[English] 日本語
Yorodumi
- PDB-6q6h: Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q6h
TitleCryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, the D2 box class
Components
  • (Anaphase-promoting complex subunit ...) x 10
  • (Cell division cycle protein ...Cell cycle) x 4
  • Apc1
  • Cyclin-A2
KeywordsCELL CYCLE / spindle assembly checkpoint / anaphase-promoting complex / cyclin / ubiquitination
Function / homology
Function and homology information


metaphase/anaphase transition of cell cycle / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / regulation of mitotic cell cycle spindle assembly checkpoint / regulation of meiotic nuclear division / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex ...metaphase/anaphase transition of cell cycle / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / regulation of mitotic cell cycle spindle assembly checkpoint / regulation of meiotic nuclear division / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Phosphorylation of Emi1 / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / cell cycle G1/S phase transition / anaphase-promoting complex-dependent catabolic process / regulation of meiotic cell cycle / positive regulation of mitotic metaphase/anaphase transition / cellular response to luteinizing hormone stimulus / metaphase/anaphase transition of mitotic cell cycle / regulation of exit from mitosis / positive regulation of synaptic plasticity / Phosphorylation of the APC/C / anaphase-promoting complex binding / mitotic cell cycle phase transition / ubiquitin ligase activator activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / positive regulation of ubiquitin protein ligase activity / protein K11-linked ubiquitination / cellular response to leptin stimulus / male pronucleus / enzyme-substrate adaptor activity / female pronucleus / regulation of mitotic metaphase/anaphase transition / response to glucagon / cellular response to cocaine / positive regulation of dendrite morphogenesis / ubiquitin-ubiquitin ligase activity / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / mitotic sister chromatid cohesion / positive regulation of DNA biosynthetic process / mitotic metaphase chromosome alignment / cochlea development / mitotic spindle assembly checkpoint signaling / cellular response to platelet-derived growth factor stimulus / cyclin A2-CDK2 complex / G2 Phase / p53-Dependent G1 DNA Damage Response / regulation of mitotic cell cycle / cullin family protein binding / regulation of DNA replication / Regulation of APC/C activators between G1/S and early anaphase / Telomere Extension By Telomerase / mitotic spindle assembly / G0 and Early G1 / Transcriptional Regulation by VENTX / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / positive regulation of axon extension / animal organ regeneration / heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Cyclin A:Cdk2-associated events at S phase entry / Resolution of Sister Chromatid Cohesion / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / nuclear periphery / post-translational protein modification / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / cellular response to estradiol stimulus / Assembly of the pre-replicative complex / RHO GTPases Activate Formins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / brain development / G1/S transition of mitotic cell cycle / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / DNA Damage/Telomere Stress Induced Senescence / spindle / mitotic spindle / kinetochore / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / spindle pole / Orc1 removal from chromatin / ubiquitin-protein transferase activity / Separation of Sister Chromatids / ubiquitin protein ligase activity / microtubule cytoskeleton / positive regulation of fibroblast proliferation / G2/M transition of mitotic cell cycle / Antigen processing: Ubiquitination & Proteasome degradation
Similarity search - Function
: / Anaphase-promoting complex subunit 15 / The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 4, metazoa / : / Anaphase-promoting complex subunit 5, N-terminal domain / Anaphase-promoting complex subunit 1, C-terminal / Anaphase-promoting complex subunit 1, middle domain / : ...: / Anaphase-promoting complex subunit 15 / The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 4, metazoa / : / Anaphase-promoting complex subunit 5, N-terminal domain / 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 16 / Anaphase-promoting complex, subunit 16 / Cdc23 / Apc13 / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 4 long domain / Anaphase promoting complex subunit 8 / Cdc23 / Apc13p protein / Anaphase-promoting complex, cyclosome, subunit 4 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 5 domain / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 5 / 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 / Anaphase-promoting complex, cyclosome, subunit 3 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / TPR repeat / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Tetratricopeptide repeat / Cyclin, C-terminal domain / Cyclin_C / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Tetratricopeptide repeat / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Cyclin, N-terminal / Cyclin, N-terminal domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Galactose-binding domain-like / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Armadillo-like helical / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / Jelly Rolls / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / Sandwich / 2-Layer Sandwich / Mainly Beta
Similarity search - Domain/homology
Cyclin-A2 / Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 15 / Cell division cycle protein 20 homolog / 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 ...Cyclin-A2 / Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 15 / Cell division cycle protein 20 homolog / 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 / Anaphase-promoting complex subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang, S. / Barford, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1021/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Cyclin A2 degradation during the spindle assembly checkpoint requires multiple binding modes to the APC/C.
Authors: Suyang Zhang / Thomas Tischer / David Barford /
Abstract: The anaphase-promoting complex/cyclosome (APC/C) orchestrates cell cycle progression by controlling the temporal degradation of specific cell cycle regulators. Although cyclin A2 and cyclin B1 are ...The anaphase-promoting complex/cyclosome (APC/C) orchestrates cell cycle progression by controlling the temporal degradation of specific cell cycle regulators. Although cyclin A2 and cyclin B1 are both targeted for degradation by the APC/C, during the spindle assembly checkpoint (SAC), the mitotic checkpoint complex (MCC) represses APC/C's activity towards cyclin B1, but not cyclin A2. Through structural, biochemical and in vivo analysis, we identify a non-canonical D box (D2) that is critical for cyclin A2 ubiquitination in vitro and degradation in vivo. During the SAC, cyclin A2 is ubiquitinated by the repressed APC/C-MCC, mediated by the cooperative engagement of its KEN and D2 boxes, ABBA motif, and the cofactor Cks. Once the SAC is satisfied, cyclin A2 binds APC/C-Cdc20 through two mutually exclusive binding modes, resulting in differential ubiquitination efficiency. Our findings reveal that a single substrate can engage an E3 ligase through multiple binding modes, affecting its degradation timing and efficiency.
History
DepositionDec 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4466
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Anaphase-promoting complex subunit 10
D: Anaphase-promoting complex subunit 15
A: Apc1
N: Anaphase-promoting complex subunit 2
I: Anaphase-promoting complex subunit 4
O: Anaphase-promoting complex subunit 5
K: Cell division cycle protein 16 homolog
C: Anaphase-promoting complex subunit 11
G: Anaphase-promoting complex subunit CDC26
W: Anaphase-promoting complex subunit CDC26
M: Anaphase-promoting complex subunit 13
H: Anaphase-promoting complex subunit 16
J: Cell division cycle protein 27 homolog
P: Cell division cycle protein 27 homolog
Q: Cell division cycle protein 16 homolog
Y: Anaphase-promoting complex subunit 7
U: Cell division cycle protein 23 homolog
V: Cell division cycle protein 23 homolog
Z: Anaphase-promoting complex subunit 7
R: Cell division cycle protein 20 homolog
S: Cyclin-A2


Theoretical massNumber of molelcules
Total (without water)1,262,16221
Polymers1,262,16221
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area112190 Å2
ΔGint-554 kcal/mol
Surface area333360 Å2
MethodPISA

-
Components

-
Anaphase-promoting complex subunit ... , 10 types, 12 molecules LDNIOCGWMHYZ

#1: Protein Anaphase-promoting complex subunit 10 / / APC10 / Cyclosome subunit 10


Mass: 21282.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC10, APC10 / Production host: unidentified baculovirus / References: UniProt: Q9UM13
#2: Protein Anaphase-promoting complex subunit 15 / / APC15


Mass: 14286.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC15, C11orf51, HSPC020 / Production host: unidentified baculovirus / References: UniProt: P60006
#4: Protein Anaphase-promoting complex subunit 2 / / APC2 / Cyclosome subunit 2


Mass: 93938.977 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: unidentified baculovirus / References: UniProt: Q9UJX6
#5: Protein Anaphase-promoting complex subunit 4 / / APC4 / Cyclosome subunit 4


Mass: 92219.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC4, APC4 / Production host: unidentified baculovirus / References: UniProt: Q9UJX5
#6: Protein Anaphase-promoting complex subunit 5 / / APC5 / Cyclosome subunit 5


Mass: 85179.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC5, APC5 / Production host: unidentified baculovirus / References: UniProt: Q9UJX4
#8: 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: unidentified baculovirus / References: UniProt: Q9NYG5
#9: Protein Anaphase-promoting complex subunit CDC26 / / Anaphase-promoting complex subunit 12 / APC12 / Cell division cycle protein 26 homolog


Mass: 9793.999 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC26, ANAPC12, C9orf17 / Production host: unidentified baculovirus / References: UniProt: Q8NHZ8
#10: 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: unidentified baculovirus / References: UniProt: Q9BS18
#11: Protein Anaphase-promoting complex subunit 16 / / APC16 / Cyclosome subunit 16


Mass: 11677.995 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: unidentified baculovirus / References: UniProt: Q96DE5
#13: Protein Anaphase-promoting complex subunit 7 / / APC7 / Cyclosome subunit 7


Mass: 66929.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC7, APC7 / Production host: unidentified baculovirus / References: UniProt: Q9UJX3

-
Protein , 2 types, 2 molecules AS

#3: Protein Apc1


Mass: 207240.234 Da / Num. of mol.: 1 / Mutation: deletion of residues 307-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified baculovirus / References: UniProt: Q9H1A4*PLUS
#16: Protein Cyclin-A2 / Cyclin-A / Cyclin A


Mass: 44427.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Production host: Escherichia coli (E. coli) / References: UniProt: P20248

-
Cell division cycle protein ... , 4 types, 7 molecules KQJPUVR

#7: Protein Cell division cycle protein 16 homolog / Cell cycle / Anaphase-promoting complex subunit 6 / APC6 / CDC16 homolog / CDC16Hs / Cyclosome subunit 6


Mass: 71747.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC16, ANAPC6 / Production host: unidentified baculovirus / References: UniProt: Q13042
#12: Protein Cell division cycle protein 27 homolog / Cell cycle / Anaphase-promoting complex subunit 3 / APC3 / CDC27 homolog / CDC27Hs / H-NUC


Mass: 91973.125 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: unidentified baculovirus / References: UniProt: P30260
#14: Protein Cell division cycle protein 23 homolog / Cell cycle / Anaphase-promoting complex subunit 8 / APC8 / Cyclosome subunit 8


Mass: 68921.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC23, ANAPC8 / Production host: unidentified baculovirus / References: UniProt: Q9UJX2
#15: Protein Cell division cycle protein 20 homolog / Cell cycle / p55CDC


Mass: 54796.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC20 / Production host: unidentified baculovirus / References: UniProt: Q12834

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, the D2 box classCOMPLEXall0MULTIPLE SOURCES
2Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, the D2 box classCOMPLEX#1-#151RECOMBINANT
3Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, the D2 box classCOMPLEX#161RECOMBINANT
Molecular weightValue: 1.3 MDa
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22unidentified baculovirus10469
33Esacherichia coli (E. coli)562
Buffer solutionpH: 8 / Details: 20mM Hepes, 150mM NaCl, 0.5mM TCEP
SpecimenConc.: 0.15 mg/ml / Embedding 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 28 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM softwareName: RELION / Version: 3 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117044 / 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