[English] 日本語
Yorodumi
- EMDB-47954: Tubulin cofactors D,E,G bound to tubulin dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47954
TitleTubulin cofactors D,E,G bound to tubulin dimer
Map data
Sample
  • Complex: Tubulin cofactors D,E,G in complex with tubulin dimer
    • Protein or peptide: Protein PAC2
    • Protein or peptide: GTP-binding protein CIN4
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: DESIGNED ANKYRIN REPEAT PROTEIN -- DARPin
    • Protein or peptide: Chromosome instability protein 1
    • Protein or peptide: Tubulin alpha-1A chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsTubulin / Tubulin cofactors / Tubulin biogenesis / Tubulin degradation / microtubules / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


post-chaperonin tubulin folding pathway / tubulin complex assembly / motile cilium / alpha-tubulin binding / beta-tubulin binding / GTPase activator activity / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / protein folding ...post-chaperonin tubulin folding pathway / tubulin complex assembly / motile cilium / alpha-tubulin binding / beta-tubulin binding / GTPase activator activity / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / protein folding / mitotic cell cycle / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
: / Tubulin-specific chaperone D-like, ARM repeats / Tubulin-folding cofactor D / Tubulin-specific chaperone D-like, ARM repeat / ADP-ribosylation factor-like protein 2/3 / : / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain ...: / Tubulin-specific chaperone D-like, ARM repeats / Tubulin-folding cofactor D / Tubulin-specific chaperone D-like, ARM repeat / ADP-ribosylation factor-like protein 2/3 / : / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Leucine Rich repeat / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Small GTP-binding protein domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tubulin alpha-1A chain / Tubulin beta chain / GTP-binding protein CIN4 / Protein PAC2 / Chromosome instability protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsTaheri A / Al-bassam J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structures of the tubulin cofactors reveal the molecular basis of alpha/beta-tubulin biogenesis.
Authors: Aryan Taheri / Zhoaqian Wang / Bharti Singal / Fei Guo / Jawdat Al-Bassam /
Abstract: Microtubule polarity and dynamic polymerization arise from the self-association properties of the αβ-tubulin heterodimer. For decades, it has remained unclear how the tubulin cofactors TBCD, TBCE, ...Microtubule polarity and dynamic polymerization arise from the self-association properties of the αβ-tubulin heterodimer. For decades, it has remained unclear how the tubulin cofactors TBCD, TBCE, TBCC, and the Arl2 GTPase mediate the biogenesis of αβ-tubulin from individual α- and β-tubulins. Here, we use cryo-electron microscopy to determine structures of tubulin cofactors bound to αβ-tubulin. TBCD, TBCE, and Arl2 form a heterotrimeric cage-like assembly, we term TBC-DEG, around the αβ-tubulin heterodimer. The TBC-DEG-αβ-tubulin structures show that TBC-DEG wraps around β-tubulin while TBCE extends along α-tubulin. The TBC-DEG/TBCC-αβ-tubulin structures reveal that TBCC forms multi-domain interactions with Arl2 and TBCD to engage the αβ-tubulin intradimer-interface, promoting TBCE rotation while TBCD holds β-tubulin. TBCC engages the GTP-bound Arl2, multiple sites of TBCD, and the native αβ-tubulin intradimer interface near the α-tubulin N-site GTP. Together, these structures uncover transition states for αβ-tubulin biogenesis and degradation, suggesting a vise-like, GTP-hydrolysis-dependent mechanism in which TBCC binding to TBC-DEG modulates αβ-tubulin interfaces. Our studies provide structural evidence that tubulin cofactors act as enzymatic regulators that assemble the invariant αβ-tubulin architecture. By catalyzing α- and β-tubulin biogenesis and degradation, the TBC-DEG and TBCC assemblies regulate the polymerization competency of αβ-tubulin for microtubule formation.
History
DepositionNov 18, 2024-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47954.png

Downloads & links

-
Map

FileDownload / File: emd_47954.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 400 pix.
= 529.6 Å		1.32 Å/pix.
x 400 pix.
= 529.6 Å		1.32 Å/pix.
x 400 pix.
= 529.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.324 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0132
Minimum - Maximum-0.0017621794 - 1.9670148
Average (Standard dev.)0.0003314822 (±0.01394983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 529.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Tubulin cofactors D,E,G in complex with tubulin dimer

EntireName: Tubulin cofactors D,E,G in complex with tubulin dimer
Components
  • Complex: Tubulin cofactors D,E,G in complex with tubulin dimer
    • Protein or peptide: Protein PAC2
    • Protein or peptide: GTP-binding protein CIN4
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: DESIGNED ANKYRIN REPEAT PROTEIN -- DARPin
    • Protein or peptide: Chromosome instability protein 1
    • Protein or peptide: Tubulin alpha-1A chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

-
Supramolecule #1: Tubulin cofactors D,E,G in complex with tubulin dimer

SupramoleculeName: Tubulin cofactors D,E,G in complex with tubulin dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Macromolecule #1: Protein PAC2

MacromoleculeName: Protein PAC2 / type: protein_or_peptide / ID: 1
Details: Chain E contains a well-resolved C-terminal region that was modeled with full side-chain identities. Density for the LRR and CAP-Gly domains is weaker and discontinuous, consistent with ...Details: Chain E contains a well-resolved C-terminal region that was modeled with full side-chain identities. Density for the LRR and CAP-Gly domains is weaker and discontinuous, consistent with flexibility of this portion of the protein in the complex. Therefore, residues in these regions are modeled as poly-alanine to represent the backbone trace and overall topology only (listed as UNK in the entry). Side-chain identities are not asserted in these low-density regions. The sequence register is anchored by the well-resolved C-terminal domain and supported by the AlphaFold prediction.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 32.341963 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)SLVL KIKIRAGKKP SSDLDYWVLP S FTVRYVKS VICRKLNFDI LNVKLFHENS EGMINEIKYN FRPISDFNVV NGDIIHVSSP VNNKSIQKVN SPS

UniProtKB: Protein PAC2

-
Macromolecule #2: GTP-binding protein CIN4

MacromoleculeName: GTP-binding protein CIN4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.096717 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGLLSIIRKQ KLRDKEIRCL ILGLDNSGKS TIVNKLLPKD EQNNDGIMPT VGFQIHSLMI KDVTISLWDI GGQRTLRPFW DNYFDKTQA MIWCIDVSLS MRFDETLQEL KELINRDENR IGYECAVIVV LNKIDLVEDK SELHRRCLLV ESELKCLFKP D IRIELVKC SGVTGEGIDN LRDRLVESCH FTQ

UniProtKB: GTP-binding protein CIN4

-
Macromolecule #3: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 49.90777 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEGEEDEA

UniProtKB: Tubulin beta chain

-
Macromolecule #4: DESIGNED ANKYRIN REPEAT PROTEIN -- DARPin

MacromoleculeName: DESIGNED ANKYRIN REPEAT PROTEIN -- DARPin / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.955262 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRGSHHHHHH GSDLGKKLLE AARAGQDDEV RVLMANGADV NATDASGLTP LHLAATYGHL EIVEVLLKHG ADVSASDLMG STPLHLAAL IGHLEIVEVL LKHGADVNAV DTWGDTPLRL AAVMGHLKIV EALLKHGADV NAQDKFGKTA YDTSIDNGSE D LAEILQKL N

-
Macromolecule #5: Chromosome instability protein 1

MacromoleculeName: Chromosome instability protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 117.608211 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHNNI RALLDSIQSG VQTVSPEKHQ QTIAAINKFQ DDPALLDTIL PRCVPLLTKS FFCMSQRDQK LVAELFYNLD KISHSKVLK SLDTSIFRLN EILNYLQDRA SPSSFSDVLC VYLNLSWLSV ILLSPYAFKD KFNKTLQVSS RFENYPICIP P INKIKAVL ...String:
MHHHHHHNNI RALLDSIQSG VQTVSPEKHQ QTIAAINKFQ DDPALLDTIL PRCVPLLTKS FFCMSQRDQK LVAELFYNLD KISHSKVLK SLDTSIFRLN EILNYLQDRA SPSSFSDVLC VYLNLSWLSV ILLSPYAFKD KFNKTLQVSS RFENYPICIP P INKIKAVL YFKNFTDAFD QLPEREQANV PFLNQFLKLF IQSSEKANYY FSNENLRHLQ QVALSNDGIK LLPKLFQISF NH GSHDILD AIVEFFHDHL SSNSTDTRFQ LAHSFAKIAK FLHQADPASF IELIDYTIEN TVSLLQAPCD SIDSNELHTS LLI IAEVAL AKILPIDLVD RVLTLIIPKT CHFQKSHFQI IKGHHIRDST NFIIWSVIRS NRSNSLSPQV LQSLLSHLLI NAFF DPELI IRYSSFAALQ ELLGRSNKSL ALNQNDIALI LQANWKDLPR SFEENSGLIR RLFNPENTSK SAVCVWKVFR DWSFN WNLL ENLHLTTMKL NIDYNLVPLI KSKLSSPALL QEVLNKAGSS VTQNCQILYL YLKLFENDVN CPKISEICID IYQKKI KFQ LTTQAKRQFN DNSPELFQIF VILKYWQLTG QNDFNQELFW KFVDIVSPQK KLNLYNEFIP IIQQIISQCV SLNYTRI VQ LIKSDNELTC RSICHMPDQE KMCSLFFSQF PLLSPQSRSL LIGELDHHWD VRISLLPSNS YRKFRNIIIN CLDDYTIT Q QGDVGRLVRI QALKLMQSHP DFLSGDCDSI NPKLTRLLAE PVPEIRKLSY QLLASATSQI TVLSDSSILN FRHKQGLSE EFWKGYAVSA GAIHFTDSQL TSSIDSFIVY YRSLSPSQQL ELCHDLIRII PSAKQIAESR IRDRNKDPLT GGMRFDTIKF TIHCVKFWT RIMESGLVVL HPNFNFQGVF AKFYNLHLLD CTTLRVSVIK FFPFLAISCY HTMRENADQK NLSNIILKRL L VLVKREYA ATKSKFMTDQ NVALQGMFQI FLELGVTRQL QALQVACQKH ELANILESDI TL

UniProtKB: Chromosome instability protein 1

-
Macromolecule #6: Tubulin alpha-1A chain

MacromoleculeName: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 50.121266 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFSVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFSVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLIGQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRAHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRTIQFVDW CPTGFKVGIN YEPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1A chain

-
Macromolecule #7: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

-
Macromolecule #8: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 275487
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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