[English] 日本語
Yorodumi
- EMDB-6902: Yeast TRiC/CCT with PA tag insertion in CCT6 subunits -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6902
TitleYeast TRiC/CCT with PA tag insertion in CCT6 subunits
Map dataYeast TRiC/CCT with PA tag in CCT6 subunits
Sample
  • Complex: Yeast TRiC/CCT with PA tag in CCT6 subunits
    • Protein or peptide: T-complex protein 1 subunit alpha
    • Protein or peptide: T-complex protein 1 subunit beta
    • Protein or peptide: T-complex protein 1 subunit gamma
    • Protein or peptide: T-complex protein 1 subunit delta
    • Protein or peptide: T-complex protein 1 subunit epsilon
    • Protein or peptide: T-complex protein 1 subunit zeta
    • Protein or peptide: T-complex protein 1 subunit eta
    • Protein or peptide: T-complex protein 1 subunit theta
Function / homology
Function and homology information


Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / : / chaperone mediated protein folding independent of cofactor / chaperonin-containing T-complex / : / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding ...Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / : / chaperone mediated protein folding independent of cofactor / chaperonin-containing T-complex / : / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit / T-complex protein 1, beta subunit / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. ...T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit / T-complex protein 1, beta subunit / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
T-complex protein 1 subunit alpha / T-complex protein 1 subunit beta / T-complex protein 1 subunit gamma / T-complex protein 1 subunit delta / T-complex protein 1 subunit zeta / T-complex protein 1 subunit epsilon / T-complex protein 1 subunit eta / T-complex protein 1 subunit theta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.4 Å
AuthorsWang H / Takagi J / Cong Y
CitationJournal: J Mol Biol / Year: 2018
Title: Yeast Inner-Subunit PA-NZ-1 Labeling Strategy for Accurate Subunit Identification in a Macromolecular Complex through Cryo-EM Analysis.
Authors: Huping Wang / Wenyu Han / Junichi Takagi / Yao Cong /
Abstract: Cryo-electron microscopy (cryo-EM) has been established as one of the central tools in the structural study of macromolecular complexes. Although intermediate- or low-resolution structural ...Cryo-electron microscopy (cryo-EM) has been established as one of the central tools in the structural study of macromolecular complexes. Although intermediate- or low-resolution structural information through negative staining or cryo-EM analysis remains highly valuable, we lack general and efficient ways to achieve unambiguous subunit identification in these applications. Here, we took advantage of the extremely high affinity between a dodecapeptide "PA" tag and the NZ-1 antibody Fab fragment to develop an efficient "yeast inner-subunit PA-NZ-1 labeling" strategy that when combined with cryo-EM could precisely identify subunits in macromolecular complexes. Using this strategy combined with cryo-EM 3D reconstruction, we were able to visualize the characteristic NZ-1 Fab density attached to the PA tag inserted into a surface-exposed loop in the middle of the sequence of CCT6 subunit present in the Saccharomyces cerevisiae group II chaperonin TRiC/CCT. This procedure facilitated the unambiguous localization of CCT6 in the TRiC complex. The PA tag was designed to contain only 12 amino acids and a tight turn configuration; when inserted into a loop, it usually has a high chance of maintaining the epitope structure and low likelihood of perturbing the native structure and function of the target protein compared to other tagging systems. We also found that the association between PA and NZ-1 can sustain the cryo freezing conditions, resulting in very high occupancy of the Fab in the final cryo-EM images. Our study demonstrated the robustness of this strategy combined with cryo-EM in efficient and accurate subunit identification in challenging multi-component complexes.
History
DepositionFeb 2, 2018-
Header (metadata) releaseApr 25, 2018-
Map releaseApr 25, 2018-
UpdateApr 25, 2018-
Current statusApr 25, 2018Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0053
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0053
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6902.png

Downloads & links

-
Map

FileDownload / File: emd_6902.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYeast TRiC/CCT with PA tag in CCT6 subunits
Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 0.0053 / Movie #1: 0.0053
Minimum - Maximum-0.016169377 - 0.034177776
Average (Standard dev.)0.00008937777 (±0.0030757887)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0160.0340.000

-
Supplemental data

-
Sample components

-
Entire : Yeast TRiC/CCT with PA tag in CCT6 subunits

EntireName: Yeast TRiC/CCT with PA tag in CCT6 subunits
Components
  • Complex: Yeast TRiC/CCT with PA tag in CCT6 subunits
    • Protein or peptide: T-complex protein 1 subunit alpha
    • Protein or peptide: T-complex protein 1 subunit beta
    • Protein or peptide: T-complex protein 1 subunit gamma
    • Protein or peptide: T-complex protein 1 subunit delta
    • Protein or peptide: T-complex protein 1 subunit epsilon
    • Protein or peptide: T-complex protein 1 subunit zeta
    • Protein or peptide: T-complex protein 1 subunit eta
    • Protein or peptide: T-complex protein 1 subunit theta

-
Supramolecule #1: Yeast TRiC/CCT with PA tag in CCT6 subunits

SupramoleculeName: Yeast TRiC/CCT with PA tag in CCT6 subunits / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: TRiC incubation with PA tag antibody NZ-1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1 MDa

-
Macromolecule #1: T-complex protein 1 subunit alpha

MacromoleculeName: T-complex protein 1 subunit alpha / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString: MSQLFNNSRS DTLFLGGEK I SGDDIRNQ NV LATMAVA NVV KSSLGP VGLD KMLVD DIGDF TVTN DGATIL SLL DVQHPAG KI LVELAQQQ D REIGDGTTS VVIIASELLK RANELVKNK I HPTTIITG FR VALREAI RFI NEVLST SVDTLGKETL INIA ...String:
MSQLFNNSRS DTLFLGGEK I SGDDIRNQ NV LATMAVA NVV KSSLGP VGLD KMLVD DIGDF TVTN DGATIL SLL DVQHPAG KI LVELAQQQ D REIGDGTTS VVIIASELLK RANELVKNK I HPTTIITG FR VALREAI RFI NEVLST SVDTLGKETL INIA KTSMS SKIIG ADSD FFSNMV VDA LLAVKTQ NS KGEIKYPV K AVNVLKAHG KSATESLLVP GYALNCTVA S QAMPKRIA GG NVKIACL DLN LQKARM AMGV QINID DPEQL EQIR KREAGI VLE RVKKIID AG AQVVLTTK G IDDLCLKEF VEAKIMGVRR CKKEDLRRI A RATGATLV SS MSNLEGE ETFESSYLGL CDE VVQAKF SDDE CILIK GTSKH SSSS IILRGA NDY SLDEMER SL HDSLSVVK R TLESGNVVP GGGCVEAALN IYLDNFATT V GSREQLAI AE FAAALLI IPK TLAVNA AKDS SELVA KLRSY HAAS QMAKPE DVK RRSYRNY GL DLIRGKIV D EIHAGVLEP TISKVKSLKS ALEACVAIL R IDTMITVD PE PPKEDPH DH

-
Macromolecule #2: T-complex protein 1 subunit beta

MacromoleculeName: T-complex protein 1 subunit beta / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString: MSVQIFGDQV TEERAENARL SAFVGAIAVG DLVKSTLGPK GMDKLLQSAS SNTCMVTNDG ATILKSIPLD NPAAKVLVNI SKVQDDEVGD GTTSVTVLSA ELLREAEKLI DQSKIHPQTI IEGYRLASAA ALDALTKAAV DNSHDKTMFR EDLIHIAKTT LSSKILSQDK ...String:
MSVQIFGDQV TEERAENARL SAFVGAIAVG DLVKSTLGPK GMDKLLQSAS SNTCMVTNDG ATILKSIPLD NPAAKVLVNI SKVQDDEVGD GTTSVTVLSA ELLREAEKLI DQSKIHPQTI IEGYRLASAA ALDALTKAAV DNSHDKTMFR EDLIHIAKTT LSSKILSQDK DHFAELATNA ILRLKGSTNL EHIQIIKILG GKLSDSFLDE GFILAKKFGN NQPKRIENAK ILIANTTLDT DKVKIFGTKF KVDSTAKLAQ LEKAEREKMK NKIAKISKFG INTFINRQLI YDYPEQLFTD LGINSIEHAD FEGVERLALV TGGEVVSTFD EPSKCKLGEC DVIEEIMLGE QPFLKFSGCK AGEACTIVLR GATDQTLDEA ERSLHDALSV LSQTTKETRT VLGGGCAEMV MSKAVDTEAQ NIDGKKSLAV EAFARALRQL PTILADNAGF DSSELVSKLR SSIYNGISTS GLDLNNGTIA DMRQLGIVES YKLKRAVVSS ASEAAEVLLR VDNIIRARPR TANRQHM

-
Macromolecule #3: T-complex protein 1 subunit gamma

MacromoleculeName: T-complex protein 1 subunit gamma / type: protein_or_peptide / ID: 3 / Details: insertion Strep-CBP-His tag between P374 and K375 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString: MQAPVVFMNA SQERTTGRQA QISNITAAKA VADVIRTCLG PKAMLKMLLD PMGGLVLTND GHAILREIDV AHPAAKSMLE LSRTQDEEVG DGTTTVIILA GEILAQCAPY LIEKNIHPVI IIQALKKALT DALEVIKQVS KPVDVENDAA MKKLIQASIG TKYVIHWSEK ...String:
MQAPVVFMNA SQERTTGRQA QISNITAAKA VADVIRTCLG PKAMLKMLLD PMGGLVLTND GHAILREIDV AHPAAKSMLE LSRTQDEEVG DGTTTVIILA GEILAQCAPY LIEKNIHPVI IIQALKKALT DALEVIKQVS KPVDVENDAA MKKLIQASIG TKYVIHWSEK MCELALDAVK TVRKDLGQTV EGEPNFEIDI KRYVRVEKIP GGDVLDSRVL KGVLLNKDVV HPKMSRHIEN PRVVLLDCPL EYKKGESQTN IEIEKEEDWN RILQIEEEQV QLMCEQILAV RPTLVITEKG VSDLAQHYLL KGGCSVLRRV KKSDNNRIAR VTGATIVNRV EDLKESDVGT NCGLFKVEMI GDEYFSFLDN CKEP(LEGSGSGWSHPQFEKGSGKRRWKKNFIAVSAANRFKKISSSGALGSGHHHHHHHHGSGLQ)KACTI MLRGGSKDIL NEIDRNLQDA MAVARNVMLS PSLSPGGGAT EMAVSVKLAE KAKQLEGIQQ WPYQAVADAM ECIPRTLIQN AGGDPIRLLS QLRAKHAQGN FTTGIDGDKG KIVDMVSYGI WEPEVIKQQS VKTAIESACL LLRVDDIVSG VRKQE

-
Macromolecule #4: T-complex protein 1 subunit delta

MacromoleculeName: T-complex protein 1 subunit delta / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString: MSAKVPSNAT FKNKEKPQEV RKANIIAARS VADAIRTSLG PKGMDKMIKT SRGEIIISND GHTILKQMAI LHPVARMLVE VSAAQDSEAG DGTTSVVILT GALLGAAERL LNKGIHPTII ADSFQSAAKR SVDILLEMCH KVSLSDREQL VRAASTSLSS KIVSQYSSFL ...String:
MSAKVPSNAT FKNKEKPQEV RKANIIAARS VADAIRTSLG PKGMDKMIKT SRGEIIISND GHTILKQMAI LHPVARMLVE VSAAQDSEAG DGTTSVVILT GALLGAAERL LNKGIHPTII ADSFQSAAKR SVDILLEMCH KVSLSDREQL VRAASTSLSS KIVSQYSSFL APLAVDSVLK ISDENSKNVD LNDIRLVKKV GGTIDDTEMI DGVVLTQTAI KSAGGPTRKE KAKIGLIQFQ ISPPKPDTEN NIIVNDYRQM DKILKEERAY LLNICKKIKK AKCNVLLIQK SILRDAVNDL ALHFLSKLNI MVVKDIEREE IEFLSKGLGC KPIADIELFT EDRLGSADLV EEIDSDGSKI VRVTGIRNNN ARPTVSVVIR GANNMIIDET ERSLHDALCV IRCLVKERGL IAGGGAPEIE ISRRLSKEAR SMEGVQAFIW QEFASALEVI PTTLAENAGL NSIKVVTELR SKHENGELND GISVRRSGTT NTYEEHILQP VLVSTSAITL ASECVKSILR IDDIAFSR

-
Macromolecule #5: T-complex protein 1 subunit epsilon

MacromoleculeName: T-complex protein 1 subunit epsilon / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString: MAARPQQPPM EMPDLSNAIV AQDEMGRPFI IVKDQGNKKR QHGLEAKKSH ILAARSVASI IKTSLGPRGL DKILISPDGE ITITNDGATI LSQMELDNEI AKLLVQLSKS QDDEIGDGTT GVVVLASALL DQALELIQKG IHPIKIANGF DEAAKLAISK LEETCDDISA ...String:
MAARPQQPPM EMPDLSNAIV AQDEMGRPFI IVKDQGNKKR QHGLEAKKSH ILAARSVASI IKTSLGPRGL DKILISPDGE ITITNDGATI LSQMELDNEI AKLLVQLSKS QDDEIGDGTT GVVVLASALL DQALELIQKG IHPIKIANGF DEAAKLAISK LEETCDDISA SNDELFRDFL LRAAKTSLGS KIVSKDHDRF AEMAVEAVIN VMDKDRKDVD FDLIKMQGRV GGSISDSKLI NGVILDKDFS HPQMPKCVLP KEGSDGVKLA ILTCPFEPPK PKTKHKLDIS SVEEYQKLQT YEQDKFKEMI DDVKKAGADV VICQWGFDDE ANHLLLQNDL PAVRWVGGQE LEHIAISTNG RIVPRFQDLS KDKLGTCSRI YEQEFGTTKD RMLIIEQSKE TKTVTCFVRG SNKMIVDEAE RALHDSLCVV RNLVKDSRVV YGGGAAEVTM SLAVSEEADK QRGIDQYAFR GFAQALDTIP MTLAENSGLD PIGTLSTLKS KQLKEKISNI GVDCLGYGSN DMKELFVVDP FIGKKQQILL ATQLCRMILK IDNVIISGKD EY

-
Macromolecule #6: T-complex protein 1 subunit zeta

MacromoleculeName: T-complex protein 1 subunit zeta / type: protein_or_peptide / ID: 6 / Details: insertion PA tag within C285 and G286 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString: MSLQLLNPKA ESLRRDAALK VNVTSAEGLQ SVLETNLGPK GTLKMLVDGA GNIKLTKDGK VLLTEMQIQS PTAVLIARAA AAQDEITGDG TTTVVCLVGE LLRQAHRFIQ EGVHPRIITD GFEIARKESM KFLDEFKISK TNLSNDREFL LQVARSSLLT KVDADLTEVL ...String:
MSLQLLNPKA ESLRRDAALK VNVTSAEGLQ SVLETNLGPK GTLKMLVDGA GNIKLTKDGK VLLTEMQIQS PTAVLIARAA AAQDEITGDG TTTVVCLVGE LLRQAHRFIQ EGVHPRIITD GFEIARKESM KFLDEFKISK TNLSNDREFL LQVARSSLLT KVDADLTEVL TPIVTDAVLS VYDAQADNLD LHMVEIMQMQ HLSPKDTTFI KGLVLDHGGR HPDMPTRVKN AYVLILNVSL EYEKTEVNSG FFYSSADQRD KLAASERKFV DAKLKKIIDL KNEVC(ggtgtagctatgccaggtgcagaagatgatgtggtg)GMDP DKGFVIINQK GIDPMSLDVF AKHNILALRR AKRRNMERLQ LVTGGEAQNS VEDLSPQILG FSGLVYQETI GEEKFTYVTE NTDPKSCTIL IKGSTHYALA QTKDAVRDGL RAVANVLKDK NIIPGAGAFY IALSRYLRSA NMNKLGAKGK TKTGIEAFAE ALLVIPKTLV KNSGFDPLDV LAMVEDELDD AQDSDETRYV GVDLNIGDSC DPTIEGIWDS YRVLRNAITG ATGIASNLLL CDELLRAGRS TLKETPQ

-
Macromolecule #7: T-complex protein 1 subunit eta

MacromoleculeName: T-complex protein 1 subunit eta / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString: MNFGSQTPTI VVLKEGTDAS QGKGQIISNI NACVAVQEAL KPTLGPLGSD ILIVTSNQKT TISNDGATIL KLLDVVHPAA KTLVDISRAQ DAEVGDGTTS VTILAGELMK EAKPFLEEGI SSHLIMKGYR KAVSLAVEKI NELAVDITSE KSSGRELLER CARTAMSSKL ...String:
MNFGSQTPTI VVLKEGTDAS QGKGQIISNI NACVAVQEAL KPTLGPLGSD ILIVTSNQKT TISNDGATIL KLLDVVHPAA KTLVDISRAQ DAEVGDGTTS VTILAGELMK EAKPFLEEGI SSHLIMKGYR KAVSLAVEKI NELAVDITSE KSSGRELLER CARTAMSSKL IHNNADFFVK MCVDAVLSLD RNDLDDKLIG IKKIPGGAME ESLFINGVAF KKTFSYAGFE QQPKKFNNPK ILSLNVELEL KAEKDNAEVR VEHVEDYQAI VDAEWQLIFE KLRQVEETGA NIVLSKLPIG DLATQFFADR NIFCAGRVSA DDMNRVIQAV GGSIQSTTSD IKPEHLGTCA LFEEMQIGSE RYNLFQGCPQ AKTCTLLLRG GAEQVIAEVE RSLHDAIMIV KRALQNKLIV AGGGATEMEV SKCLRDYSKT IAGKQQMIIN AFAKALEVIP RQLCENAGFD AIEILNKLRL AHSKGEKWYG VVFETENIGD NFAKFVWEPA LVKINALNSA TEATNLILSV DETITNKGSE SANAGMMPPQ GAGRGRGMPM

-
Macromolecule #8: T-complex protein 1 subunit theta

MacromoleculeName: T-complex protein 1 subunit theta / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString: MSLRLPQNPN AGLFKQGYNS YSNADGQIIK SIAAIRELHQ MCLTSMGPCG RNKIIVNHLG KIIITNDAAT MLRELDIVHP AVKVLVMATE QQKIDMGDGT NLVMILAGEL LNVSEKLISM GLSAVEIIQG YNMARKFTLK ELDEMVVGEI TDKNDKNELL KMIKPVISSK ...String:
MSLRLPQNPN AGLFKQGYNS YSNADGQIIK SIAAIRELHQ MCLTSMGPCG RNKIIVNHLG KIIITNDAAT MLRELDIVHP AVKVLVMATE QQKIDMGDGT NLVMILAGEL LNVSEKLISM GLSAVEIIQG YNMARKFTLK ELDEMVVGEI TDKNDKNELL KMIKPVISSK KYGSEDILSE LVSEAVSHVL PVAQQAGEIP YFNVDSIRVV KIMGGSLSNS TVIKGMVFNR EPEGHVKSLS EDKKHKVAVF TCPLDIANTE TKGTVLLHNA QEMLDFSKGE EKQIDAMMKE IADMGVECIV AGAGVGELAL HYLNRYGILV LKVPSKFELR RLCRVCGATP LPRLGAPTPE ELGLVETVKT MEIGGDRVTV FKQEQGEISR TSTIILRGAT QNNLDDIERA IDDGVAAVKG LMKPSGGKLL PGAGATEIEL ISRITKYGER TPGLLQLAIK QFAVAFEVVP RTLAETAGLD VNEVLPNLYA AHNVTEPGAV KTDHLYKGVD IDGESDEGVK DIREENIYDM LATKKFAINV ATEAATTVLS IDQIIMAKKA GGPRAPQGPR PGNWDQED

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 38.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14805

+
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