[English] 日本語
Yorodumi
- EMDB-34453: Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a tetrameric complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34453
TitleCryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a tetrameric complex
Map data
Sample
  • Complex: KBTBD2-CUL3-Rbx1-p85a tetrameric complex
    • Protein or peptide: Cullin-3
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: Kelch repeat and BTB domain-containing protein 2
    • Protein or peptide: Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Ligand: ZINC ION
Keywordsligase / complex
Function / homology
Function and homology information


positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / nuclear protein quality control by the ubiquitin-proteasome system / polar microtubule / COPII vesicle coating / phosphatidylinositol kinase activity ...positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / nuclear protein quality control by the ubiquitin-proteasome system / polar microtubule / COPII vesicle coating / phosphatidylinositol kinase activity / anaphase-promoting complex-dependent catabolic process / phosphatidylinositol 3-kinase regulator activity / positive regulation of focal adhesion disassembly / phosphatidylinositol 3-kinase activator activity / IRS-mediated signalling / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / interleukin-18-mediated signaling pathway / T follicular helper cell differentiation / myeloid leukocyte migration / phosphatidylinositol 3-kinase complex / PI3K events in ERBB4 signaling / embryonic cleavage / regulation protein catabolic process at postsynapse / cullin-RING-type E3 NEDD8 transferase / RHOBTB3 ATPase cycle / NEDD8 transferase activity / phosphatidylinositol 3-kinase regulatory subunit binding / cell projection organization / neurotrophin TRKA receptor binding / cullin-RING ubiquitin ligase complex / positive regulation of mitotic metaphase/anaphase transition / Activated NTRK2 signals through PI3K / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / cis-Golgi network / ErbB-3 class receptor binding / Activated NTRK3 signals through PI3K / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / transmembrane receptor protein tyrosine kinase adaptor activity / stem cell division / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / kinase activator activity / Signaling by cytosolic FGFR1 fusion mutants / positive regulation of protein autoubiquitination / RHOD GTPase cycle / RHOF GTPase cycle / protein neddylation / phosphatidylinositol 3-kinase complex, class IA / Nephrin family interactions / Notch binding / Signaling by LTK in cancer / Regulation of T cell activation by CD28 family / positive regulation of leukocyte migration / NEDD8 ligase activity / fibroblast apoptotic process / enzyme-substrate adaptor activity / Signaling by LTK / MET activates PI3K/AKT signaling / PI3K/AKT activation / growth hormone receptor signaling pathway / RHOBTB1 GTPase cycle / negative regulation of response to oxidative stress / RND1 GTPase cycle / Cul5-RING ubiquitin ligase complex / negative regulation of stress fiber assembly / positive regulation of filopodium assembly / RND2 GTPase cycle / RND3 GTPase cycle / insulin binding / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / Signaling by ALK / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / GP1b-IX-V activation signalling / RHOB GTPase cycle / Cul3-RING ubiquitin ligase complex / natural killer cell mediated cytotoxicity / RHOV GTPase cycle / mitotic metaphase chromosome alignment / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / PI-3K cascade:FGFR2 / stress fiber assembly / PI-3K cascade:FGFR4 / negative regulation of Rho protein signal transduction / PI-3K cascade:FGFR1 / Prolactin receptor signaling / RHOC GTPase cycle / positive regulation of cytokinesis / RHOJ GTPase cycle / intracellular glucose homeostasis / negative regulation of osteoclast differentiation / phosphatidylinositol phosphate biosynthetic process / Synthesis of PIPs at the plasma membrane
Similarity search - Function
Kelch repeat and BTB domain-containing protein 2 / : / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain ...Kelch repeat and BTB domain-containing protein 2 / : / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Cullin protein neddylation domain / Kelch / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Kelch motif / Kelch repeat type 1 / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Kelch-type beta propeller / Rho GTPase activation protein / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Zinc finger RING-type profile. / Zinc finger, RING-type / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Phosphatidylinositol 3-kinase regulatory subunit alpha / E3 ubiquitin-protein ligase RBX1 / Cullin-3 / Kelch repeat and BTB domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.52 Å
AuthorsHu Y / Mao Q / Chen Z / Sun L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81900729 China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Dynamic molecular architecture and substrate recruitment of cullin3-RING E3 ligase CRL3.
Authors: Yuxia Hu / Zhao Zhang / Qiyu Mao / Xiang Zhang / Aihua Hao / Yu Xun / Yeda Wang / Lin Han / Wuqiang Zhan / Qianying Liu / Yue Yin / Chao Peng / Eva Marie Y Moresco / Zhenguo Chen / Bruce Beutler / Lei Sun /
Abstract: Phosphatidylinositol 3-kinase α, a heterodimer of catalytic p110α and one of five regulatory subunits, mediates insulin- and insulin like growth factor-signaling and, frequently, oncogenesis. ...Phosphatidylinositol 3-kinase α, a heterodimer of catalytic p110α and one of five regulatory subunits, mediates insulin- and insulin like growth factor-signaling and, frequently, oncogenesis. Cellular levels of the regulatory p85α subunit are tightly controlled by regulated proteasomal degradation. In adipose tissue and growth plates, failure of K48-linked p85α ubiquitination causes diabetes, lipodystrophy and dwarfism in mice, as in humans with SHORT syndrome. Here we elucidated the structures of the key ubiquitin ligase complexes regulating p85α availability. Specificity is provided by the substrate receptor KBTBD2, which recruits p85α to the cullin3-RING E3 ubiquitin ligase (CRL3). CRL3 forms multimers, which disassemble into dimers upon substrate binding (CRL3-p85α) and/or neddylation by the activator NEDD8 (CRL3~N8), leading to p85α ubiquitination and degradation. Deactivation involves dissociation of NEDD8 mediated by the COP9 signalosome and displacement of KBTBD2 by the inhibitor CAND1. The hereby identified structural basis of p85α regulation opens the way to better understanding disturbances of glucose regulation, growth and cancer.
History
DepositionOct 8, 2022-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_34453.png

Downloads & links

-
Map

FileDownload / File: emd_34453.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.66 Å/pix.
x 192 pix.
= 511.488 Å		2.66 Å/pix.
x 192 pix.
= 511.488 Å		2.66 Å/pix.
x 192 pix.
= 511.488 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.664 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.0013982126 - 1.6030204
Average (Standard dev.)0.0016076874 (±0.026238957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 511.488 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_34453_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34453_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : KBTBD2-CUL3-Rbx1-p85a tetrameric complex

EntireName: KBTBD2-CUL3-Rbx1-p85a tetrameric complex
Components
  • Complex: KBTBD2-CUL3-Rbx1-p85a tetrameric complex
    • Protein or peptide: Cullin-3
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: Kelch repeat and BTB domain-containing protein 2
    • Protein or peptide: Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Ligand: ZINC ION

-
Supramolecule #1: KBTBD2-CUL3-Rbx1-p85a tetrameric complex

SupramoleculeName: KBTBD2-CUL3-Rbx1-p85a tetrameric complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Cullin-3

MacromoleculeName: Cullin-3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.063328 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN AYTMVLHKHG EKLYTGLREV VTEHLINKV REDVLNSLNN NFLQTLNQAW NDHQTAMVMI RDILMYMDRV YVQQNNVENV YNLGLIIFRD QVVRYGCIRD H LRQTLLDM ...String:
MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN AYTMVLHKHG EKLYTGLREV VTEHLINKV REDVLNSLNN NFLQTLNQAW NDHQTAMVMI RDILMYMDRV YVQQNNVENV YNLGLIIFRD QVVRYGCIRD H LRQTLLDM IARERKGEVV DRGAIRNACQ MLMILGLEGR SVYEEDFEAP FLEMSAEFFQ MESQKFLAEN SASVYIKKVE AR INEEIER VMHCLDKSTE EPIVKVVERE LISKHMKTIV EMENSGLVHM LKNGKTEDLG CMYKLFSRVP NGLKTMCECM SSY LREQGK ALVSEEGEGK NPVDYIQGLL DLKSRFDRFL LESFNNDRLF KQTIAGDFEY FLNLNSRSPE YLSLFIDDKL KKGV KGLTE QEVETILDKA MVLFRFMQEK DVFERYYKQH LARRLLTNKS VSDDSEKNMI SKLKTECGCQ FTSKLEGMFR DMSIS NTTM DEFRQHLQAT GVSLGGVDLT VRVLTTGYWP TQSATPKCNI PPAPRHAFEI FRRFYLAKHS GRQLTLQHHM GSADLN ATF YGPVKKEDGS EVGVGGAQVT GSNTRKHILQ VSTFQMTILM LFNNREKYTF EEIQQETDIP ERELVRALQS LACGKPT QR VLTKEPKSKE IENGHIFTVN DQFTSKLHRV KIQTVAAKQG ESDPERKETR QKVDDDRKHE IEAAIVRIMK SRKKMQHN V LVAEVTQQLK ARFLPSPVVI KKRIEGLIER EYLARTPEDR KVYTYVA

UniProtKB: Cullin-3

-
Macromolecule #2: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.289977 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

-
Macromolecule #3: Kelch repeat and BTB domain-containing protein 2

MacromoleculeName: Kelch repeat and BTB domain-containing protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.431375 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSTQDERQIN TEYAVSLLEQ LKLFYEQQLF TDIVLIVEGT EFPCHKMVLA TCSSYFRAMF MSGLSESKQT HVHLRNVDAA TLQIIITYA YTGNLAMNDS TVEQLYETAC FLQVEDVLQR CREYLIKKIN AENCVRLLSF ADLFSCEELK QSAKRMVEHK F TAVYHQDA ...String:
MSTQDERQIN TEYAVSLLEQ LKLFYEQQLF TDIVLIVEGT EFPCHKMVLA TCSSYFRAMF MSGLSESKQT HVHLRNVDAA TLQIIITYA YTGNLAMNDS TVEQLYETAC FLQVEDVLQR CREYLIKKIN AENCVRLLSF ADLFSCEELK QSAKRMVEHK F TAVYHQDA FMQLSHDLLI DILSSDNLNV EKEETVREAA MLWLEYNTES RSQYLSSVLS QIRIDALSEV TQRAWFQGLP PN DKSVVVQ GLYKDMPKFF KPRLGMTKEE MMIFIEASSE NPCSLYSSVC YSPQAEKVYK LCSPPADLHK VGTVVTPDND IYI AGGQVP LKNTKTNHSK TSKLQTAFRT VNCFYWFDAQ QNTWFPKTPM LFVRIKPSLV CCEGYIYAIG GDSVGGELNR RTVE RYDTE KDEWTMVSPL PCAWQWSAAV VVHDCIYVMT LNLMYCYFPR SDSWVEMAMR QTSRSFASAA AFGDKIFYIG GLHIA TNSG IRLPSGTVDG SSVTVEIYDV NKNEWKMAAN IPAKRYSDPC VRAVVISNSL CVFMRETHLN ERAKYVTYQY DLELDR WSL RQHISERVLW DLGRDFRCTV GKLYPSCLEE SPWKPPTYLF STDGTEEFEL DGEMVALPPV

UniProtKB: Kelch repeat and BTB domain-containing protein 2

-
Macromolecule #4: Phosphatidylinositol 3-kinase regulatory subunit alpha

MacromoleculeName: Phosphatidylinositol 3-kinase regulatory subunit alpha
type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.710281 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSAEGYQYRA LYDYKKEREE DIDLHLGDIL TVNKGSLVAL GFSDGQEARP EEIGWLNGYN ETTGERGDFP GTYVEYIGRK KISPPTPKP RPPRPLPVAP GSSKTEADVE QQALTLPDLA EQFAPPDIAP PLLIKLVEAI EKKGLECSTL YRTQSSSNLA E LRQLLDCD ...String:
MSAEGYQYRA LYDYKKEREE DIDLHLGDIL TVNKGSLVAL GFSDGQEARP EEIGWLNGYN ETTGERGDFP GTYVEYIGRK KISPPTPKP RPPRPLPVAP GSSKTEADVE QQALTLPDLA EQFAPPDIAP PLLIKLVEAI EKKGLECSTL YRTQSSSNLA E LRQLLDCD TPSVDLEMID VHVLADAFKR YLLDLPNPVI PAAVYSEMIS LAPEVQSSEE YIQLLKKLIR SPSIPHQYWL TL QYLLKHF FKLSQTSSKN LLNARVLSEI FSPMLFRFSA ASSDNTENLI KVIEILISTE WNERQPAPAL PPKPPKPTTV ANN GMNNNM SLQDAEWYWG DISREEVNEK LRDTADGTFL VRDASTKMHG DYTLTLRKGG NNKLIKIFHR DGKYGFSDPL TFSS VVELI NHYRNESLAQ YNPKLDVKLL YPVSKYQQDQ VVKEDNIEAV GKKLHEYNTQ FQEKSREYDR LYEEYTRTSQ EIQMK RTAI EAFNETIKIF EEQCQTQERY SKEYIEKFKR EGNEKEIQRI MHNYDKLKSR ISEIIDSRRR LEEDLKKQAA EYREID KRM NSIKPDLIQL RKTRDQYLMW LTQKGVRQKK LNEWLGNENT EDQYSLVEDD EDLPHHDEKT WNVGSSNRNK AENLLRG KR DGTFLVRESS KQGCYACSVV VDGEVKHCVI NKTATGYGFA EPYNLYSSLK ELVLHYQHTS LVQHNDSLNV TLAYPVYA Q QRR

UniProtKB: Phosphatidylinositol 3-kinase regulatory subunit alpha

-
Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 12 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4ovu


Details: 7CIO
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 239068
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
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