+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-19477 | |||||||||
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タイトル | Saccharomyces cerevisiae FAS type I | |||||||||
マップデータ | sharp map from cryosparc software | |||||||||
試料 |
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キーワード | Fatty acid synthase / complex / TRANSFERASE | |||||||||
機能・相同性 | 機能・相同性情報 : / 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 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.3 Å | |||||||||
データ登録者 | Mann D / Grininger M / Ludig D / Sachse C | |||||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: Acta Crystallogr D Struct Biol / 年: 2024 タイトル: VitroJet: new features and case studies. 著者: 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 ...著者: 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 / 要旨: 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. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_19477.map.gz | 483.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-19477-v30.xml emd-19477.xml | 21.2 KB 21.2 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_19477_fsc.xml | 17 KB | 表示 | FSCデータファイル |
画像 | emd_19477.png | 215.7 KB | ||
マスクデータ | emd_19477_msk_1.map | 512 MB | マスクマップ | |
Filedesc metadata | emd-19477.cif.gz | 7.7 KB | ||
その他 | emd_19477_half_map_1.map.gz emd_19477_half_map_2.map.gz | 474.2 MB 474.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-19477 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19477 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_19477_validation.pdf.gz | 1.2 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_19477_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | emd_19477_validation.xml.gz | 26.8 KB | 表示 | |
CIF形式データ | emd_19477_validation.cif.gz | 34.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19477 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19477 | HTTPS FTP |
-関連構造データ
関連構造データ | C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_19477.map.gz / 形式: CCP4 / 大きさ: 512 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | sharp map from cryosparc software | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.816 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
ファイル | emd_19477_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: half map B
ファイル | emd_19477_half_map_1.map | ||||||||||||
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注釈 | half map B | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: half map A
ファイル | emd_19477_half_map_2.map | ||||||||||||
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注釈 | half map A | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Saccharomyces cerevisiae FAS type I
全体 | 名称: Saccharomyces cerevisiae FAS type I |
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要素 |
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-超分子 #1: Saccharomyces cerevisiae FAS type I
超分子 | 名称: Saccharomyces cerevisiae FAS type I / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) |
-分子 #1: Fatty acid synthase subunit alpha
分子 | 名称: Fatty acid synthase subunit alpha / タイプ: protein_or_peptide / ID: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) |
配列 | 文字列: MKPEVEQELA HILLTELLAY QFASPVRWIE TQDVFLKDFN TERVVEIGPS PTLAGMAQRT LKNKYESYDA ALSLHREILC YSKDAKEIYY TPDPSELAAK EEPAKEEAPA PTPAASAPAP AAAAPAPVAA AAPAAAAAEI ADEPVKASLL LHVLVAHKLK KSLDSIPMSK ...文字列: 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 |
-分子 #2: Fatty acid synthase subunit beta
分子 | 名称: Fatty acid synthase subunit beta / タイプ: protein_or_peptide / ID: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) |
配列 | 文字列: MDAYSTRPLT LSHGSLEHVL LVPTASFFIA SQLQEQFNKI LPEPTEGFAA DDEPTTPAEL VGKFLGYVSS LVEPSKVGQF DQVLNLCLTE FENCYLEGND IHALAAKLLQ ENDTTLVKTK ELIKNYITAR IMAKRPFDKK SNSALFRAVG EGNAQLVAIF GGQGNTDDYF ...文字列: 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 |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 6.5 / 構成要素 - 濃度: 100.0 mM / 構成要素 - 式: KPi / 構成要素 - 名称: potassium phosphate |
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グリッド | モデル: UltrAuFoil R1.2/1.3 / 材質: GOLD / メッシュ: 300 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 60 sec. |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 278 K / 装置: OTHER 詳細: 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 ...詳細: 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. |
-電子顕微鏡法
顕微鏡 | TFS TALOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 実像数: 3696 / 平均電子線量: 48.0 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 0.5 µm / 倍率(公称値): 100000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |