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- PDB-6o7u: Saccharomyces cerevisiae V-ATPase Stv1-VO -

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基本情報

登録情報
データベース: PDB / ID: 6o7u
タイトルSaccharomyces cerevisiae V-ATPase Stv1-VO
要素
  • (V-type proton ATPase subunit ...) x 6
  • Putative protein YPR170W-B
  • V0 assembly protein 1
キーワードMEMBRANE PROTEIN / Proton pump
機能・相同性
機能・相同性情報


cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / P-type proton-exporting transporter activity / plasma membrane proton-transporting V-type ATPase complex / endosomal lumen acidification ...cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / P-type proton-exporting transporter activity / plasma membrane proton-transporting V-type ATPase complex / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar transport / vacuole organization / protein targeting to vacuole / proton-transporting V-type ATPase complex / fungal-type vacuole / fungal-type vacuole membrane / vacuolar proton-transporting V-type ATPase complex / phosphatidylinositol-4-phosphate binding / vacuolar acidification / proton transmembrane transporter activity / intracellular copper ion homeostasis / proton transmembrane transport / Neutrophil degranulation / RNA endonuclease activity / proton-transporting ATPase activity, rotational mechanism / cell periphery / transmembrane transport / endocytosis / late endosome / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / early endosome / endosome membrane / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / membrane
類似検索 - 分子機能
Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / V-ATPase proteolipid subunit / ATPase, V0 complex, c/d subunit ...Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / V-ATPase proteolipid subunit / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
類似検索 - ドメイン・相同性
V-type proton ATPase subunit f / V-type proton ATPase subunit c'' / V-type proton ATPase subunit c / V-type proton ATPase subunit d / V-type proton ATPase subunit c' / V-type proton ATPase subunit a, Golgi isoform / V0 assembly protein 1 / V-type proton ATPase subunit e
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
手法電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.1 Å
データ登録者Vasanthakumar, T. / Bueler, S.A. / Wu, D. / Beilsten-Edmands, V. / Robinson, C.V. / Rubinstein, J.L.
資金援助 カナダ, 1件
組織認可番号国
Canadian Institutes of Health Research (CIHR)MOP81294 カナダ
引用ジャーナル: Proc Natl Acad Sci U S A / 年: 2019
タイトル: Structural comparison of the vacuolar and Golgi V-ATPases from .
著者: Thamiya Vasanthakumar / Stephanie A Bueler / Di Wu / Victoria Beilsten-Edmands / Carol V Robinson / John L Rubinstein /
要旨: Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal ...Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal acidification. In mammals, V-ATPase subunit isoforms are differentially targeted to various intracellular compartments or tissues, but how these subunit isoforms influence enzyme activity is not clear. In the yeast , isoform diversity is limited to two different versions of the proton-translocating subunit a: Vph1p, which is targeted to the vacuole, and Stv1p, which is targeted to the Golgi apparatus and endosomes. We show that purified V-ATPase complexes containing Vph1p have higher ATPase activity than complexes containing Stv1p and that the relative difference in activity depends on the presence of lipids. We also show that V complexes containing Stv1p could be readily purified without attached V regions. We used this effect to determine structures of the membrane-embedded V region with Stv1p at 3.1-Å resolution, which we compare with a structure of the V region with Vph1p that we determine to 3.2-Å resolution. These maps reveal differences in the surface charge near the cytoplasmic proton half-channel. Both maps also show the presence of bound lipids, as well as regularly spaced densities that may correspond to ergosterol or bound detergent, around the c-ring.
履歴
登録2019年3月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年4月3日Provider: repository / タイプ: Initial release
改定 1.12019年4月10日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22019年4月24日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32019年12月18日Group: Author supporting evidence / Other / カテゴリ: atom_sites / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _pdbx_audit_support.funding_organization
改定 1.42024年3月20日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

ムービー
  • 登録構造単位
  • Jmolによる作画
  • ダウンロード
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-0645
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
a: V-type proton ATPase subunit a, Golgi isoform
b: V0 assembly protein 1
c: V-type proton ATPase subunit c''
d: V-type proton ATPase subunit d
e: V-type proton ATPase subunit e
f: Putative protein YPR170W-B
g: V-type proton ATPase subunit c
h: V-type proton ATPase subunit c
i: V-type proton ATPase subunit c
j: V-type proton ATPase subunit c
k: V-type proton ATPase subunit c
l: V-type proton ATPase subunit c
m: V-type proton ATPase subunit c
n: V-type proton ATPase subunit c
o: V-type proton ATPase subunit c'


分子量 (理論値)分子数
合計 (水以外)362,27315
ポリマ－362,27315
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: microscopy
タイプ名称対称操作数
identity operation1_5551

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要素

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V-type proton ATPase subunit ... , 6種, 13分子 acdeghijklmno

#1: タンパク質 V-type proton ATPase subunit a, Golgi isoform / V-ATPase a 2 subunit / Similar to VPH1 protein 1 / V-ATPase 101 kDa subunit / V-ATPase subunit ...V-ATPase a 2 subunit / Similar to VPH1 protein 1 / V-ATPase 101 kDa subunit / V-ATPase subunit AC115 / Vacuolar proton translocating ATPase subunit a 2


分子量: 104481.141 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P37296
#3: タンパク質 V-type proton ATPase subunit c'' / V-ATPase subunit c'' / V-ATPase 22 kDa proteolipid subunit / Vacuolar proton pump c'' subunit


分子量: 22610.641 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P23968
#4: タンパク質