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- EMDB-26254: Structure of the yeast TRAPPII-Rab11/Ypt32 complex in the closed/... -

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基本情報

登録情報
データベース: EMDB / ID: EMD-26254
タイトルStructure of the yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (composite structure)
マップデータComposite map of TRAPPII-Ypt32 symmetric closed/closed dimer
試料
  • 複合体: TRAPPII complex bound to Rab11/Ypt32
    • タンパク質・ペプチド: x 13種
  • リガンド: x 1種
キーワードcomplex / GTPase / Guanosine Exchange Factor / GEF / PROTEIN TRANSPORT
機能・相同性
機能・相同性情報


Anchoring of the basal body to the plasma membrane / beta-glucan biosynthetic process / TRAPPI protein complex / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / early endosome to Golgi transport / COPII-mediated vesicle transport ...Anchoring of the basal body to the plasma membrane / beta-glucan biosynthetic process / TRAPPI protein complex / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / early endosome to Golgi transport / COPII-mediated vesicle transport / cis-Golgi network membrane / cytoplasm to vacuole targeting by the Cvt pathway / protein localization to phagophore assembly site / intra-Golgi vesicle-mediated transport / cellular bud neck / cis-Golgi network / protein-containing complex localization / phagophore assembly site / retrograde transport, endosome to Golgi / cellular response to nitrogen starvation / exocytosis / positive regulation of macroautophagy / chromosome organization / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / Neutrophil degranulation / macroautophagy / trans-Golgi network / recycling endosome / cell wall organization / autophagy / protein transport / protein-containing complex assembly / mitochondrial outer membrane / early endosome / endosome / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum / Golgi apparatus / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
TRAPP II complex, Trs120 / TRAPP II complex TRAPPC10, C-terminal / Trafficking protein particle complex II-specific subunit 65 / Trafficking protein particle complex subunit TRAPPC10/Trs130 / : / : / : / Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit / Trafficking protein particle complex subunit 10, TRAPPC10 / TRAPP trafficking subunit Trs65 IgD3 ...TRAPP II complex, Trs120 / TRAPP II complex TRAPPC10, C-terminal / Trafficking protein particle complex II-specific subunit 65 / Trafficking protein particle complex subunit TRAPPC10/Trs130 / : / : / : / Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit / Trafficking protein particle complex subunit 10, TRAPPC10 / TRAPP trafficking subunit Trs65 IgD3 / Trafficking protein particle complex subunit 10-like, N-terminal / TRAPP trafficking subunit Trs65 IgD1 / TRAPP trafficking subunit Trs65 IgD2 / Trafficking protein particle complex subunit 2 / Sedlin, N-terminal conserved region / Trafficking protein particle complex subunit / Sybindin-like family / Sybindin-like family / TRAPP I complex, subunit 5 / TRAPP complex, Trs33 subunit / Bet3 family / Transport protein particle (TRAPP) component / Transport protein particle (TRAPP) component / : / NO signalling/Golgi transport ligand-binding domain superfamily / Longin-like domain superfamily / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
TRAPP-associated protein TCA17 / Trafficking protein particle complex II-specific subunit 65 / Trafficking protein particle complex subunit BET3 / Trafficking protein particle complex subunit 20 / GTP-binding protein YPT32/YPT11 / Trafficking protein particle complex subunit 31 / Trafficking protein particle complex subunit BET5 / Trafficking protein particle complex II-specific subunit 130 / Trafficking protein particle complex subunit 23 / Trafficking protein particle complex II-specific subunit 120 / Trafficking protein particle complex subunit 33
類似検索 - 構成要素
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: 3.7 Å
データ登録者Bagde SR / Fromme JC
資金援助 米国, 2件
OrganizationGrant number国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM136258 米国
National Science Foundation (NSF, United States)DMR-1719875 米国
引用ジャーナル: Sci Adv / 年: 2022
タイトル: Structure of a TRAPPII-Rab11 activation intermediate reveals GTPase substrate selection mechanisms.
著者: Saket R Bagde / J Christopher Fromme /
要旨: Rab1 and Rab11 are essential regulators of the eukaryotic secretory and endocytic recycling pathways. The transport protein particle (TRAPP) complexes activate these guanosine triphosphatases via ...Rab1 and Rab11 are essential regulators of the eukaryotic secretory and endocytic recycling pathways. The transport protein particle (TRAPP) complexes activate these guanosine triphosphatases via nucleotide exchange using a shared set of core subunits. The basal specificity of the TRAPP core is toward Rab1, yet the TRAPPII complex is specific for Rab11. A steric gating mechanism has been proposed to explain TRAPPII counterselection against Rab1. Here, we present cryo-electron microscopy structures of the 22-subunit TRAPPII complex from budding yeast, including a TRAPPII-Rab11 nucleotide exchange intermediate. The Trs130 subunit provides a "leg" that positions the active site distal to the membrane surface, and this leg is required for steric gating. The related TRAPPIII complex is unable to activate Rab11 because of a repulsive interaction, which TRAPPII surmounts using the Trs120 subunit as a "lid" to enclose the active site. TRAPPII also adopts an open conformation enabling Rab11 to access and exit from the active site chamber.
履歴
登録2022年2月17日-
ヘッダ(付随情報) 公開2022年4月27日-
マップ公開2022年4月27日-
更新2024年10月16日-
現状2024年10月16日処理サイト: RCSB / 状態: 公開

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構造の表示

添付画像

emd_26254.png

ダウンロードとリンク

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マップ

ファイルダウンロード / ファイル: emd_26254.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈Composite map of TRAPPII-Ypt32 symmetric closed/closed dimer
投影像・断面図

画像のコントロール

大きさ
明度
コントラスト
その他
軸Z (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 400 pix.
= 572.8 Å		1.43 Å/pix.
x 400 pix.
= 572.8 Å		1.43 Å/pix.
x 400 pix.
= 572.8 Å

表面

投影像

断面 (1/3)

断面 (1/2)

断面 (2/3)

画像は Spider により作成

ボクセルのサイズX=Y=Z: 1.432 Å
密度

ヒストグラム

ヒストグラム (対数)
表面レベル登録者による: 2.5
最小 - 最大-22.622871 - 39.608699999999999
平均 (標準偏差)0.005271441 (±0.65724874)
対称性空間群: 1
詳細

EMDB XML:

マップ形状
Axis orderXYZ
Origin000
サイズ400400400
Spacing400400400
セルA=B=C: 572.8 Å
α=β=γ: 90.0 °

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添付データ

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試料の構成要素

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全体 : TRAPPII complex bound to Rab11/Ypt32

全体名称: TRAPPII complex bound to Rab11/Ypt32
要素
  • 複合体: TRAPPII complex bound to Rab11/Ypt32
    • タンパク質・ペプチド: Trafficking protein particle complex II-specific subunit 130
    • タンパク質・ペプチド: Trafficking protein particle complex II-specific subunit 65
    • タンパク質・ペプチド: TRAPP-associated protein TCA17
    • タンパク質・ペプチド: Trafficking protein particle complex subunit 33
    • タンパク質・ペプチド: Trafficking protein particle complex subunit BET3
    • タンパク質・ペプチド: Trafficking protein particle complex subunit BET5
    • タンパク質・ペプチド: Trafficking protein particle complex subunit 23
    • タンパク質・ペプチド: Trafficking protein particle complex subunit 31
    • タンパク質・ペプチド: Trafficking protein particle complex subunit 20
    • タンパク質・ペプチド: GTP-binding protein YPT32/YPT11
    • タンパク質・ペプチド: Trafficking protein particle complex II-specific subunit 130
    • タンパク質・ペプチド: Trafficking protein particle complex II-specific subunit 120
    • タンパク質・ペプチド: Trafficking protein particle complex II-specific subunit 65
  • リガンド: PALMITIC ACID

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超分子 #1: TRAPPII complex bound to Rab11/Ypt32

超分子名称: TRAPPII complex bound to Rab11/Ypt32 / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#13
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 1.1 MDa

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分子 #1: Trafficking protein particle complex II-specific subunit 130

分子名称: Trafficking protein particle complex II-specific subunit 130
タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 20.61332 KDa
配列文字列: (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) ...文字列:
(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)

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分子 #2: Trafficking protein particle complex II-specific subunit 65

分子名称: Trafficking protein particle complex II-specific subunit 65
タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 63.434473 KDa
配列文字列: MECFVPLRCD LDGSNIEQLR QSHLSRKFII FDEQLNLWLW FQGNSQENKR FVLQNMIILI NEAQVTRTST IDDYFTQVEN NENLWRLKN DCCSKILFKS NVVMNNGYNN QIKFVFEYKS VDANFNNQDS LQDPQAKYTL DKYSSEEILP SFEPVYSWSS A ATKSSKNT ...文字列:
MECFVPLRCD LDGSNIEQLR QSHLSRKFII FDEQLNLWLW FQGNSQENKR FVLQNMIILI NEAQVTRTST IDDYFTQVEN NENLWRLKN DCCSKILFKS NVVMNNGYNN QIKFVFEYKS VDANFNNQDS LQDPQAKYTL DKYSSEEILP SFEPVYSWSS A ATKSSKNT NNHLEKNNRA THRVSSKNSE VHEADVSRNP NTFTLKLQYP IFSLLNMRLR NISLKSEHCI LSSLDFQTSK AS EQLTKKF IYPQEHNSFL KLNFQEISYK LIDGTSQIEL DPICPLKVPL TAFSYDSISA TFKLVLLPKS TQPHRVKITL AYE LELHPN LKLPVRTSWE TEVTLKRSMP ISSTSSQYSS NNNNTNHSAS FNGAANNVNS GGLANLRLGG VSSSRFSLGA ASTT SLVNS KLSNVKFKFI NSNIKVIKGE KFTMRLQIIN SSSSPLDLVV YYNNTINPIP SANNVRNSNG INNCGMNNGT IPNSP LTLE NQYQLHNKYR KIAEGIILLS NDYKIPVVPP RETYFADLRF IGIMSGYYGT LSGLKVLDLN TNELIEVGNG ASVLIQ

UniProtKB: Trafficking protein particle complex II-specific subunit 65

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分子 #3: TRAPP-associated protein TCA17

分子名称: TRAPP-associated protein TCA17 / タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 17.371008 KDa
配列文字列:
MSLRPCFVSL IDESDKPILI YVPNEAENEM NDVLKYNVLS NISLDYFESA LVEWHSLDSK PLLKSIFQLE GVSVFAMLIK QTGLKIVIG FEQKSLSGAD DEFEAINQIF ETVRKIYIRV KCNPLLVSGD EKSIIKSLER KFDELFISTE VEL

UniProtKB: TRAPP-associated protein TCA17

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分子 #4: Trafficking protein particle complex subunit 33

分子名称: Trafficking protein particle complex subunit 33 / タイプ: protein_or_peptide / ID: 4 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 30.786176 KDa
配列文字列: MSSTHSNNVG HPQSSPQGPL TEQQRAQQQY QIFENSLPKV SQSVYQMLLN EMVPLAMGIE RQISGDVISS DSNVTSENGN INNMIKRLK IEEHHTVDII RSHNLIHELY KADEEEKEKV LARLRNIGFQ IGLKLSELLI FSNNPNLKFK EMDLLLIMKF I CRDVWKQI ...文字列:
MSSTHSNNVG HPQSSPQGPL TEQQRAQQQY QIFENSLPKV SQSVYQMLLN EMVPLAMGIE RQISGDVISS DSNVTSENGN INNMIKRLK IEEHHTVDII RSHNLIHELY KADEEEKEKV LARLRNIGFQ IGLKLSELLI FSNNPNLKFK EMDLLLIMKF I CRDVWKQI FGKQIDNLKT NHRGTFYLLD YDYRPIQSFS LEEDAKNEEL KMIEPFLEIP VGIIRGVLSS LGYSSEEVIC LA SFIDRPT DRPKTAFPKG VSFHVQVTMP Q

UniProtKB: Trafficking protein particle complex subunit 33

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分子 #5: Trafficking protein particle complex subunit BET3

分子名称: Trafficking protein particle complex subunit BET3 / タイプ: protein_or_peptide / ID: 5 / コピー数: 4 / 光学異性体: LEVO
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 22.152445 KDa
配列文字列: MVSTTQSRSL KAMGEEIWKN KTEKINTELF TLTYGSIVAQ LCQDYERDFN KVNDHLYSMG YNIGCRLIED FLARTALPRC ENLVKTSEV LSKCAFKIFL NITPNITNWS HNKDTFSLIL DENPLADFVE LPMDAMKSLW YSNILCGVLK GSLEMVQLDC D VWFVSDIL ...文字列:
MVSTTQSRSL KAMGEEIWKN KTEKINTELF TLTYGSIVAQ LCQDYERDFN KVNDHLYSMG YNIGCRLIED FLARTALPRC ENLVKTSEV LSKCAFKIFL NITPNITNWS HNKDTFSLIL DENPLADFVE LPMDAMKSLW YSNILCGVLK GSLEMVQLDC D VWFVSDIL RGDSQTEIKV KLNRILKDEI PIGED

UniProtKB: Trafficking protein particle complex subunit BET3

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分子 #6: Trafficking protein particle complex subunit BET5

分子名称: Trafficking protein particle complex subunit BET5 / タイプ: protein_or_peptide / ID: 6 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 18.453875 KDa
配列文字列:
MGIYSFWIFD RHCNCIFDRE WTLASNSASG TINSKQNEED AKLLYGMIFS LRSITQKLSK GSVKNDIRSI STGKYRVHTY CTASGLWFV LLSDFKQQSY TQVLQYIYSH IYVKYVSNNL LSPYDFAENE NEMRGQGTRK ITNRNFISVL ESFLAPMVNQ

UniProtKB: Trafficking protein particle complex subunit BET5

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分子 #7: Trafficking protein particle complex subunit 23

分子名称: Trafficking protein particle complex subunit 23 / タイプ: protein_or_peptide / ID: 7 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 24.889262 KDa
配列文字列: MAIETILVIN KSGGLIYQRN FTNDEQKLNS NEYLILASTL HGVFAIASQL TPKALQLTQQ TNIENTIPYI PYVGMSSNRS DTRNGGGNN NKHTNNEKLG SFKGDDFFKE PFTNWNKSGL RQLCTDQFTM FIYQTLTGLK FVAISSSVMP QRQPTIATTD K PDRPKSTS ...文字列:
MAIETILVIN KSGGLIYQRN FTNDEQKLNS NEYLILASTL HGVFAIASQL TPKALQLTQQ TNIENTIPYI PYVGMSSNRS DTRNGGGNN NKHTNNEKLG SFKGDDFFKE PFTNWNKSGL RQLCTDQFTM FIYQTLTGLK FVAISSSVMP QRQPTIATTD K PDRPKSTS NLAIQIADNF LRKVYCLYSD YVMKDPSYSM EMPIRSNLFD EKVKKMVENL Q

UniProtKB: Trafficking protein particle complex subunit 23

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分子 #8: Trafficking protein particle complex subunit 31

分子名称: Trafficking protein particle complex subunit 31 / タイプ: protein_or_peptide / ID: 8 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 31.755689 KDa
配列文字列: MSQRIIQPSA SDQQFPGKSD GYEYTVGPKQ AITSEASTTY IPSRIYSESL LFKRQEASLS AMAFLFQEMI SQLHRTCKTA GDFETKLSD YGHNIGIRLL ELLNFRASVS PSSLPRASAF LSQNESSSKL SNASNSPGML ANSSTATSAS ANERLQEKQT E SLSNYITK ...文字列:
MSQRIIQPSA SDQQFPGKSD GYEYTVGPKQ AITSEASTTY IPSRIYSESL LFKRQEASLS AMAFLFQEMI SQLHRTCKTA GDFETKLSD YGHNIGIRLL ELLNFRASVS PSSLPRASAF LSQNESSSKL SNASNSPGML ANSSTATSAS ANERLQEKQT E SLSNYITK MRRRDLKILD ILQFIHGTLW SYLFNHVSDD LVKSSERDNE YMIVDNFPTL TQFIPGENVS CEYFVCGIIK GF LFNAGFP CGVTAHRMPQ GGHSQRTVYL IQFDRQVLDR EGLRFG

UniProtKB: Trafficking protein particle complex subunit 31

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分子 #9: Trafficking protein particle complex subunit 20

分子名称: Trafficking protein particle complex subunit 20 / タイプ: protein_or_peptide / ID: 9 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 19.721154 KDa
配列文字列:
MPQYFAIIGK KDNPVYEIEF TNAENPQGFP QDLKELNPFI LHASLDIVED LQWQINPTSQ LNGNGGNGSN GGGGFLRSRA VNNTDNCYL GKVDHFYGLA ITAYISYSGM KFVMIHGNSA NSSVVIDDNN MRSFYQEVHE LYVKTLMNPF YKITDPIRSP A FDSRVRTL ARKHLSK

UniProtKB: Trafficking protein particle complex subunit 20

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分子 #10: GTP-binding protein YPT32/YPT11

分子名称: GTP-binding protein YPT32/YPT11 / タイプ: protein_or_peptide / ID: 10 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 25.309145 KDa
組換発現生物種: Escherichia coli BL21 (大腸菌)
配列文字列: MSNEDYGYDY DYLFKIVLIG DSGVGKSNLL SRFTTDEFNI ESKSTIGVEF ATRTIEVENK KIKAQIWDTA GQERYRAITS AYYRGAVGA LIVYDISKSS SYENCNHWLT ELRENADDNV AVGLIGNKSD LAHLRAVPTD EAKNFAMENQ MLFTETSALN S DNVDKAFR ...文字列:
MSNEDYGYDY DYLFKIVLIG DSGVGKSNLL SRFTTDEFNI ESKSTIGVEF ATRTIEVENK KIKAQIWDTA GQERYRAITS AYYRGAVGA LIVYDISKSS SYENCNHWLT ELRENADDNV AVGLIGNKSD LAHLRAVPTD EAKNFAMENQ MLFTETSALN S DNVDKAFR ELIVAIFQMV SKHQVDLSGS GTNNMGSNGA PKGPTISLTP APKEDKKKKS SNHHHHHHH

UniProtKB: GTP-binding protein YPT32/YPT11

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分子 #11: Trafficking protein particle complex II-specific subunit 130

分子名称: Trafficking protein particle complex II-specific subunit 130
タイプ: protein_or_peptide / ID: 11 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 128.42425 KDa
配列文字列: MDKEIYCGSV PVSYFDPFDL FESLRPEFQQ ILPLDNIHWK AFDGTVRTVN RLPIELIPEG RGEADKSNDE QPFIRFLIVN CISIDQYRA KVRPLVRQWL PNLESVSSST GEKMIYKPII LLYANSEVVD SNLFKSVSLM EKFGKDFPHV QTLEVRSVYR S PKERQEFW ...文字列:
MDKEIYCGSV PVSYFDPFDL FESLRPEFQQ ILPLDNIHWK AFDGTVRTVN RLPIELIPEG RGEADKSNDE QPFIRFLIVN CISIDQYRA KVRPLVRQWL PNLESVSSST GEKMIYKPII LLYANSEVVD SNLFKSVSLM EKFGKDFPHV QTLEVRSVYR S PKERQEFW NQFSQKIKAS VLSIFQKRLT HLQHSLANLQ KGNNFEEQLL TREKLYELYV VFNILEDASL ELQKIKKEIL RR NMNMPDG KLQVPFESSS KSDESLGSII IEGTLDKFQL HKYFFIRRLR LLKLEDQTLT AFVGAFQLIK NFIESISIEY RKS VRLLEF KHYFITSMLS YFEFENVSNP LLCEIKAELL MLKRDNWVQG VMATSGYRLM DKNYPNSDVK YKFDLLKETF VDET VFQEN FLTLTKEILS LFNKCEGKRQ RIVDILSIEI GLLYYQGKKY EEAVSLFLSC YEYYTQTNWN SIGLKILQVF IDSLS HCPK LDVLQIDGES VSASAVLTNA FLNILKLCKD NDSKEIWWKK FMDLQMKNNI HLMYPLDGLF EVTLNSKVHL ARANVS AIE VNLKSYGFPE DISTKTMRLS LKNMGGDVIV FGASDFLLKK GENKLILECR DIMYGEFSLL SFEIIVEGIT FVKEFPE NQ DEFIVVPEIY CKESTKVLVK QAHNLNLGEY ALELKSVQSD ALESLQVEVE VQKNIGNMKN LPVSFSMDEI QARKRYNT P FENVRLEYYL LDQITAFDLI IKTSFTKKND QGTFGETKKV RIQCYLQLSV SVEDIFKKDI FFFKFLLNSS VREEPVILY SSELSAPDTR NDYNIRGDYI ATTPALITFD GNESFINCYE ITANNNFDSK DIFNLKVRYN TLKEQLDCFI TDAVLIEGDV EWFILFEKW KTFWELEILK KLKYDYDAFK ENRIIRLLKT SIDLNKTKSK IRNLCIEKAV LDKILICLNK VSRGIAVCNT D MDEYVRNL VPKQLTVPVQ LPGFEQFFHV QFEQMETSHD ALHDTIATIG NSLSYTVIVE NLSGQWGQDV IDDGGYIFEI LS SNEWLIH GQKRCAIKEK RKEFEVHLIP LKKGYLNFPR VEITNINGKS CRVDHSNAFE SILIFAA

UniProtKB: Trafficking protein particle complex II-specific subunit 130

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分子 #12: Trafficking protein particle complex II-specific subunit 120

分子名称: Trafficking protein particle complex II-specific subunit 120
タイプ: protein_or_peptide / ID: 12 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 147.823281 KDa
配列文字列: MNILKHFPSY VGPSKIRTLV IPIGHWTRKE FNNAVQKLSE FNEIHLSDVT PIDSPIFTPQ GFPHGKLFFD FLTIDHDDAL ELFLYDFEP FRKTFVIIGL VNDYSDPLTN LNFMKEKYPT LISPNLVYAS STPTKELEQT IDTMENVFAS SPDMQKNIET I MCDIARNF ...文字列:
MNILKHFPSY VGPSKIRTLV IPIGHWTRKE FNNAVQKLSE FNEIHLSDVT PIDSPIFTPQ GFPHGKLFFD FLTIDHDDAL ELFLYDFEP FRKTFVIIGL VNDYSDPLTN LNFMKEKYPT LISPNLVYAS STPTKELEQT IDTMENVFAS SPDMQKNIET I MCDIARNF LTALNSYYSS YKHVTLRSPG AIGGNAVLKT TLIRQNSYTS SSSSTPMSAV QSSVSSSSKA GSVTTASKRL SS FEMTTNS LKRSASLKLA TTLSTSENRS QQKSLGRQMK ILGNFQLLAG RYVDALNSFV DAITTLYKVR DYLWLGSALD GIS ICFLLL SYLGLSYQIP QIVSLICPVE KLNFESSSTG ISPVDSNSKA TASTTASSTP RNSISIAAMQ SPRNSIMSLS APAL NIDVE NINLPLLIKC ISDKVLYYYD LSLMHNSEYA PQVVYCEFLL KTLTFMTSCY KSSEFSKDVL DNIVKNQHRA LSDIP NSPM FPRFEVYFYS NKLFELQLKE MQVEAQIKIY STMAEVYRLL GYKRKQLFVL RLLMVALLAT PNKIAWHPDY RTLIDT IIE LLNINESEAK INVDDPSQST WLILQKKILQ LCIKVSRKIN DFEYVAKFSS ILITKYTHLL NQSEQDALFK EYIQPSI TN ESITSYWDPF ILREVVINRI LDSDPTSNEI PLESDVSSLE SLENRQKTQD INPQEVFNPF KRVQPTSFVS NNSTKVPI L VFLVGDKAEF TCRVQNPFKF DFTINDIQLD EEISEFCEID RKAVSYSGPY NVKAESIRSI TLPLIIKKPT YKKIYEISC LKISILKLPL QKFDIINDSR RSNPVEEEAE YSKCIYGKLK IKILPEQPQL ELLSTSKMTR NSWMMLDGTK TDFHITVRNK SLSCAINHI KIIPMNNIEQ MLKPDYWKKM PPDDLYIMEK QLDWLSKSCV RIIKLPTVIK PNETITFDLE LDNTAVPFNF T GFDLLIEY GMSATDESCI YLKKLSIPYE VTLRRTIEVP SMDIIPLNEL FSSQVENVDW IEYVMSKIRA ESNLHSRDFI LL LLDFRNS WIDGIKLNVQ FEDFTSNEYH VEASHTSRII VPIKKIDYKK YNFENTPIPR IYPGRQFIQS GLNEEQTIEM RQK FWCREH IISKLKCNWK LTTDQSVTGS VDFNKFIEKF DHKMVYTIYP GRLFYGVQLL LDEPKVKVGE IINLKIITEP TSTC RRKQN STVNFLDIVI FDSKTSKILP RSNRRILYNG SLTKPISTTK VSEINLEIIP IEKGRYEFSV CISKSNNQDG IIQFD SENV ILSVI

UniProtKB: Trafficking protein particle complex II-specific subunit 120

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分子 #13: Trafficking protein particle complex II-specific subunit 65

分子名称: Trafficking protein particle complex II-specific subunit 65
タイプ: protein_or_peptide / ID: 13 / コピー数: 2 / 光学異性体: LEVO
由来(天然)生物種: Saccharomyces cerevisiae (パン酵母)
分子量理論値: 17.889996 KDa
配列文字列: (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) ...文字列:
(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)

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分子 #14: PALMITIC ACID

分子名称: PALMITIC ACID / タイプ: ligand / ID: 14 / コピー数: 4 / 式: PLM
分子量理論値: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID / パルミチン酸

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実験情報

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構造解析

手法クライオ電子顕微鏡法
解析単粒子再構成法
試料の集合状態particle

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試料調製

濃度5.6 mg/mL
緩衝液pH: 8
構成要素:
濃度名称
10.0 mMTris
150.0 mMSodium chloride
0.1 %CHAPS
1.0 mMMagnesium acetate
1.0 mMDTT
グリッドモデル: UltrAuFoil R1.2/1.3 / 材質: GOLD / メッシュ: 300 / 支持フィルム - 材質: GOLD / 支持フィルム - トポロジー: HOLEY / 支持フィルム - Film thickness: 50 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 30 sec. / 前処理 - 雰囲気: AIR
凍結凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV
詳細: The sample was incubated on the grid for 10 seconds followed by blotting for 5 seconds before plunging in liquid ethane..

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電子顕微鏡法

顕微鏡FEI TALOS ARCTICA
特殊光学系エネルギーフィルター - 名称: GIF Bioquantum / エネルギーフィルター - スリット幅: 20 eV
撮影フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k)
デジタル化 - サイズ - 横: 5760 pixel / デジタル化 - サイズ - 縦: 4092 pixel / 撮影したグリッド数: 3 / 実像数: 4998 / 平均露光時間: 3.5 sec. / 平均電子線量: 53.0 e/Å2 / 詳細: Images were collected as 50 frame movies.
電子線加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN
電子光学系C2レンズ絞り径: 50.0 µm / 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）: 2.5 µm / 最小 デフォーカス（公称値）: 0.8 µm / 倍率（公称値）: 63000
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
実験機器
モデル: Talos Arctica / 画像提供: FEI Company

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画像解析

粒子像選択選択した数: 979187
初期モデルモデルのタイプ: INSILICO MODEL
In silico モデル: Used Ab-initio Reconstruction job in cryoSPARC to generate starting map.
最終 再構成想定した対称性 - 点群: C2 (2回回転対称) / 解像度のタイプ: BY AUTHOR / 解像度: 3.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: PHENIX
詳細: The composite map was generated by combining the consensus dimer map (EMD-26221) with focused refinement maps deposited in the entries EMD-26223, EMD-26224. EMD-26225, EMD-26226, EMD-26227, ...詳細: The composite map was generated by combining the consensus dimer map (EMD-26221) with focused refinement maps deposited in the entries EMD-26223, EMD-26224. EMD-26225, EMD-26226, EMD-26227, EMD-26228, EMD-26229, EMD-26230, EMD-26231 and EMD-26232 using Combine Focused Maps in Phenix.
使用した粒子像数: 369488
初期 角度割当タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: cryoSPARC (ver. 3.2.0)
最終 角度割当タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.1)

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原子モデル構築 1

初期モデル
PDB IDChain

3cue

source_name: PDB, initial_model_type: experimental model

3rwo

source_name: PDB, initial_model_type: experimental model

3pr6

source_name: PDB, initial_model_type: experimental model
詳細Model was rebuilt in coot and refined using phenix.real_space_refine.
精密化空間: REAL / プロトコル: OTHER
得られたモデル

PDB-7u05:
Structure of the yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (composite structure)

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る