[English] 日本語
Yorodumi
- EMDB-10314: Tc holotoxin prepore TcdA1-TcdB2-TccC3-Cdc42 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10314
TitleTc holotoxin prepore TcdA1-TcdB2-TccC3-Cdc42
Map dataEM density map of ABC holotoxin formed by TcdA1 and TcdB2-TccC3-Cdc42
Sample
  • Complex: Complex of TcdA1 pentamer and TcdB2-TccC3-Cdc42
    • Protein or peptide: TcdA1
    • Protein or peptide: chimeric protein TcdB2-TccC3-cdc42
Function / homology
Function and homology information


GBD domain binding / submandibular salivary gland formation / Golgi transport complex / positive regulation of pinocytosis / actin filament branching / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole ...GBD domain binding / submandibular salivary gland formation / Golgi transport complex / positive regulation of pinocytosis / actin filament branching / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / organelle transport along microtubule / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / GTP-dependent protein binding / Inactivation of CDC42 and RAC1 / cardiac conduction system development / modulation by host of viral process / establishment of Golgi localization / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / thioesterase binding / regulation of modification of postsynaptic structure / regulation of stress fiber assembly / regulation of lamellipodium assembly / adherens junction organization / embryonic heart tube development / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / sprouting angiogenesis / positive regulation of filopodium assembly / Wnt signaling pathway, planar cell polarity pathway / nuclear migration / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / small GTPase-mediated signal transduction / Myogenesis / heart contraction / establishment of cell polarity / establishment or maintenance of cell polarity / Golgi organization / RHOJ GTPase cycle / positive regulation of cytokinesis / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / phagocytic vesicle / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / secretory granule / small monomeric GTPase / actin filament organization / positive regulation of DNA replication / integrin-mediated signaling pathway / filopodium / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / positive regulation of JNK cascade / RHO GTPases Activate Formins / EGFR downregulation / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / G beta:gamma signalling through CDC42 / endocytosis / mitotic spindle / ubiquitin protein ligase activity / positive regulation of neuron apoptotic process / apical part of cell / intracellular protein localization
Similarity search - Function
Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat / Tripartite Tc toxins repeat / Cdc42 / Rhs repeat-associated core ...Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat / Tripartite Tc toxins repeat / Cdc42 / Rhs repeat-associated core / : / Small GTPase Rho / small GTPase Rho family profile. / Integrin alpha, N-terminal / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cell division control protein 42 homolog / TccC3 / TcdB2
Similarity search - Component
Biological speciesPhotorhabdus luminescens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsRoderer D / Raunser S / Schubert E / Sitsel O
Funding support Germany, 1 items
OrganizationGrant numberCountry
European Research Council615984 Germany
CitationJournal: Nat Commun / Year: 2019
Title: Towards the application of Tc toxins as a universal protein translocation system.
Authors: Daniel Roderer / Evelyn Schubert / Oleg Sitsel / Stefan Raunser /
Abstract: Tc toxins are bacterial protein complexes that inject cytotoxic enzymes into target cells using a syringe-like mechanism. Tc toxins are composed of a membrane translocator and a cocoon that ...Tc toxins are bacterial protein complexes that inject cytotoxic enzymes into target cells using a syringe-like mechanism. Tc toxins are composed of a membrane translocator and a cocoon that encapsulates a toxic enzyme. The toxic enzyme varies between Tc toxins from different species and is not conserved. Here, we investigate whether the toxic enzyme can be replaced by other small proteins of different origin and properties, namely Cdc42, herpes simplex virus ICP47, Arabidopsis thaliana iLOV, Escherichia coli DHFR, Ras-binding domain of CRAF kinase, and TEV protease. Using a combination of electron microscopy, X-ray crystallography and in vitro translocation assays, we demonstrate that it is possible to turn Tc toxins into customizable molecular syringes for delivering proteins of interest across membranes. We also infer the guidelines that protein cargos must obey in terms of size, charge, and fold in order to apply Tc toxins as a universal protein translocation system.
History
DepositionSep 14, 2019-
Header (metadata) releaseDec 11, 2019-
Map releaseDec 11, 2019-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.041
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.041
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10314.png

Downloads & links

-
Map

FileDownload / File: emd_10314.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM density map of ABC holotoxin formed by TcdA1 and TcdB2-TccC3-Cdc42
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 480 pix.
= 547.2 Å		1.14 Å/pix.
x 480 pix.
= 547.2 Å		1.14 Å/pix.
x 480 pix.
= 547.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.041 / Movie #1: 0.041
Minimum - Maximum-0.07510522 - 0.16168544
Average (Standard dev.)0.00057571457 (±0.0055799535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 547.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.141.141.14
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z547.200547.200547.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0750.1620.001

-
Supplemental data

-
Sample components

-
Entire : Complex of TcdA1 pentamer and TcdB2-TccC3-Cdc42

EntireName: Complex of TcdA1 pentamer and TcdB2-TccC3-Cdc42
Components
  • Complex: Complex of TcdA1 pentamer and TcdB2-TccC3-Cdc42
    • Protein or peptide: TcdA1
    • Protein or peptide: chimeric protein TcdB2-TccC3-cdc42

-
Supramolecule #1: Complex of TcdA1 pentamer and TcdB2-TccC3-Cdc42

SupramoleculeName: Complex of TcdA1 pentamer and TcdB2-TccC3-Cdc42 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.7 MDa

-
Macromolecule #1: TcdA1

MacromoleculeName: TcdA1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNESVKEIPD VLKSQCGFNC LTDISHSSFN EFRQQVSEHL SWSETHDLYH DAQQAQKDNR LYEARILKRA NPQLQNAVHL AILAPNAELI GYNNQFSGRA SQYVAPGTVS SMFSPAAYLT ELYREARNLH ASDSVYYLDT RRPDLKSMAL SQQNMDIELS TLSLSNELLL ...String:
MNESVKEIPD VLKSQCGFNC LTDISHSSFN EFRQQVSEHL SWSETHDLYH DAQQAQKDNR LYEARILKRA NPQLQNAVHL AILAPNAELI GYNNQFSGRA SQYVAPGTVS SMFSPAAYLT ELYREARNLH ASDSVYYLDT RRPDLKSMAL SQQNMDIELS TLSLSNELLL ESIKTESKLE NYTKVMEMLS TFRPSGATPY HDAYENVREV IQLQDPGLEQ LNASPAIAGL MHQASLLGIN ASISPELFNI LTEEITEGNA EELYKKNFGN IEPASLAMPE YLKRYYNLSD EELSQFIGKA SNFGQQEYSN NQLITPVVNS SDGTVKVYRI TREYTTNAYQ MDVELFPFGG ENYRLDYKFK NFYNASYLSI KLNDKRELVR TEGAPQVNIE YSANITLNTA DISQPFEIGL TRVLPSGSWA YAAAKFTVEE YNQYSFLLKL NKAIRLSRAT ELSPTILEGI VRSVNLQLDI NTDVLGKVFL TKYYMQRYAI HAETALILCN APISQRSYDN QPSQFDRLFN TPLLNGQYFS TGDEEIDLNS GSTGDWRKTI LKRAFNIDDV SLFRLLKITD HDNKDGKIKN NLKNLSNLYI GKLLADIHQL TIDELDLLLI AVGEGKTNLS AISDKQLATL IRKLNTITSW LHTQKWSVFQ LFIMTSTSYN KTLTPEIKNL LDTVYHGLQG FDKDKADLLH VMAPYIAATL QLSSENVAHS VLLWADKLQP GDGAMTAEKF WDWLNTKYTP GSSEAVETQE HIVQYCQALA QLEMVYHSTG INENAFRLFV TKPEMFGAAT GAAPAHDALS LIMLTRFADW VNALGEKASS VLAAFEANSL TAEQLADAMN LDANLLLQAS IQAQNHQHLP PVTPENAFSC WTSINTILQW VNVAQQLNVA PQGVSALVGL DYIQSMKETP TYAQWENAAG VLTAGLNSQQ ANTLHAFLDE SRSAALSTYY IRQVAKAAAA IKSRDDLYQY LLIDNQVSAA IKTTRIAEAI ASIQLYVNRA LENVEENANS GVISRQFFID WDKYNKRYST WAGVSQLVYY PENYIDPTMR IGQTKMMDAL LQSVSQSQLN ADTVEDAFMS YLTSFEQVAN LKVISAYHDN INNDQGLTYF IGLSETDAGE YYWRSVDHSK FNDGKFAANA WSEWHKIDCP INPYKSTIRP VIYKSRLYLL WLEQKEITKQ TGNSKDGYQT ETDYRYELKL AHIRYDGTWN TPITFDVNKK ISELKLEKNR APGLYCAGYQ GEDTLLVMFY NQQDTLDSYK NASMQGLYIF ADMASKDMTP EQSNVYRDNS YQQFDTNNVR RVNNRYAEDY EIPSSVSSRK DYGWGDYYLS MVYNGDIPTI NYKAASSDLK IYISPKLRII HNGYEGQKRN QCNLMNKYGK LGDKFIVYTS LGVNPNNSSN KLMFYPVYQY SGNTSGLNQG RLLFHRDTTY PSKVEAWIPG AKRSLTNQNA AIGDDYATDS LNKPDDLKQY IFMTDSKGTA TDVSGPVEIN TAISPAKVQI IVKAGGKEQT FTADKDVSIQ PSPSFDEMNY QFNALEIDGS GLNFINNSAS IDVTFTAFAE DGRKLGYESF SIPVTLKVST DNALTLHHNE NGAQYMQWQS YRTRLNTLFA RQLVARATTG IDTILSMETQ NIQEPQLGKG FYATFVIPPY NLSTHGDERW FKLYIKHVVD NNSHIIYSGQ LTDTNINITL FIPLDDVPLN QDYHAKVYMT FKKSPSDGTW WGPHFVRDDK GIVTINPKSI LTHFESVNVL NNISSEPMDF SGANSLYFWE LFYYTPMLVA QRLLHEQNFD EANRWLKYVW SPSGYIVHGQ IQNYQWNVRP LLEDTSWNSD PLDSVDPDAV AQHDPMHYKV STFMRTLDLL IARGDHAYRQ LERDTLNEAK MWYMQALHLL GDKPYLPLST TWSDPRLDRA ADITTQNAHD SAIVALRQNI PTPAPLSLRS ANTLTDLFLP QINEVMMNYW QTLAQRVYNL RHNLSIDGQP LYLPIYATPA DPKALLSAAV ATSQGGGKLP ESFMSLWRFP HMLENARGMV SQLTQFGSTL QNIIERQDAE ALNALLQNQA AELILTNLSI QDKTIEELDA EKTVLEKSKA GAQSRFDSYG KLYDENINAG ENQAMTLRAS AAGLTTAVQA SRLAGAAADL VPNIFGFAGG GSRWGAIAEA TGYVMEFSAN VMNTEADKIS QSETYRRRRQ EWEIQRNNAE AELKQIDAQL KSLAVRREAA VLQKTSLKTQ QEQTQSQLAF LQRKFSNQAL YNWLRGRLAA IYFQFYDLAV ARCLMAEQAY RWELNDDSAR FIKPGAWQGT YAGLLAGETL MLSLAQMEDA HLKRDKRALE VERTVSLAEV YAGLPKDNGP FSLAQEIDKL VSQGSGSAGS GNNNLAFGAG TDTKTSLQAS VSFADLKIRE DYPASLGKIR RIKQISVTLP ALLGPYQDVQ AILSYGDKAG LANGCEALAV SHGMNDSGQF QLDFNDGKFL PFEGIAIDQG TLTLSFPNAS MPEKGKQATM LKTLNDIILH IRYTIK

-
Macromolecule #2: chimeric protein TcdB2-TccC3-cdc42

MacromoleculeName: chimeric protein TcdB2-TccC3-cdc42 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQNSQDFSIT ELSLPKGGGA ITGMGEALTP TGPDGMAALS LPLPISAGRG YAPAFTLNYN SGAGNSPFGL GWDCNVMTIR RRTHFGVPHY DETDTFLGPE GEVLVVADQP RDESTLQGIN LGATFTVTGY RSRLESHFSR LEYWQPKTTG KTDFWLIYSP DGQVHLLGKS ...String:
MQNSQDFSIT ELSLPKGGGA ITGMGEALTP TGPDGMAALS LPLPISAGRG YAPAFTLNYN SGAGNSPFGL GWDCNVMTIR RRTHFGVPHY DETDTFLGPE GEVLVVADQP RDESTLQGIN LGATFTVTGY RSRLESHFSR LEYWQPKTTG KTDFWLIYSP DGQVHLLGKS PQARISNPSQ TTQTAQWLLE ASVSSRGEQI YYQYRAEDDT GCEADEITHH LQATAQRYLH IVYYGNRTAS ETLPGLDGSA PSQADWLFYL VFDYGERSNN LKTPPAFSTT GSWLCRQDRF SRYEYGFEIR TRRLCRQVLM YHHLQALDSK ITEHNGPTLV SRLILNYDES AIASTLVFVR RVGHEQDGNV VTLPPLELAY QDFSPRHHAH WQPMDVLANF NAIQRWQLVD LKGEGLPGLL YQDKGAWWYR SAQRLGEIGS DAVTWEKMQP LSVIPSLQSN ASLVDINGDG QLDWVITGPG LRGYHSQRPD GSWTRFTPLN ALPVEYTHPR AQLADLMGAG LSDLVLIGPK SVRLYANTRD GFAKGKDVVQ SGDITLPVPG TDPRKLVAFS DVLGSGQAHL VEVSATKVTC WPNLGRGRFG QPITLPGFSQ PATEFNPAQV YLADLDGSGP TDLIYVHTNR LDIFLNKSGN GFAEPVTLRF PEGLRFDHTC QLQMADVQGL GVASLILSVP HMSPHHWRCD LTNMKPWLLN EMNNNMGVHH TLRYRSSSQF WLDEKAAALT TGQTPVCYLP FPIHTLWQTE TEDEISGNKL VTTLRYARGA WDGREREFRG FGYVEQTDSH QLAQGNAPER TPPALTKNWY ATGLPVIDNA LSTEYWRDDQ AFAGFSPRFT TWQDNKDVPL TPEDDNSRYW FNRALKGQLL RSELYGLDDS TNKHVPYTVT EFRSQVRRLQ HTDSRYPVLW SSVVESRNYH YERIASDPQC SQNITLSSDR FGQPLKQLSV QYPRRQQPAI NLYPDTLPDK LLANSYDDQQ RQLRLTYQQS SWHHLTNNTV RVLGLPDSTR SDIFTYVAEN VPAGGLNLEL LSDKNSLIAD DKPREYLGQQ KTAYTDGQNT TPLQTPTRQA LIAFTETTVF NQSTLSAFNG SIPSDKLSTT LEQAGYQQTN YLFPRTGEDK VWVAHHGYTD YGTAAQFWRP QKQSNTQLTG KITLIWDANY CVVVQTRDAA GLTTSAKYDW RFLTPVQLTD INDNQHLITL DALGRPITLR FWGTENGKMT GYSSPEKASF SPPSDVNAAI ELKKPLPVAQ CQVYAPESWM PVLSQKTFNR LAEQDWQKLY NARIITEDGR ICTLAYRRWV QSQKAIPQLI SLLNNGPRLP PHSLTLTTDR YDHDPEQQIR QQVVFSDGFG RLLQAAARHE AGMARQRNED GSLIINVQHT ENRWAVTGRT EYDNKGQPIR TYQPYFLNDW RYVSNDSARQ EKEAYADTHV YDPIGREIKV ITAKGWFRRT LFTPWFTVNE DENDTAAEVK KVKMPGSRPM KNIDPKLYQK TPTVSVYDNR GLIIRNIDFH RTTANGDPDT RITRHQYDIH GHLNQSIDPR LYEAKQTNNT IKPNFLWQYD LTGNPLCTES IDAGRTVTLN DIEGRPLLTV TATGVIQTRQ YETSSLPGRL LSVAEQTPEE KTSRITERLI WAGNTEAEKD HNLAGQCVRH YDTAGVTRLE SLSLTGTVLS QSSQLLIDTQ EANWTGDNET VWQNMLADDI YTTLSTFDAT GALLTQTDAK GNIQRLAYDV AGQLNGSWLT LKGQTEQVII KSLTYSAAGQ KLREEHGNDV ITEYSYEPET QRLIGIKTRR PSDTKVLQDL RYEYDPVGNV ISIRNDAEAT RFWHNQKVMP ENTYTYDSLY QLISATGREM ANIGQQSHQF PSPALPSDNN TYTNYTRTYT YDRGGNLTKI QHSSPATQNN YTTNITVSNR SNRAVLSTLT EDPAQVDALF DAGGHQNTLI SGQNLNWNTR GELQQVTLVK RDKGANDDRE WYRYSGDGRR MLKINEQQAS NNAQTQRVTY LPNLELRLTQ NSTATTEDLQ VITVGEAGRA QVRVLHWESG KPEDIDNNQL RYSYDNLIGS SQLELDSEGQ IISEEEYYPY GGTALWAARN QTEASYKTIR YSGKERDATG LYYYGYRYYQ PWIGRWLSSD PAGTIDGLNL YRMVRNNPVT LLDPDGLEPM AMQTIKCVVV GDGAVGKTCL LISYTTNKFP SEYVPTVFDN YAVTVMIGGE PYTLGLFDTA GQEDYDRLRP LSYPQTDVFL VCFSVVSPSS FENVKEKWVP EITHHCPKTP FLLVGTQIDL RDDPSTIEKL AKNKQKPITP ETAEKLARDL KAVKYVECSA LTQRGLKNVF DEAILAALEP

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 56665
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
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