
    • Protein or peptide: E3 ubiquitin-protein ligase HECTD3
KeywordsE3-ligase / ubiquitin / ubiquitination / HECT-ligase / LIGASE
Function / homology
Function and homology information


HECT-type E3 ubiquitin transferase / syntaxin binding / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / perinuclear region of cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase HECTD3 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase HECTD3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.06 Å
AuthorsEsposito D / Huber J / Maslen S / Rittinger K
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
The Francis Crick InstituteCC2075, CC2000 United Kingdom
UK Research and Innovation (UKRI)CC2075, CC2000 United Kingdom
Cancer Research UKCC2075, CC2000 United Kingdom
Wellcome TrustCC2075, CC2000 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 16, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53836.png

Downloads & links

-
Map

FileDownload / File: emd_53836.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map after non-uniform refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 296 pix.
= 281.2 Å		0.95 Å/pix.
x 296 pix.
= 281.2 Å		0.95 Å/pix.
x 296 pix.
= 281.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.06343789 - 0.20457971
Average (Standard dev.)0.00033313685 (±0.0074399826)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 281.19998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_53836_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Locally filtered map using a local resolution map

Fileemd_53836_additional_1.map
AnnotationLocally filtered map using a local resolution map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: EMReady sharpened map

Fileemd_53836_additional_2.map
AnnotationEMReady sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map

Fileemd_53836_half_map_1.map
AnnotationHalf-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map

Fileemd_53836_half_map_2.map
AnnotationHalf-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HECTD3 ligase

EntireName: HECTD3 ligase
Components
  • Complex: HECTD3 ligase
    • Protein or peptide: E3 ubiquitin-protein ligase HECTD3

-
Supramolecule #1: HECTD3 ligase

SupramoleculeName: HECTD3 ligase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: E3 ubiquitin-protein ligase HECTD3

MacromoleculeName: E3 ubiquitin-protein ligase HECTD3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.441055 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPGMAGPGPG AVLESPRQLL GRVRFLAEAA RSLRAGRPLP AALAFVPREV LYKLYKDPAG PSRVLLPVWE AEGLGLRVGA AGPAPGTGS GPLRAARDSI ELRRGACVRT TGEELCNGHG LWVKLTKEQL AEHLGDCGLQ EGWLLVCRPA EGGARLVPID T PNHLQRQQ ...String:
GPGMAGPGPG AVLESPRQLL GRVRFLAEAA RSLRAGRPLP AALAFVPREV LYKLYKDPAG PSRVLLPVWE AEGLGLRVGA AGPAPGTGS GPLRAARDSI ELRRGACVRT TGEELCNGHG LWVKLTKEQL AEHLGDCGLQ EGWLLVCRPA EGGARLVPID T PNHLQRQQ QLFGVDYRPV LRWEQVVDLT YSHRLGSRPQ PAEAYAEAVQ RLLYVPPTWT YECDEDLIHF LYDHLGKEDE NL GSVKQYV ESIDVSSYTE EFNVSCLTDS NADTYWESDG SQCQHWVRLT MKKGTIVKKL LLTVDTTDDN FMPKRVVVYG GEG DNLKKL SDVSIDETLI GDVCVLEDMT VHLPIIEIRI VECRDDGIDV RLRGVKIKSS RQRELGLNAD LFQPTSLVRY PRLE GTDPE VLYRRAVLLQ RFIKILDSVL HHLVPAWDHT LGTFSEIKQV KQFLLLSRQR PGLVAQCLRD SESSKPSFMP RLYIN RRLA MEHRACPSRD PACKNAVFTQ VYEGLKPSDK YEKPLDYRWP MRYDQWWECK FIAEGIIDQG GGFRDSLADM SEELCP SSA DTPVPLPFFV RTANQGNGTG EARDMYVPNP SCRDFAKYEW IGQLMGAALR GKEFLVLALP GFVWKQLSGE EVSWSKD FP AVDSVLVKLL EVMEGMDKET FEFKFGKELT FTTVLSDQQV VELIPGGAGI VVGYGDRSRF IQLVQKARLE ESKEQVAA M QAGLLKVVPQ AVLDLLTWQE LEKKVCGDPE VTVDALRKLT RFEDFEPSDS RVQYFWEALN NFTNEDRSRF LRFVTGRSR LPARIYIYPD KLGYETTDAL PESSTCSSTL FLPHYASAKV CEEKLRYAAY NCVAIDTDMS PWEE

UniProtKB: E3 ubiquitin-protein ligase HECTD3

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.92 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
50.0 mMNa-PPhosphate
200.0 mMNaClSodium Chloride
0.5 mMTCEP
2.0 %Glycerol
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 25560 / Average electron dose: 40.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3537942
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 91869
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

t447


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-9r8t:
Cryo-EM structure of the E3 ligase HECTD3

+
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