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- EMDB-19477: Saccharomyces cerevisiae FAS type I -

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Basic information

Entry
Database: EMDB / ID: EMD-19477
TitleSaccharomyces cerevisiae FAS type I
Map datasharp map from cryosparc software
Sample
  • Complex: Saccharomyces cerevisiae FAS type I
    • Protein or peptide: Fatty acid synthase subunit alpha
    • Protein or peptide: Fatty acid synthase subunit beta
KeywordsFatty acid synthase / complex / TRANSFERASE
Function / homology
Function and homology information


: / fatty-acyl-CoA synthase system / : / fatty-acyl-CoA synthase activity / fatty acid synthase complex / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase activity / oleoyl-[acyl-carrier-protein] hydrolase ...: / fatty-acyl-CoA synthase system / : / fatty-acyl-CoA synthase activity / fatty acid synthase complex / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase activity / oleoyl-[acyl-carrier-protein] hydrolase / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / holo-[acyl-carrier-protein] synthase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid synthase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / long-chain fatty acid biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / lipid droplet / magnesium ion binding / mitochondrion / cytosol / cytoplasm
Similarity search - Function
: / Fatty acid synthase, meander beta sheet domain / Fatty acid synthase subunit beta, N-terminal domain / N-terminal domain in fatty acid synthase subunit beta / Fatty acid synthase meander beta sheet domain / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase alpha subunit, yeast ...: / Fatty acid synthase, meander beta sheet domain / Fatty acid synthase subunit beta, N-terminal domain / N-terminal domain in fatty acid synthase subunit beta / Fatty acid synthase meander beta sheet domain / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase alpha subunit, yeast / Fatty acid synthase subunit beta/Fas1-like, helical / Fatty acid synthase type I, helical / Fatty acid synthase type I helical domain / Fatty acid synthase / N-terminal of MaoC-like dehydratase / N-terminal half of MaoC dehydratase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / MaoC-like dehydratase domain / MaoC like domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / HotDog domain superfamily / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Phosphopantetheine attachment site. / Thiolase-like / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Fatty acid synthase subunit beta / Fatty acid synthase subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMann D / Grininger M / Ludig D / Sachse C
Funding support Germany, 1 items
OrganizationGrant numberCountry
Helmholtz AssociationPoF 5352 Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: VitroJet: new features and case studies.
Authors: Rene J M Henderikx / Daniel Mann / Aušra Domanska / Jing Dong / Saba Shahzad / Behnam Lak / Aikaterini Filopoulou / Damian Ludig / Martin Grininger / Jeffrey Momoh / Elina Laanto / Hanna M ...Authors: Rene J M Henderikx / Daniel Mann / Aušra Domanska / Jing Dong / Saba Shahzad / Behnam Lak / Aikaterini Filopoulou / Damian Ludig / Martin Grininger / Jeffrey Momoh / Elina Laanto / Hanna M Oksanen / Kyrylo Bisikalo / Pamela A Williams / Sarah J Butcher / Peter J Peters / Bart W A M M Beulen /
Abstract: Single-particle cryo-electron microscopy has become a widely adopted method in structural biology due to many recent technological advances in microscopes, detectors and image processing. Before ...Single-particle cryo-electron microscopy has become a widely adopted method in structural biology due to many recent technological advances in microscopes, detectors and image processing. Before being able to inspect a biological sample in an electron microscope, it needs to be deposited in a thin layer on a grid and rapidly frozen. The VitroJet was designed with this aim, as well as avoiding the delicate manual handling and transfer steps that occur during the conventional grid-preparation process. Since its creation, numerous technical developments have resulted in a device that is now widely utilized in multiple laboratories worldwide. It features plasma treatment, low-volume sample deposition through pin printing, optical ice-thickness measurement and cryofixation of pre-clipped Autogrids through jet vitrification. This paper presents recent technical improvements to the VitroJet and the benefits that it brings to the cryo-EM workflow. A wide variety of applications are shown: membrane proteins, nucleosomes, fatty-acid synthase, Tobacco mosaic virus, lipid nanoparticles, tick-borne encephalitis viruses and bacteriophages. These case studies illustrate the advancement of the VitroJet into an instrument that enables accurate control and reproducibility, demonstrating its suitability for time-efficient cryo-EM structure determination.
History
DepositionJan 25, 2024-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19477.png

Downloads & links

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Map

FileDownload / File: emd_19477.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharp map from cryosparc software
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 417.792 Å		0.82 Å/pix.
x 512 pix.
= 417.792 Å		0.82 Å/pix.
x 512 pix.
= 417.792 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.816 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.3728831 - 0.69717646
Average (Standard dev.)0.0026049875 (±0.026240263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 417.792 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19477_msk_1.map
Projections & Slices
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Half map: half map B

Fileemd_19477_half_map_1.map
Annotationhalf map B
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_19477_half_map_2.map
Annotationhalf map A
Projections & Slices
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Sample components

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Entire : Saccharomyces cerevisiae FAS type I

EntireName: Saccharomyces cerevisiae FAS type I
Components
  • Complex: Saccharomyces cerevisiae FAS type I
    • Protein or peptide: Fatty acid synthase subunit alpha
    • Protein or peptide: Fatty acid synthase subunit beta

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Supramolecule #1: Saccharomyces cerevisiae FAS type I

SupramoleculeName: Saccharomyces cerevisiae FAS type I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Fatty acid synthase subunit alpha

MacromoleculeName: Fatty acid synthase subunit alpha / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKPEVEQELA HILLTELLAY QFASPVRWIE TQDVFLKDFN TERVVEIGPS PTLAGMAQRT LKNKYESYDA ALSLHREILC YSKDAKEIYY TPDPSELAAK EEPAKEEAPA PTPAASAPAP AAAAPAPVAA AAPAAAAAEI ADEPVKASLL LHVLVAHKLK KSLDSIPMSK ...String:
MKPEVEQELA HILLTELLAY QFASPVRWIE TQDVFLKDFN TERVVEIGPS PTLAGMAQRT LKNKYESYDA ALSLHREILC YSKDAKEIYY TPDPSELAAK EEPAKEEAPA PTPAASAPAP AAAAPAPVAA AAPAAAAAEI ADEPVKASLL LHVLVAHKLK KSLDSIPMSK TIKDLVGGKS TVQNEILGDL GKEFGTTPEK PEETPLEELA ETFQDTFSGA LGKQSSSLLS RLISSKMPGG FTITVARKYL QTRWGLPSGR QDGVLLVALS NEPAARLGSE ADAKAFLDSM AQKYASIVGV DLSSAASASG AAGAGAAAGA AMIDAGALEE ITKDHKVLAR QQLQVLARYL KMDLDNGERK FLKEKDTVAE LQAQLDYLNA ELGEFFVNGV ATSFSRKKAR TFDSSWNWAK QSLLSLYFEI IHGVLKNVDR EVVSEAINIM NRSNDALIKF MEYHISNTDE TKGENYQLVK TLGEQLIENC KQVLDVDPVY KDVAKPTGPK TAIDKNGNIT YSEEPREKVR KLSQYVQEMA LGGPITKESQ PTIEEDLTRV YKAISAQADK QDISSSTRVE FEKLYSDLMK FLESSKEIDP SQTTQLAGMD VEDALDKDST KEVASLPNKS TISKTVSSTI PRETIPFLHL RKKTPAGDWK YDRQLSSLFL DGLEKAAFNG VTFKDKYVLI TGAGKGSIGA EVLQGLLQGG AKVVVTTSRF SKQVTDYYQS IYAKYGAKGS TLIVVPFNQG SKQDVEALIE FIYDTEKNGG LGWDLDAIIP FAAIPEQGIE LEHIDSKSEF AHRIMLTNIL RMMGCVKKQK SARGIETRPA QVILPMSPNH GTFGGDGMYS ESKLSLETLF NRWHSESWAN QLTVCGAIIG WTRGTGLMSA NNIIAEGIEK MGVRTFSQKE MAFNLLGLLT PEVVELCQKS PVMADLNGGL QFVPELKEFT AKLRKELVET SEVRKAVSIE TALEHKVVNG NSADAAYAQV EIQPRANIQL DFPELKPYKQ VKQIAPAELE GLLDLERVIV VTGFAEVGPW GSARTRWEME AFGEFSLEGC VEMAWIMGFI SYHNGNLKGR PYTGWVDSKT KEPVDDKDVK AKYETSILEH SGIRLIEPEL FNGYNPEKKE MIQEVIVEED LEPFEASKET AEQFKHQHGD KVDIFEIPET GEYSVKLLKG ATLYIPKALR FDRLVAGQIP TGWNAKTYGI SDDIISQVDP ITLFVLVSVV EAFIASGITD PYEMYKYVHV SEVGNCSGSG MGGVSALRGM FKDRFKDEPV QNDILQESFI NTMSAWVNML LISSSGPIKT PVGACATSVE SVDIGVETIL SGKARICIVG GYDDFQEEGS FEFGNMKATS NTLEEFEHGR TPAEMSRPAT TTRNGFMEAQ GAGIQIIMQA DLALKMGVPI YGIVAMAATA TDKIGRSVPA PGKGILTTAR EHHSSVKYAS PNLNMKYRKR QLVTREAQIK DWVENELEAL KLEAEEIPSE DQNEFLLERT REIHNEAESQ LRAAQQQWGN DFYKRDPRIA PLRGALATYG LTIDDLGVAS FHGTSTKAND KNESATINEM MKHLGRSEGN PVIGVFQKFL TGHPKGAAGA WMMNGALQIL NSGIIPGNRN ADNVDKILEQ FEYVLYPSKT LKTDGVRAVS ITSFGFGQKG GQAIVVHPDY LYGAITEDRY NEYVAKVSAR EKSAYKFFHN GMIYNKLFVS KEHAPYTDEL EEDVYLDPLA RVSKDKKSGS LTFNSKNIQS KDSYINANTI ETAKMIENMT KEKVSNGGVG VDVELITSIN VENDTFIERN FTPQEIEYCS AQPSVQSSFA GTWSAKEAVF KSLGVKSLGG GAALKDIEIV RVNKNAPAVE LHGNAKKAAE EAGVTDVKVS ISHDDLQAVA VAVSTKK

UniProtKB: Fatty acid synthase subunit alpha

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Macromolecule #2: Fatty acid synthase subunit beta

MacromoleculeName: Fatty acid synthase subunit beta / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDAYSTRPLT LSHGSLEHVL LVPTASFFIA SQLQEQFNKI LPEPTEGFAA DDEPTTPAEL VGKFLGYVSS LVEPSKVGQF DQVLNLCLTE FENCYLEGND IHALAAKLLQ ENDTTLVKTK ELIKNYITAR IMAKRPFDKK SNSALFRAVG EGNAQLVAIF GGQGNTDDYF ...String:
MDAYSTRPLT LSHGSLEHVL LVPTASFFIA SQLQEQFNKI LPEPTEGFAA DDEPTTPAEL VGKFLGYVSS LVEPSKVGQF DQVLNLCLTE FENCYLEGND IHALAAKLLQ ENDTTLVKTK ELIKNYITAR IMAKRPFDKK SNSALFRAVG EGNAQLVAIF GGQGNTDDYF EELRDLYQTY HVLVGDLIKF SAETLSELIR TTLDAEKVFT QGLNILEWLE NPSNTPDKDY LLSIPISCPL IGVIQLAHYV VTAKLLGFTP GELRSYLKGA TGHSQGLVTA VAIAETDSWE SFFVSVRKAI TVLFFIGVRC YEAYPNTSLP PSILEDSLEN NEGVPSPMLS ISNLTQEQVQ DYVNKTNSHL PAGKQVEISL VNGAKNLVVS GPPQSLYGLN LTLRKAKAPS GLDQSRIPFS ERKLKFSNRF LPVASPFHSH LLVPASDLIN KDLVKNNVSF NAKDIQIPVY DTFDGSDLRV LSGSISERIV DCIIRLPVKW ETTTQFKATH ILDFGPGGAS GLGVLTHRNK DGTGVRVIVA GTLDINPDDD YGFKQEIFDV TSNGLKKNPN WLEEYHPKLI KNKSGKIFVE TKFSKLIGRP PLLVPGMTPC TVSPDFVAAT TNAGYTIELA GGGYFSAAGM TAAIDSVVSQ IEKGSTFGIN LIYVNPFMLQ WGIPLIKELR SKGYPIQFLT IGAGVPSLEV ASEYIETLGL KYLGLKPGSI DAISQVINIA KAHPNFPIAL QWTGGRGGGH HSFEDAHTPM LQMYSKIRRH PNIMLIFGSG FGSADDTYPY LTGEWSTKFD YPPMPFDGFL FGSRVMIAKE VKTSPDAKKC IAACTGVPDD KWEQTYKKPT GGIVTVRSEM GEPIHKIATR GVMLWKEFDE TIFNLPKNKL VPTLEAKRDY IISRLNADFQ KPWFATVNGQ ARDLATMTYE EVAKRLVELM FIRSTNSWFD VTWRTFTGDF LRRVEERFTK SKTLSLIQSY SLLDKPDEAI EKVFNAYPAA REQFLNAQDI DHFLSMCQNP MQKPVPFVPV LDRRFEIFFK KDSLWQSEHL EAVVDQDVQR TCILHGPVAA QFTKVIDEPI KSIMDGIHDG HIKKLLHQYY GDDESKIPAV EYFGGESPVD VQSQVDSSSV SEDSAVFKAT SSTDEESWFK ALAGSEINWR HASFLCSFIT QDKMFVSNPI RKVFKPSQGM VVEISNGNTS SKTVVTLSEP VQGELKPTVI LKLLKENIIQ MEMIENRTMD GKPVSLPLLY NFNPDNGFAP ISEVMEDRNQ RIKEMYWKLW IDEPFNLDFD PRDVIKGKDF EITAKEVYDF THAVGNNCED FVSRPDRTML APMDFAIVVG WRAIIKAIFP NTVDGDLLKL VHLSNGYKMI PGAKPLQVGD VVSTTAVIES VVNQPTGKIV DVVGTLSRNG KPVMEVTSSF FYRGNYTDFE NTFQKTVEPV YQMHIKTSKD IAVLRSKEWF QLDDEDFDLL NKTLTFETET EVTFKNANIF SSVKCFGPIK VELPTKETVE IGIVDYEAGA SHGNPVVDFL KRNGSTLEQK VNLENPIPIA VLDSYTPSTN EPYARVSGDL NPIHVSRHFA SYANLPGTIT HGMFSSASVR ALIENWAADS VSSRVRGYTC QFVDMVLPNT ALKTSIQHVG MINGRKLIKF ETRNEDDVVV LTGEAEIEQP VTTFVFTGQG SQEQGMGMDL YKTSKAAQDV WNRADNHFKD TYGFSILDIV INNPVNLTIH FGGEKGKRIR ENYSAMIFET IVDGKLKTEK IFKEINEHST SYTFRSEKGL LSATQFTQPA LTLMEKAAFE DLKSKGLIPA DATFAGHSLG EYAALASLAD VMSIESLVEV VFYRGMTMQV AVPRDELGRS NYGMIAINPG RVAASFSQEA LQYVVERVGK RTGWLVEIVN YNVENQQYVA AGDLRALDTV TNVLNFIKLQ KIDIIELQKS LSLEEVEGHL FEIIDEASKK SAVKPRPLKL ERGFACIPLV GISVPFHSTY LMNGVKPFKS FLKKNIIKEN VKVARLAGKY IPNLTAKPFQ VTKEYFQDVY DLTGSEPIKE IIDNWEKYEQ S

UniProtKB: Fatty acid synthase subunit beta

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5 / Component - Concentration: 100.0 mM / Component - Formula: KPi / Component - Name: potassium phosphate
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: OTHER
Details: External glow discharge with Pelco EasiGlow plus internal glow discharging in VitroJet. VitroJet pins were cleaned with detergent and 70% EtOH in an ultrasonic bath (5 minutes each), ...Details: External glow discharge with Pelco EasiGlow plus internal glow discharging in VitroJet. VitroJet pins were cleaned with detergent and 70% EtOH in an ultrasonic bath (5 minutes each), followed by 1 min drying under nitrogen stream. Freshly purified FAS was pin printed at 4 degC climate chamber temperature with a 70 micrometer spiral, 15 micrometer standoff with a velocity of 5 mm per second.. The value given for _em_vitrification.instrument is CRYOSOL VITROJET. This is not in a list of allowed values {'HOMEMADE PLUNGER', 'FEI VITROBOT MARK III', 'FEI VITROBOT MARK II', 'FEI VITROBOT MARK I', 'GATAN CRYOPLUNGE 3', 'LEICA PLUNGER', 'LEICA EM GP', 'REICHERT-JUNG PLUNGER', 'LEICA EM CPC', 'OTHER', 'FEI VITROBOT MARK IV', 'SPOTITON', 'EMS-002 RAPID IMMERSION FREEZER', 'LEICA KF80'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS TALOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 3696 / Average electron dose: 48.0 e/Å2

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Image processing

Startup modelType of model: NONE / Details: ab initio 3D
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 10000 / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45979
DetailsCDS mode
FSC plot (resolution estimation)

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