+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19477 | |||||||||
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Title | Saccharomyces cerevisiae FAS type I | |||||||||
Map data | sharp map from cryosparc software | |||||||||
Sample |
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Keywords | Fatty acid synthase / complex / TRANSFERASE | |||||||||
Function / homology | Function and homology information : / fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase activity / fatty acyl-[ACP] hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase ...: / fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase activity / fatty acyl-[ACP] hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / : / holo-[acyl-carrier-protein] synthase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / 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 / fatty acid synthase activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / lipid droplet / magnesium ion binding / mitochondrion / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Mann D / Grininger M / Ludig D / Sachse C | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19477.map.gz | 483.9 MB | EMDB map data format | |
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Header (meta data) | emd-19477-v30.xml emd-19477.xml | 21.2 KB 21.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19477_fsc.xml | 17 KB | Display | FSC data file |
Images | emd_19477.png | 215.7 KB | ||
Masks | emd_19477_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-19477.cif.gz | 7.7 KB | ||
Others | emd_19477_half_map_1.map.gz emd_19477_half_map_2.map.gz | 474.2 MB 474.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19477 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19477 | HTTPS FTP |
-Validation report
Summary document | emd_19477_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_19477_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_19477_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | emd_19477_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19477 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19477 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_19477.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | sharp map from cryosparc software | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.816 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19477_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_19477_half_map_1.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_19477_half_map_2.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Saccharomyces cerevisiae FAS type I
Entire | Name: Saccharomyces cerevisiae FAS type I |
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Components |
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-Supramolecule #1: Saccharomyces cerevisiae FAS type I
Supramolecule | Name: Saccharomyces cerevisiae FAS type I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Fatty acid synthase subunit alpha
Macromolecule | Name: Fatty acid synthase subunit alpha / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: 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 |
-Macromolecule #2: Fatty acid synthase subunit beta
Macromolecule | Name: Fatty acid synthase subunit beta / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 / Component - Concentration: 100.0 mM / Component - Formula: KPi / Component - Name: potassium phosphate |
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen 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. |
-Electron microscopy
Microscope | TFS TALOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 3696 / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 100000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |