[English] 日本語
Yorodumi
- EMDB-18182: Closed conformation of the g-tubulin ring complex nucleating micr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18182
TitleClosed conformation of the g-tubulin ring complex nucleating microtubules
Map dataRefined map of the closed gTuRC conformation
Sample
  • Complex: gamma-tubulin ring complex
    • Protein or peptide: GCP2
    • Protein or peptide: GCP3
    • Protein or peptide: GCP4
    • Protein or peptide: GCP5
    • Protein or peptide: GCP6
    • Protein or peptide: gamma-tubulin
KeywordsMicrotubule / cytoskeleton / g-tubulin ring complex / tubulin / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.39 Å
AuthorsLlorca O / Serna M
Funding support Spain, European Union, 2 items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)AEI/10.13039/501100011 003 Spain
European Regional Development FundPID2020-114429RB-I00European Union
CitationJournal: Science / Year: 2024
Title: Transition of human γ-tubulin ring complex into a closed conformation during microtubule nucleation.
Authors: Cláudia Brito / Marina Serna / Pablo Guerra / Oscar Llorca / Thomas Surrey /
Abstract: Microtubules are essential for intracellular organization and chromosome segregation. They are nucleated by the γ-tubulin ring complex (γTuRC). However, isolated vertebrate γTuRC adopts an open ...Microtubules are essential for intracellular organization and chromosome segregation. They are nucleated by the γ-tubulin ring complex (γTuRC). However, isolated vertebrate γTuRC adopts an open conformation that deviates from the microtubule structure, raising the question of the nucleation mechanism. In this study, we determined cryo-electron microscopy structures of human γTuRC bound to a nascent microtubule. Structural changes of the complex into a closed conformation ensure that γTuRC templates the 13-protofilament microtubules that exist in human cells. Closure is mediated by a latch that interacts with incorporating tubulin, making it part of the closing mechanism. Further rearrangements involve all γTuRC subunits and the removal of the actin-containing luminal bridge. Our proposed mechanism of microtubule nucleation by human γTuRC relies on large-scale structural changes that are likely the target of regulation in cells.
History
DepositionAug 10, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18182.png

Downloads & links

-
Map

FileDownload / File: emd_18182.map.gz / Format: CCP4 / Size: 259.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefined map of the closed gTuRC conformation
Voxel sizeX=Y=Z: 1.36754 Å
Density
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.0067491014 - 0.028027507
Average (Standard dev.)0.00015980071 (±0.0016922144)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions408408408
Spacing408408408
CellA=B=C: 557.9563 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_18182_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Sharpened map of the closed gTuRC conformation

Fileemd_18182_additional_1.map
AnnotationSharpened map of the closed gTuRC conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half 2 map of the refined closed gTuRC conformation structure

Fileemd_18182_half_map_1.map
AnnotationHalf 2 map of the refined closed gTuRC conformation structure
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half 1 map of the refined closed gTuRC conformation structure

Fileemd_18182_half_map_2.map
AnnotationHalf 1 map of the refined closed gTuRC conformation structure
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : gamma-tubulin ring complex

EntireName: gamma-tubulin ring complex
Components
  • Complex: gamma-tubulin ring complex
    • Protein or peptide: GCP2
    • Protein or peptide: GCP3
    • Protein or peptide: GCP4
    • Protein or peptide: GCP5
    • Protein or peptide: GCP6
    • Protein or peptide: gamma-tubulin

-
Supramolecule #1: gamma-tubulin ring complex

SupramoleculeName: gamma-tubulin ring complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: GCP2

MacromoleculeName: GCP2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MSEFRIHHDV NELLSLLRVH GGDGAEVYID LLQKNRTPYV TTTVSAHSAK VKIAEFSRTP EDFLKKYDE LKSKNTRNLD PLVYLLSKLT EDKETLQYLQ QNAKERAELA AAAVGSSTTS I NVPAAASK ISMQELEELR KQLGSVATGS TLQQSLELKR KMLRDKQNKK ...String:
MSEFRIHHDV NELLSLLRVH GGDGAEVYID LLQKNRTPYV TTTVSAHSAK VKIAEFSRTP EDFLKKYDE LKSKNTRNLD PLVYLLSKLT EDKETLQYLQ QNAKERAELA AAAVGSSTTS I NVPAAASK ISMQELEELR KQLGSVATGS TLQQSLELKR KMLRDKQNKK NSGQHLPIFP AW VYERPAL IGDFLIGAGI STDTALPIGT LPLASQESAV VEDLLYVLVG VDGRYVSAQP LAG RQSRTF LVDPNLDLSI RELVHRILPV AASYSAVTRF IEEKSSFEYG QVNHALAAAM RTLV KEHLI LVSQLEQLHR QGLLSLQKLW FYIQPAMRTM DILASLATSV DKGECLGGST LSLLH DRSF SYTGDSQAQE LCLYLTKAAS APYFEVLEKW IYRGIIHDPY SEFMVEEHEL RKERIQ EDY NDKYWDQRYT IVQQQIPSFL QKMADKILST GKYLNVVREC GHDVTCPVAK EIIYTLK ER AYVEQIEKAF NYASKVLLDF LMEEKELVAH LRSIKRYFLM DQGDFFVHFM DLAEEELR K PVEDITPPRL EALLELALRM STANTDPFKD DLKIDLMPHD LITQLLRVLA IETKQEKAM AHADPTELAL SGLEAFSFDY IVKWPLSLII NRKALTRYQM LFRHMFYCKH VERQLCSVWI SNKTAKQHS LHSAQWFAGA FTLRQRMLNF VQNIQYYMMF EVMEPTWHIL EKNLKSASNI D DVLGHHTG FLDTCLKDCM LTNPELLKVF SKLMSVCVMF TNCMQKFTQS MKLDGELGGQ TL EHSTVLG LPAGAEERAR KELARKHLAE HADTVQLVSG FEATINKFDK NFSAHLLDLL ARL SIYSTS DCEHGMASVI SRLDFNGFYT ERLERLSAER SQKATPQVPV LRGPPAPAPR VAVT AQ

-
Macromolecule #2: GCP3

MacromoleculeName: GCP3 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MATPDQKSPN VLLQNLCCRI LGRSEADVAQ QFQYAVRVIG SNFAPTVERD EFLVAEKIKK ELIRQRREA DAALFSELHR KLHSQGVLKN KWSILYLLLS LSEDPRRQPS KVSSYATLFA Q ALPRDAHS TPYYYARPQT LPLSYQDRSA QSAQSSGSVG SSGISSIGLC ...String:
MATPDQKSPN VLLQNLCCRI LGRSEADVAQ QFQYAVRVIG SNFAPTVERD EFLVAEKIKK ELIRQRREA DAALFSELHR KLHSQGVLKN KWSILYLLLS LSEDPRRQPS KVSSYATLFA Q ALPRDAHS TPYYYARPQT LPLSYQDRSA QSAQSSGSVG SSGISSIGLC ALSGPAPAPQ SL LPGQSNQ APGVGDCLRQ QLGSRLAWTL TANQPSSQAT TSKGVPSAVS RNMTRSRREG DTG GTMEIT EAALVRDILY VFQGIDGKNI KMNNTENCYK VEGKANLSRS LRDTAVRLSE LGWL HNKIR RYTDQRSLDR SFGLVGQSFC AALHQELREY YRLLSVLHSQ LQLEDDQGVN LGLES SLTL RRLLVWTYDP KIRLKTLAAL VDHCQGRKGG ELASAVHAYT KTGDPYMRSL VQHILS LVS HPVLSFLYRW IYDGELEDTY HEFFVASDPT VKTDRLWHDK YTLRKSMIPS FMTMDQS RK VLLIGKSINF LHQVCHDQTP TTKMIAVTKS AESPQDAADL FTDLENAFQG KIDAAYFE T SKYLLDVLNK KYSLLDHMQA MRRYLLLGQG DFIRHLMDLL KPELVRPATT LYQHNLTGI LETAVRATNA QFDSPEILRR LDVRLLEVSP GDTGWDVFSL DYHVDGPIAT VFTRECMSHY LRVFNFLWR AKRMEYILTD IRKGHMCNAK LLRNMPEFSG VLHQCHILAS EMVHFIHQMQ Y YITFEVLE CSWDELWNKV QQAQDLDHII AAHEVFLDTI ISRCLLDSDS RALLNQLRAV FD QIIELQN AQDAIYRAAL EELQRRLQFE EKKKQREIEG QWGVTAAEEE EENKRIGEFK ESI PKMCSQ LRILTHFYQG IVQQFLVLLT TSSDESLRFL SFRLDFNEHY KAREPRLRVS LGTR GRRSS HT

-
Macromolecule #3: GCP4

MacromoleculeName: GCP4 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MIHELLLALS GYPGSIFTWN KRSGLQVSQD FPFLHPSETS VLNRLCRLGT DYIRFTEFIE QYTGHVQQQ DHHPSQQGQG GLHGIYLRAF CTGLDSVLQP YRQALLDLEQ EFLGDPHLSI S HVNYFLDQ FQLLFPSVMV VVEQIKSQKI HGCQILETVY KHSCGGLPPV ...String:
MIHELLLALS GYPGSIFTWN KRSGLQVSQD FPFLHPSETS VLNRLCRLGT DYIRFTEFIE QYTGHVQQQ DHHPSQQGQG GLHGIYLRAF CTGLDSVLQP YRQALLDLEQ EFLGDPHLSI S HVNYFLDQ FQLLFPSVMV VVEQIKSQKI HGCQILETVY KHSCGGLPPV RSALEKILAV CH GVMYKQL SAWMLHGLLL DQHEEFFIKQ GPSSGNVSAQ PEEDEEDLGI GGLTGKQLRE LQD LRLIEE ENMLAPSLKQ FSLRVEILPS YIPVRVAEKI LFVGESVQMF ENQNVNLTRK GSIL KNQED TFAAELHRLK QQPLFSLVDF EQVVDRIRST VAEHLWKLMV EESDLLGQLK IIKDF YLLG RGELFQAFID TAQHMLKTPP TAVTEHDVNV AFQQSAHKVL LDDDNLLPLL HLTIEY HGK EHKADATQAR EGPSRETSPR EAPASGWAAL GLSYKVQWPL HILFTPAVLE KYNVVFK YL LSVRRVQAEL QHCWALQMQR KHLKSNQTDA IKWRLRNHMA FLVDNLQYYL QVDVLESQ F SQLLHQINST RDFESIRLAH DHFLSNLLAQ SFILLKPVFH CLNEILDLCH SFCSLVSQN LGPLDERGAA QLSILVKGFS RQSSLLFKIL SSVRNHQINS DLAQLLLRLD YNKYYTQAGG TLGSFGM

-
Macromolecule #4: GCP5

MacromoleculeName: GCP5 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MARHGPPWSR LDAQQERDVR ELVRGVAGLQ DEADPNFQLA LNFAWSNFRF HRFLDVNSHK IEKTIEGIY EKFVIHSDLS KAASWKRLTE EFLNAPLPSI KEIKTDAHYS ILSLLLCLSD S PSNSSYVE TPRNKEVEKK DDFDWGKYLM EDEEMDIGPY MDTPNWSEES ...String:
MARHGPPWSR LDAQQERDVR ELVRGVAGLQ DEADPNFQLA LNFAWSNFRF HRFLDVNSHK IEKTIEGIY EKFVIHSDLS KAASWKRLTE EFLNAPLPSI KEIKTDAHYS ILSLLLCLSD S PSNSSYVE TPRNKEVEKK DDFDWGKYLM EDEEMDIGPY MDTPNWSEES EEENDQQPLS RE DSGIQVD RTPLEEQDQN RKLDPCISWK DEPDDRSWLE HHVVHQYWTA RPSQFPHSLH LHS NLAAVW DQHLYSSDPL YVPDDRVLVT ETQVIRETLW LLSGVKKLFI FQLIDGKVTV RNNI IVTHL THSCLRSVLE QIAAYGQVVF RLQEFIDEVM GHSSESMLPG SGSVPKKSTE APFRT YQAF MWALYKYFIS FKEELAEIEK CIINNDTTIT LAIVVDKLAP RLSQLKVLHK VFSTGV AEV PPDTRNVVRA SHLLNTLYKA ILEYDNVGEA SEQTVSLLFS LWVETVRPYL QTVDEWI VH GHLWDGAREF IIQRNKNVPV NHRDFWYATY TLYSVSEKTE NEEKMSDNAS ASSGSDQG P SSRQHTMVSF LKPVLKQIIM AGKSMQLLKN LQCAESTTCQ AGARDAERKS LYTLFLESV QSRLRHGEDS TPQVLTEQQA TKENLMKMQS IAESHLELDD VHDPLLAINF ARMYLEQSDF HEKFAGGDV CVDRSSESVT CQTFELTLRS CLYPHIDKQY LDCCGNLMQT LKKDYRLVEY L QAMRNFFL MEGGDTMYDF YTSIFDKIRE KETWQNVSFL NVQLQEAVGQ RYPEDSSRLS IS FENVDTA KKKLPVHILD GLTLSYKVPW PVDIVISLEC QKIYNQVFLL LLQIKWAKYS LDV LLFGEL VSTAEKPRLK EGLIHEQDTV AQFGPQKEPV RQQIHRMFLL RVKLMHFVNS LHNY IMTRI LHSTGLEFQH QVEEAKDLDQ LIKIHYRYLS TIHDRCLLRE KVSFVKEAIM KVLNL ALMF ADGWQAGLGT WRMESIEKME SDFKNCHMFL VTILNKAVCR GSFPHLESLA LSLMAG MEQ S

-
Macromolecule #5: GCP6

MacromoleculeName: GCP6 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MASITQLFDD LCEALLPAAK THLGQRSVNR KRAKRSLKKV AYNALFTNLF QDETQQLQPD MSKLPARNK ILMLSFDLRV GGLGPKADRL EELVEELEAA PCCPLLEVGS VLDLLVQLAG S GPPQVLPR KRDYFLNNKH VGRNVPYSGY DCDDLSVFEM DVQSLISREE ...String:
MASITQLFDD LCEALLPAAK THLGQRSVNR KRAKRSLKKV AYNALFTNLF QDETQQLQPD MSKLPARNK ILMLSFDLRV GGLGPKADRL EELVEELEAA PCCPLLEVGS VLDLLVQLAG S GPPQVLPR KRDYFLNNKH VGRNVPYSGY DCDDLSVFEM DVQSLISREE CLCHSMIQET LQ VMEAAPG TGLPTVGLFS FGDPCGDRFE RDTRVSLFGA LVHSRTYDMD VRLGLPPVPD NAD LSGLAI KVPPSVDQWE DEGFQSASNL TPDSQSEPSV TPDVDLWEAA LTYEASKRRC WERV GCPPG HREEPYLTEA GRDAFDKFCR LHQGELQLLA GGVLQAPQPV LVKECELVKD VLNVL IGVV SATFSLCQPA QAFVVKRGVH VSGASPESIS SLLSEVAEYG TCYTRLSHFS LQPVLD SLY SKGLVFQAFT SGLRRYLQYY RACVLSTPPT LSLLTIGFLF KKLGRQLRYL AELCGVG AV LPGTCGGGPR AAFPTGVKLL SYLYQEALHN CSNEHYPVLL SLLKTSCEPY TRFIHDWV Y SGVFRDAYGE FMIQVNHEYL SFRDKLYWTH GYVLISKEVE DCVPVFLKHI AHDIYVCGK TINLLKLCCP RHYLCWSDVP VPRISVIFSL EELKEIEKDC AVYVGRMERV ARHSSVSKEE KELRMEIAK QELIAHAREA ASRVLSALSD RQMSERMALD ARKREQFQRL KEQFVKDQER R QAARQEEL DDDFSYAREL RDRERRLKSL EEELERKARQ ALVDHYSKLS AEAARREQKA LW RIQRHRL ESARLRFLLE DEKHIQEMLK AVSEAHQPQE PPDVLLSVHP QVTSPGPEHP EGG QGCDSG SAEQHSPAWD GWNRPGLLTP QPLKPLAVGA GGRGLQQAEG ARPFSDSLSI GDFL PVGPG AEPSVQTGMV PLLEVALQTI NLDLPPSAPG EAPAAASTQP SRPQEYDFST VLRPA VATS PAPGPLQAAE CSLGSSGLQL WEDSCGKMDA CGSASRETLL PSHPPRRAAL EEGSSQ PTE RLFGQVSGGG LPTGDYASEI APTRPRWNTH GHVSDASIRV GENVSDVAPT QPRWNTH GH VSNASISLGE SVSDVAPTRP RWNIHGHVSN ASIRVGENVS DVAPTRPRWN THGHVSNA S IRVGENVSDV APTRPRWNTH GHVSDASISL GESVSDMAPA RPRWNTHGHV SDASISLGE SVSDMAPTRP RWNTHGHVSD TSIRVGENVS DVAPIRSRCN THGHVSDASI SLGEPVSDVV STRPRWNTH VPIPPPHMVL GALSPEAEPN TPRPQQSPPG HTSQSALSLG AQSTVLDCGP R LPVEVGPS LSSPSSGCGE GSISVGENVS DVAPTQPWWP NTPGDSVSEE LGPGRSGDTE DL SPNWPLN SQEDTAAQSS PGRGEEAEAS AAEAQGGEQA YLAGLAGQYH LERYPDSYES MSE PPIAHL LRPVLPRAFA FPVDPQVQSA ADETAVQLSE LLTLPVLMKR SITAPLAAHI SLVN KAAVD YFFVELHLEA HYEALRHFLL MEDGEFAQSL SDLLFEKLGA GQTPGELLNP LVLNS VLSK ALQCSLHGDT PHASNLSLAL KYLPEVFAPN APDVLSCLEL RYKVDWPLNI VITEGC VSK YSGVFSFLLQ LKLMMWALKD VCFHLKRTAL LSHMAGSVQF RQLQLFKHEM QHFVKVI QG YIANQILHVT WCEFRARLAT VGDLEEIQRA HAEYLHKAVF RGLLTEKAAP VMNVIHSI F SLVLKFRSQL ISQAWGPPGG PRGAEHPNFA LMQQSYNTFK YYSHFLFKVV TKLVNRGYQ PHLEDFLLRI NFNNYYQDA

-
Macromolecule #6: gamma-tubulin

MacromoleculeName: gamma-tubulin / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MPREIITLQL GQCGNQIGFE FWKQLCAEHG ISPEGIVEEF ATEGTDRKDV FFYQADDEHY IPRAVLLDL EPRVIHSILN SPYAKLYNPE NIYLSEHGGG AGNNWASGFS QGEKIHEDIF D IIDREADG SDSLEGFVLC HSIAGGTGSG LGSYLLERLN DRYPKKLVQT ...String:
MPREIITLQL GQCGNQIGFE FWKQLCAEHG ISPEGIVEEF ATEGTDRKDV FFYQADDEHY IPRAVLLDL EPRVIHSILN SPYAKLYNPE NIYLSEHGGG AGNNWASGFS QGEKIHEDIF D IIDREADG SDSLEGFVLC HSIAGGTGSG LGSYLLERLN DRYPKKLVQT YSVFPNQDEM SD VVVQPYN SLLTLKRLTQ NADCVVVLDN TALNRIATDR LHIQNPSFSQ INQLVSTIMS AST TTLRYP GYMNNDLIGL IASLIPTPRL HFLMTGYTPL TTDQSVASVR KTTVLDVMRR LLQP KNVMV STGRDRQTNH CYIAILNIIQ GEVDPTQVHK SLQRIRERKL ANFIPWGPAS IQVAL SRKS PYLPSAHRVS GLMMANHTSI SSLFERTCRQ YDKLRKREAF LEQFRKEDMF KDNFDE MDT SREIVQQLID EYHAATRPDY ISWGTQEQ

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.9
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 310 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 46276 / Average exposure time: 1.3 sec. / Average electron dose: 46.276 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1580023
Startup modelType of model: INSILICO MODEL / In silico model: CryoSPARC Ab Initio Reconstruction
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 77306
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software: (Name: RELION (ver. 4.0), cryoSPARC (ver. 4.0+))
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4.0)
Final 3D classificationSoftware: (Name: RELION (ver. 4.0), cryoSPARC (ver. 4.0+), cryoDRGN (ver. 2.0))
Details: Several 3D classification and heterogeneity analysis methods
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

7as4

source_name: PDB, initial_model_type: experimental model

6x0u

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

+
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://pdbjlvh1.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