[English] 日本語
Yorodumi
- EMDB-27782: Structure of human cytoplasmic dynein-1 bound to two Lis1 proteins -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27782
TitleStructure of human cytoplasmic dynein-1 bound to two Lis1 proteins
Map data
Sample
  • Complex: Human cytoplasmic dynein-1 bound to two Lis1 WD40 domains.
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
    • Protein or peptide: Platelet-activating factor acetylhydrolase IB subunit beta
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordsdynein / motor protein / transport
Function / homology
Function and homology information


corpus callosum morphogenesis / establishment of planar polarity of embryonic epithelium / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / 1-alkyl-2-acetylglycerophosphocholine esterase complex / interneuron migration / maintenance of centrosome location / platelet activating factor metabolic process / microtubule sliding / microtubule organizing center organization ...corpus callosum morphogenesis / establishment of planar polarity of embryonic epithelium / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / 1-alkyl-2-acetylglycerophosphocholine esterase complex / interneuron migration / maintenance of centrosome location / platelet activating factor metabolic process / microtubule sliding / microtubule organizing center organization / acrosome assembly / radial glia-guided pyramidal neuron migration / cerebral cortex neuron differentiation / positive regulation of intracellular transport / central region of growth cone / regulation of metaphase plate congression / establishment of centrosome localization / positive regulation of embryonic development / positive regulation of cytokine-mediated signaling pathway / establishment of spindle localization / astral microtubule / positive regulation of spindle assembly / nuclear membrane disassembly / layer formation in cerebral cortex / auditory receptor cell development / vesicle transport along microtubule / cortical microtubule organization / positive regulation of dendritic spine morphogenesis / reelin-mediated signaling pathway / myeloid leukocyte migration / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / microtubule plus-end binding / stereocilium / retrograde axonal transport / negative regulation of JNK cascade / cytoplasmic dynein complex / osteoclast development / dynein light intermediate chain binding / P-body assembly / stem cell division / brain morphogenesis / nuclear migration / kinesin complex / microtubule associated complex / motile cilium / dynein intermediate chain binding / dynein complex binding / cochlea development / cytoplasmic microtubule / transmission of nerve impulse / cell leading edge / establishment of mitotic spindle orientation / germ cell development / phospholipase binding / dynactin binding / neuromuscular process controlling balance / protein secretion / neuroblast proliferation / positive regulation of axon extension / microtubule-based process / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / lipid catabolic process / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / Mitotic Prometaphase / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / EML4 and NUDC in mitotic spindle formation / Recruitment of mitotic centrosome proteins and complexes / JNK cascade / axon cytoplasm / stress granule assembly / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of mitotic spindle organization / Resolution of Sister Chromatid Cohesion / MHC class II antigen presentation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / positive regulation of mitotic cell cycle / mitotic spindle organization / adult locomotory behavior / filopodium / RHO GTPases Activate Formins / phosphoprotein binding / hippocampus development / neuron migration / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / cerebral cortex development / kinetochore / microtubule cytoskeleton organization / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition
Similarity search - Function
Dynein regulator LIS1 / LIS1, N-terminal / : / LisH / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / Lissencephaly type-1-like homology motif ...Dynein regulator LIS1 / LIS1, N-terminal / : / LisH / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / Lissencephaly type-1-like homology motif / : / Dynein heavy chain, ATPase lid domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / LIS1 homology (LisH) motif profile. / LIS1 homology motif / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Platelet-activating factor acetylhydrolase IB subunit beta / Cytoplasmic dynein 1 heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsReimer JM / DeSantis M / Reck-Peterson SL / Leschziner AE
Funding support United States, 2 items
OrganizationGrant numberCountry
Damon Runyon Cancer Research FoundationDRG-2370-19 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM107214 United States
Citation
Journal: Elife / Year: 2023
Title: Structures of human dynein in complex with the lissencephaly 1 protein, LIS1.
Authors: Janice M Reimer / Morgan E DeSantis / Samara L Reck-Peterson / Andres E Leschziner /
Abstract: The lissencephaly 1 protein, LIS1, is mutated in type-1 lissencephaly and is a key regulator of cytoplasmic dynein-1. At a molecular level, current models propose that LIS1 activates dynein by ...The lissencephaly 1 protein, LIS1, is mutated in type-1 lissencephaly and is a key regulator of cytoplasmic dynein-1. At a molecular level, current models propose that LIS1 activates dynein by relieving its autoinhibited form. Previously we reported a 3.1 Å structure of yeast dynein bound to Pac1, the yeast homologue of LIS1, which revealed the details of their interactions (Gillies et al., 2022). Based on this structure, we made mutations that disrupted these interactions and showed that they were required for dynein's function in vivo in yeast. We also used our yeast dynein-Pac1 structure to design mutations in human dynein to probe the role of LIS1 in promoting the assembly of active dynein complexes. These mutations had relatively mild effects on dynein activation, suggesting that there may be differences in how dynein and Pac1/LIS1 interact between yeast and humans. Here, we report cryo-EM structures of human dynein-LIS1 complexes. Our new structures reveal the differences between the yeast and human systems, provide a blueprint to disrupt the human dynein-LIS1 interactions more accurately, and map type-1 lissencephaly disease mutations, as well as mutations in dynein linked to malformations of cortical development/intellectual disability, in the context of the dynein-LIS1 complex.
#1: Journal: Elife / Year: 2022
Title: Structural basis for cytoplasmic dynein-1 regulation by Lis1.
Authors: Gillies JP / Reimer JM / Karasmanis EP / Lahiri I / Htet ZM / Leschziner AE / Reck-Peterson SL
History
DepositionAug 5, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27782.png

Downloads & links

-
Map

FileDownload / File: emd_27782.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 352 pix.
= 408.32 Å		1.16 Å/pix.
x 352 pix.
= 408.32 Å		1.16 Å/pix.
x 352 pix.
= 408.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-0.527888 - 0.9157968
Average (Standard dev.)-0.00027608298 (±0.024737578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 408.31998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_27782_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_27782_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human cytoplasmic dynein-1 bound to two Lis1 WD40 domains.

EntireName: Human cytoplasmic dynein-1 bound to two Lis1 WD40 domains.
Components
  • Complex: Human cytoplasmic dynein-1 bound to two Lis1 WD40 domains.
    • Protein or peptide: Cytoplasmic dynein 1 heavy chain 1
    • Protein or peptide: Platelet-activating factor acetylhydrolase IB subunit beta
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: Human cytoplasmic dynein-1 bound to two Lis1 WD40 domains.

SupramoleculeName: Human cytoplasmic dynein-1 bound to two Lis1 WD40 domains.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Cytoplasmic dynein 1 heavy chain 1

MacromoleculeName: Cytoplasmic dynein 1 heavy chain 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 380.953594 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GQVALEELQD LKGVWSELSK VWEQIDQMKE QPWVSVQPRK LRQNLDALLN QLKSFPARLR QYASYEFVQR LLKGYMKINM LVIELKSEA LKDRHWKQLM KRLHVNWVVS ELTLGQIWDV DLQKNEAIVK DVLLVAQGEM ALEEFLKQIR EVWNTYELDL V NYQNKCRL ...String:
GQVALEELQD LKGVWSELSK VWEQIDQMKE QPWVSVQPRK LRQNLDALLN QLKSFPARLR QYASYEFVQR LLKGYMKINM LVIELKSEA LKDRHWKQLM KRLHVNWVVS ELTLGQIWDV DLQKNEAIVK DVLLVAQGEM ALEEFLKQIR EVWNTYELDL V NYQNKCRL IRGWDDLFNK VKEHINSVSA MKLSPYYKVF EEDALSWEDK LNRIMALFDV WIDVQRRWVY LEGIFTGSAD IK HLLPVET QRFQSISTEF LALMKKVSKS PLVMDVLNIQ GVQRSLERLA DLLGKIQKAL GEYLERERSS FPRFYFVGDE DLL EIIGNS KNVAKLQKHF KKMFAGVSSI ILNEDNSVVL GISSREGEEV MFKTPVSITE HPKINEWLTL VEKEMRVTLA KLLA ESVTE VEIFGKATSI DPNTYITWID KYQAQLVVLS AQIAWSENVE TALSSMGGGG DAAPLHSVLS NVEVTLNVLA DSVLM EQPP LRRRKLEHLI TELVHQRDVT RSLIKSKIDN AKSFEWLSQM RFYFDPKQTD VLQQLSIQMA NAKFNYGFEY LGVQDK LVQ TPLTDRCYLT MTQALEARLG GSPFGPAGTG KTESVKALGH QLGRFVLVFN CDETFDFQAM GRIFVGLCQV GAWGCFD EF NRLEERMLSA VSQQVQCIQE ALREHSNPNY DKTSAPITCE LLNKQVKVSP DMAIFITMNP GYAGRSNLPD NLKKLFRS L AMTKPDRQLI AQVMLYSQGF RTAEVLANKI VPFFKLCDEQ LSSQSHYDFG LRALKSVLVS AGNVKRERIQ KIKREKEER GEAVDEGEIA ENLPEQEILI QSVCETMVPK LVAEDIPLLF SLLSDVFPGV QYHRGEMTAL REELKKVCQE MYLTYGDGEE VGGMWVEKV LQLYQITQIN HGLMMVGPSG SGKSMAWRVL LKALERLEGV EGVAHIIDPK AISKDHLYGT LDPNTREWTD G LFTHVLRK IIDSVRGELQ KRQWIVFDGD VDPEWVENLN SVLDDNKLLT LPNGERLSLP PNVRIMFEVQ DLKYATLATV SR CGMVWFS EDVLSTDMIF NNFLARLRSI PLDEGEDEAQ RRRKGKEDEG EEAASPMLQI QRDAATIMQP YFTSNGLVTK ALE HAFQLE HIMDLTRLRC LGSLFSMLHQ ACRNVAQYNA NHPDFPMQIE QLERYIQRYL VYAILWSLSG DSRLKMRAEL GEYI RRITT VPLPTAPNIP IIDYEVSISG EWSPWQAKVP QIEVETHKVA APDVVVPTLD TVRHEALLYT WLAEHKPLVL CGPPG SGKT MTLFSALRAL PDMEVVGLNF SSATTPELLL KTFDHYCEYR RTPNGVVLAP VQLGKWLVLF CDEINLPDMD KYGTQR VIS FIRQMVEHGG FYRTSDQTWV KLERIQFVGA CNPPTDPGRK PLSHRFLRHV PVVYVDYPGP ASLTQIYGTF NRAMLRL IP SLRTYAEPLT AAMVEFYTMS QERFTQDTQP HYIYSPREMT RWVRGIFEAL RPLETLPVEG LIRIWAHEAL RLFQDRLV E DEERRWTDEN IDTVALKHFP NIDREKAMSR PILYSNWLSK DYIPVDQEEL RDYVKARLKV FYEEELDVPL VLFNEVLDH VLRIDRIFRQ PQGHLLLIGV SGAGKTTLSR FVAWMNGLSV YQIKVHRKYT GEDFDEDLRT VLRRSGCKNE KIAFIMDESN VLDSGFLER MNTLLANGEV PGLFEGDEYA TLMTQCKEGA QKEGLMLDSH EELYKWFTSQ VIRNLHVVFT MNPSSEGLKD R AATSPALF NRCVLNWFGD WSTEALYQVG KEFTSKMDLE KPNYIVPDYM PVVYDKLPQP PSHREAIVNS CVFVHQTLHQ AN ARLAKRG GRTMAITPRH YLDFINHYAN LFHEKRSELE EQQMHLNVGL RKIKETVDQV EELRRDLRIK SQELEVKNAA AND KLKKMV KDQQEAEKKK VMSQEIQEQL HKQQEVIADK QMSVKEDLDK VEPAVIEAQN AVKSIKKQHL VEVRSMANPP AAVK LALES ICLLLGESTT DWKQIRSIIM RENFIPTIVN FSAEEISDAI REKMKKNYMS NPSYNYEIVN RASLACGPMV KWAIA QLNY ADMLKRVEPL RNELQKLEDD AKDNQQKANE VEQMIRDLEA SIARYKEEYA VLISEAQAIK ADLAAVEAKV NRSTAL LKS LSAERERWEK TSETFKNQMS TIAGDCLLSA AFIAYAGYFD QQMRQNLFTT WSHHLQQANI QFRTDIARTE YLSNADE RL RWQASSLPAD DLCTENAIML KRFNRYPLII DPSGQATEFI MNEYKDRKIT RTSFLDDAFR KNLESALRFG NPLLVQDV E SYDPVLNPVL NREVRRTGGR VLITLGDQDI DLSPSFVIFL STRDPTVEFP PDLCSRVTFV NFTVTRSSLQ SQCLNEVLK AERPDVDEKR SDLLKLQGEF QLRLRQLEKS LLQALNEVKG RILDDDTIIT TLENLKREAA EVTRKVEETD IVMQEVETVS QQYLPLSTA CSSIYFTMES LKQIHFLYQY SLQFFLDIYH NVLYENPNLK GVTDHTQRLS IITKDLFQVA FNRVARGMLH Q DHITFAML LARIKLKGTV GEPTYDAEFQ HFLRGNEIVL SAGSTPRIQG LTVEQAEAVV RLSCLPAFKD LIAKVQADEQ FG IWLDSSS PEQTVPYLWS EETPATPIGQ AIHRLLLIQA FRPDRLLAMA HMFVSTNLGE SFMSIMEQPL DLTHIVGTEV KPN TPVLMC SVPGYDASGH VEDLAAEQNT QITSIAIGSA EGFNQADKAI NTAVKSGRWV MLKNVHLAPG WLMQLEKKLH SLQP HACFR LFLTMEINPK VPVNLLRAGR IFVFEPPPGV KANMLRTFSS IPVSRICKSP NERARLYFLL AWFHAIIQER LRYAP LGWS KKYEFGESDL RSACDTVDTW LDDTAKGRQN ISPDKIPWSA LKTLMAQSIY GGRVDNEFDQ RLLNTFLERL FTTRSF DSE FKLACKVDGH KDIQMPDGIR REEFVQWVEL LPDTQTPSWL GLPNNAERVL LTTQGVDMIS KMLKMQMLED EDDLAYA ET EKKTRTDSTS DGRPAWMRTL HTTASNWLHL IPQTLSHLKR TVENIKDPLF RFFEREVKMG AKLLQDVRQD LADVVQVC E GKKKQTNYLR TLINELVKGI LPRSWSHYTV PAGMTVIQWV SDFSERIKQL QNISLAAASG GAKELKNIHV CLGGLFVPE AYITATRQYV AQANSWSLEE LCLEVNVTTS QGATLDACSF GVTGLKLQGA TCNNNKLSLS NAISTALPLT QLRWVKQTNT EKKASVVTL PVYLNFTRAD LIFTVDFEIA TKEDPRSFYE RGVAVLCTE

UniProtKB: Cytoplasmic dynein 1 heavy chain 1

-
Macromolecule #2: Platelet-activating factor acetylhydrolase IB subunit beta

MacromoleculeName: Platelet-activating factor acetylhydrolase IB subunit beta
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.722918 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSVLSQRQRD ELNRAIADYL RSNGYEEAYS VFKKEAELDV NEELDKKYAG LLEKKWTSVI RLQKKVMELE SKLNEAKEEF TSGGPLGQK RDPKEWIPRP PEKYALSGHR SPVTRVIFHP VFSVMVSASE DATIKVWDYE TGDFERTLKG HTDSVQDISF D HSGKLLAS ...String:
GSVLSQRQRD ELNRAIADYL RSNGYEEAYS VFKKEAELDV NEELDKKYAG LLEKKWTSVI RLQKKVMELE SKLNEAKEEF TSGGPLGQK RDPKEWIPRP PEKYALSGHR SPVTRVIFHP VFSVMVSASE DATIKVWDYE TGDFERTLKG HTDSVQDISF D HSGKLLAS CSADMTIKLW DFQGFECIRT MHGHDHNVSS VAIMPNGDHI VSASRDKTIK MWEVQTGYCV KTFTGHREWV RM VRPNQDG TLIASCSNDQ TVRVWVVATK ECKAELREHE HVVECISWAP ESSYSSISEA TGSETKKSGK PGPFLLSGSR DKT IKMWDV STGMCLMTLV GHDNWVRGVL FHSGGKFILS CADDKTLRVW DYKNKRCMKT LNAHEHFVTS LDFHKTAPYV VTGS VDQTV KVWECR

UniProtKB: Platelet-activating factor acetylhydrolase IB subunit beta

-
Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

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

5nug

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37288
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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