[English] 日本語
Yorodumi
- PDB-8tar: APC/C-CDH1-UBE2C-Ubiquitin-CyclinB-NTD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tar
TitleAPC/C-CDH1-UBE2C-Ubiquitin-CyclinB-NTD
Components
  • (Anaphase-promoting complex subunit ...) x 11
  • (Cell division cycle protein ...) x 3
  • Fizzy-related protein homolog
  • G2/mitotic-specific cyclin-B1
  • Ubiquitin-conjugating enzyme E2 C
KeywordsTRANSFERASE / E3 RING Ligase / Ubiquitin Ligase / LIGASE
Function / homology
Function and homology information


response to DDT / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / regulation of chromosome condensation / positive regulation of anaphase-promoting complex-dependent catabolic process / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina ...response to DDT / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / regulation of chromosome condensation / positive regulation of anaphase-promoting complex-dependent catabolic process / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / positive regulation of attachment of spindle microtubules to kinetochore / positive regulation of exit from mitosis / positive regulation of mRNA 3'-end processing / MASTL Facilitates Mitotic Progression / regulation of meiotic nuclear division / free ubiquitin chain polymerization / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of mitotic cell cycle spindle assembly checkpoint / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Activation of NIMA Kinases NEK9, NEK6, NEK7 / positive regulation of synaptic plasticity / Phosphorylation of Emi1 / patched binding / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / protein branched polyubiquitination / metaphase/anaphase transition of mitotic cell cycle / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / lens fiber cell differentiation / Transcriptional regulation by RUNX2 / Phosphorylation of the APC/C / regulation of exit from mitosis / Nuclear Pore Complex (NPC) Disassembly / anaphase-promoting complex binding / tissue regeneration / outer kinetochore / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of mitotic metaphase/anaphase transition / positive regulation of dendrite morphogenesis / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / exit from mitosis / Initiation of Nuclear Envelope (NE) Reformation / Polo-like kinase mediated events / cyclin-dependent protein serine/threonine kinase activator activity / protein K11-linked ubiquitination / Golgi Cisternae Pericentriolar Stack Reorganization / cellular response to fatty acid / digestive tract development / Condensation of Prometaphase Chromosomes / oocyte maturation / regulation of mitotic metaphase/anaphase transition / cyclin-dependent protein serine/threonine kinase regulator activity / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / mitotic metaphase chromosome alignment / mitotic G2 DNA damage checkpoint signaling / microtubule organizing center / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin-like protein ligase binding / cullin family protein binding / Transcriptional Regulation by VENTX / negative regulation of cellular senescence / ubiquitin ligase complex / enzyme-substrate adaptor activity / response to mechanical stimulus / ubiquitin-like ligase-substrate adaptor activity / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of axon extension / protein K48-linked ubiquitination / APC-Cdc20 mediated degradation of Nek2A / heterochromatin / Cyclin A/B1/B2 associated events during G2/M transition / intercellular bridge / Cyclin A:Cdk2-associated events at S phase entry / Nuclear events stimulated by ALK signaling in cancer / positive regulation of cardiac muscle cell proliferation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of G2/M transition of mitotic cell cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / positive regulation of mitotic cell cycle / nuclear periphery / SCF-beta-TrCP mediated degradation of Emi1 / regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / Assembly of the pre-replicative complex / Condensation of Prophase Chromosomes / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / mitotic spindle organization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / cellular response to iron(III) ion / CDK-mediated phosphorylation and removal of Cdc6
Similarity search - Function
: / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 15 / : / CDC20/Fizzy WD40 domain / The WD repeat Cdc20/Fizzy family / : / APC4, WD40 domain C-terminal half / Anaphase-promoting complex subunit 4, metazoa / Anaphase-promoting complex subunit 1, C-terminal ...: / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 15 / : / CDC20/Fizzy WD40 domain / The WD repeat Cdc20/Fizzy family / : / APC4, WD40 domain C-terminal half / Anaphase-promoting complex subunit 4, metazoa / Anaphase-promoting complex subunit 1, C-terminal / Anaphase-promoting complex subunit 1, middle domain / : / : / : / Anaphase-promoting complex subunit 1 WD40 beta-propeller domain / Anaphase-promoting complex sub unit 1 C-terminal domain / Anaphase-promoting complex subunit 1 middle domain / APC1 beta sandwich domain / Anaphase-promoting complex subunit 5, N-terminal domain / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex, subunit 16 / Cdc23 / Apc13 / Anaphase promoting complex subunit 8 / Cdc23 / Apc13p protein / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 4 long domain / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 5 domain / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex, cyclosome, subunit 4 / Anaphase-promoting complex subunit APC10/Doc1 / Anaphase-promoting complex, subunit CDC26 / Anaphase-promoting complex APC subunit CDC26 / Anaphase-promoting complex subunit 11, RING-H2 finger / Anaphase-promoting complex subunit 11 RING-H2 finger / Anaphase-promoting complex subunit 2, C-terminal / Anaphase-promoting complex subunit 2 / Anaphase promoting complex (APC) subunit 2 / Anaphase promoting complex (APC) subunit 2 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / Anaphase-promoting complex, cyclosome, subunit 3 / TPR repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / : / Cyclin, C-terminal domain / Tetratricopeptide repeat / : / Cyclins signature. / Cyclin / : / : / Cyclin, C-terminal domain / Cyclin_C / Cullin / Tetratricopeptide repeat / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Tetratricopeptide repeat / Cyclin, N-terminal / Cyclin, N-terminal domain / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Tetratricopeptide repeat / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Ubiquitin-conjugating enzyme/RWD-like / Cyclin-like superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 C / G2/mitotic-specific cyclin-B1 / Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 15 / Cell division cycle protein 16 homolog / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 11 ...Ubiquitin-conjugating enzyme E2 C / G2/mitotic-specific cyclin-B1 / Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 15 / Cell division cycle protein 16 homolog / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 11 / Cell division cycle protein 23 homolog / Anaphase-promoting complex subunit 7 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 2 / Fizzy-related protein homolog / Anaphase-promoting complex subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsBodrug, T. / Welsh, K.A. / Bolhuis, D.L. / Paulakonis, E. / Martinez-Chacin, R.C. / Liu, B. / Pinkin, N. / Bonacci, T. / Cui, L. / Xu, P. ...Bodrug, T. / Welsh, K.A. / Bolhuis, D.L. / Paulakonis, E. / Martinez-Chacin, R.C. / Liu, B. / Pinkin, N. / Bonacci, T. / Cui, L. / Xu, P. / Roscow, O. / Amann, S.J. / Grishkovskaya, I. / Emanuele, M.J. / Harrison, J.S. / Steimel, J.P. / Hahn, K.M. / Zhang, W. / Zhong, E. / Haselbach, D. / Brown, N.G.
Funding support United States, Austria, 4items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)T32GM008570 United States
Vienna Science and Technology Fund (WWTF)WWTF-LS19-029 Austria
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R35GM128855 United States
National Science Foundation (NSF, United States)DGE-1650116 United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Time-resolved cryo-EM (TR-EM) analysis of substrate polyubiquitination by the RING E3 anaphase-promoting complex/cyclosome (APC/C).
Authors: Tatyana Bodrug / Kaeli A Welsh / Derek L Bolhuis / Ethan Paulаkonis / Raquel C Martinez-Chacin / Bei Liu / Nicholas Pinkin / Thomas Bonacci / Liying Cui / Pengning Xu / Olivia Roscow / ...Authors: Tatyana Bodrug / Kaeli A Welsh / Derek L Bolhuis / Ethan Paulаkonis / Raquel C Martinez-Chacin / Bei Liu / Nicholas Pinkin / Thomas Bonacci / Liying Cui / Pengning Xu / Olivia Roscow / Sascha Josef Amann / Irina Grishkovskaya / Michael J Emanuele / Joseph S Harrison / Joshua P Steimel / Klaus M Hahn / Wei Zhang / Ellen D Zhong / David Haselbach / Nicholas G Brown /
Abstract: Substrate polyubiquitination drives a myriad of cellular processes, including the cell cycle, apoptosis and immune responses. Polyubiquitination is highly dynamic, and obtaining mechanistic insight ...Substrate polyubiquitination drives a myriad of cellular processes, including the cell cycle, apoptosis and immune responses. Polyubiquitination is highly dynamic, and obtaining mechanistic insight has thus far required artificially trapped structures to stabilize specific steps along the enzymatic process. So far, how any ubiquitin ligase builds a proteasomal degradation signal, which is canonically regarded as four or more ubiquitins, remains unclear. Here we present time-resolved cryogenic electron microscopy studies of the 1.2 MDa E3 ubiquitin ligase, known as the anaphase-promoting complex/cyclosome (APC/C), and its E2 co-enzymes (UBE2C/UBCH10 and UBE2S) during substrate polyubiquitination. Using cryoDRGN (Deep Reconstructing Generative Networks), a neural network-based approach, we reconstruct the conformational changes undergone by the human APC/C during polyubiquitination, directly visualize an active E3-E2 pair modifying its substrate, and identify unexpected interactions between multiple ubiquitins with parts of the APC/C machinery, including its coactivator CDH1. Together, we demonstrate how modification of substrates with nascent ubiquitin chains helps to potentiate processive substrate polyubiquitination, allowing us to model how a ubiquitin ligase builds a proteasomal degradation signal.
History
DepositionJun 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Anaphase-promoting complex subunit 1
B: G2/mitotic-specific cyclin-B1
C: Anaphase-promoting complex subunit 11
D: Anaphase-promoting complex subunit 15
G: Anaphase-promoting complex subunit CDC26
H: Anaphase-promoting complex subunit 16
I: Anaphase-promoting complex subunit 4
J: Cell division cycle protein 27 homolog
K: Cell division cycle protein 16 homolog
L: Anaphase-promoting complex subunit 10
M: Anaphase-promoting complex subunit 13
N: Anaphase-promoting complex subunit 2
O: Anaphase-promoting complex subunit 5
P: Cell division cycle protein 27 homolog
Q: Ubiquitin-conjugating enzyme E2 C
R: Fizzy-related protein homolog
S: Cell division cycle protein 16 homolog
U: Cell division cycle protein 23 homolog
V: Cell division cycle protein 23 homolog
W: Anaphase-promoting complex subunit CDC26
Y: Anaphase-promoting complex subunit 7
Z: Anaphase-promoting complex subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,228,92226
Polymers1,228,66022
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Anaphase-promoting complex subunit ... , 11 types, 13 molecules ACDGWHILMNOYZ

#1: Protein Anaphase-promoting complex subunit 1


Mass: 217566.141 Da / Num. of mol.: 1
Mutation: S202E, S286E, T291E, S313E, T316E, S317E, S334E, S341E, S343E, S355E, S362E, S372E, S377E, T537E, S547E, S555E, S569E, S688E, S699E, S916E, S1347E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H1A4
#3: Protein Anaphase-promoting complex subunit 11 / APC11 / Cyclosome subunit 11 / Hepatocellular carcinoma-associated RING finger protein


Mass: 9854.647 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC11, HSPC214 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NYG5
#4: Protein Anaphase-promoting complex subunit 15


Mass: 6556.302 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC15 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P60006
#5: Protein Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 12 / APC12 / Cell division cycle protein 26 homolog


Mass: 9920.108 Da / Num. of mol.: 2 / Mutation: S51E, S52E, S82E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC26, ANAPC12, C9orf17 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NHZ8
#6: Protein Anaphase-promoting complex subunit 16 / APC16 / Cyclosome subunit 16


Mass: 6764.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC16, C10orf104, CENP-27 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96DE5
#7: Protein Anaphase-promoting complex subunit 4 / APC4 / Cyclosome subunit 4


Mass: 92303.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC4, APC4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UJX5
#10: Protein Anaphase-promoting complex subunit 10 / APC10 / Cyclosome subunit 10


Mass: 21310.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC10, APC10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UM13
#11: Protein Anaphase-promoting complex subunit 13 / APC13 / Cyclosome subunit 13


Mass: 8528.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC13 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BS18
#12: Protein Anaphase-promoting complex subunit 2 / APC2 / Cyclosome subunit 2


Mass: 94149.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC2, APC2, KIAA1406 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UJX6
#13: Protein Anaphase-promoting complex subunit 5 / APC5 / Cyclosome subunit 5


Mass: 85445.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC5, APC5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UJX4
#17: Protein Anaphase-promoting complex subunit 7 / APC7 / Cyclosome subunit 7


Mass: 63204.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC7, APC7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UJX3

-
Cell division cycle protein ... , 3 types, 6 molecules JPKSUV

#8: Protein Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 3 / APC3 / CDC27 homolog / CDC27Hs / H-NUC


Mass: 92519.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC27, ANAPC3, D0S1430E, D17S978E / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30260
#9: Protein Cell division cycle protein 16 homolog / Anaphase-promoting complex subunit 6 / APC6 / CDC16 homolog / CDC16Hs / Cyclosome subunit 6


Mass: 71929.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC16, ANAPC6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13042
#16: Protein Cell division cycle protein 23 homolog / Anaphase-promoting complex subunit 8 / APC8 / Cyclosome subunit 8


Mass: 69075.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC23, ANAPC8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UJX2

-
Protein , 2 types, 2 molecules QR

#14: Protein Ubiquitin-conjugating enzyme E2 C


Mass: 16346.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2C / Production host: Escherichia coli (E. coli) / References: UniProt: O00762
#15: Protein Fizzy-related protein homolog


Mass: 55253.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UM11

-
Protein/peptide / Non-polymers , 2 types, 5 molecules B

#18: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#2: Protein/peptide G2/mitotic-specific cyclin-B1


Mass: 1284.467 Da / Num. of mol.: 1 / Fragment: NTD (residues 39-50)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNB1, CCNB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14635

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Anaphase-promoting complex/cyclosome in complex with CHD1, UBE2C, and Cyclin-B
Type: COMPLEX / Entity ID: #1-#17 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 42 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 661289 / Symmetry type: POINT

+
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