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- PDB-5lc5: Structure of mammalian respiratory Complex I, class2 -

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登録情報
データベース: PDB / ID: 5lc5
タイトルStructure of mammalian respiratory Complex I, class2
要素
  • (Acyl carrier protein, ...) x 2
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 12
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 11
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 3
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 7
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, NDUFS1
キーワードOXIDOREDUCTASE / NADH:ubiquinone oxidoreductase / multienzyme complexes / Complex I / mitochondria
機能・相同性
機能・相同性情報


Complex I biogenesis / RHOG GTPase cycle / Respiratory electron transport / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / gliogenesis / neural precursor cell proliferation / [2Fe-2S] cluster assembly / oxygen sensor activity / Neutrophil degranulation ...Complex I biogenesis / RHOG GTPase cycle / Respiratory electron transport / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / gliogenesis / neural precursor cell proliferation / [2Fe-2S] cluster assembly / oxygen sensor activity / Neutrophil degranulation / mitochondrial ATP synthesis coupled electron transport / Mitochondrial protein degradation / acyl binding / ubiquinone binding / acyl carrier activity / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / neurogenesis / reactive oxygen species metabolic process / aerobic respiration / fatty acid binding / respiratory electron transport chain / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / fatty acid biosynthetic process / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / mitochondrial matrix / negative regulation of DNA-templated transcription / apoptotic process / mitochondrion / nucleoplasm / metal ion binding / cytoplasm
類似検索 - 分子機能
SLBB domain / Complex1_LYR-like / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / Tim17/Tim22/Tim23/Pmp24 family / NADH-ubiquinone oxidoreductase, subunit 10 ...SLBB domain / Complex1_LYR-like / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / Tim17/Tim22/Tim23/Pmp24 family / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / 2Fe-2S iron-sulfur cluster binding domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / : / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / : / : / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase subunit 2 C-terminus / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase 1 alpha subcomplex subunit 3 / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / GRIM-19 / GRIM-19 protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NDUFB9, LYR domain / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NDUFA6, LYR domain / Deoxynucleoside kinase domain / Deoxynucleoside kinase / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / : / SLBB domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / : / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / Complex 1 LYR protein domain / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Complex 1 protein (LYR family) / NADH:ubiquinone oxidoreductase / : / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit
類似検索 - ドメイン・相同性
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / IRON/SULFUR CLUSTER / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 ...FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / IRON/SULFUR CLUSTER / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / Acyl carrier protein, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
類似検索 - 構成要素
生物種Bos taurus (ウシ)
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: 4.35 Å
データ登録者Vinothkumar, K.R. / Zhu, J. / Hirst, J.
資金援助 英国, 1件
組織認可番号国
Medical Research Council (United Kingdom)U105184322/U105663141 英国
引用ジャーナル: Nature / 年: 2016
タイトル: Structure of mammalian respiratory complex I.
著者: Jiapeng Zhu / Kutti R Vinothkumar / Judy Hirst /
要旨: Complex I (NADH:ubiquinone oxidoreductase), one of the largest membrane-bound enzymes in the cell, powers ATP synthesis in mammalian mitochondria by using the reducing potential of NADH to drive ...Complex I (NADH:ubiquinone oxidoreductase), one of the largest membrane-bound enzymes in the cell, powers ATP synthesis in mammalian mitochondria by using the reducing potential of NADH to drive protons across the inner mitochondrial membrane. Mammalian complex I (ref. 1) contains 45 subunits, comprising 14 core subunits that house the catalytic machinery (and are conserved from bacteria to humans) and a mammalian-specific cohort of 31 supernumerary subunits. Knowledge of the structures and functions of the supernumerary subunits is fragmentary. Here we describe a 4.2-Å resolution single-particle electron cryomicroscopy structure of complex I from Bos taurus. We have located and modelled all 45 subunits, including the 31 supernumerary subunits, to provide the entire structure of the mammalian complex. Computational sorting of the particles identified different structural classes, related by subtle domain movements, which reveal conformationally dynamic regions and match biochemical descriptions of the 'active-to-de-active' enzyme transition that occurs during hypoxia. Our structures therefore provide a foundation for understanding complex I assembly and the effects of mutations that cause clinically relevant complex I dysfunctions, give insights into the structural and functional roles of the supernumerary subunits and reveal new information on the mechanism and regulation of catalysis.
履歴
登録2016年6月19日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02016年9月7日Provider: repository / タイプ: Initial release
改定 1.12017年8月2日Group: Data collection / Refinement description / カテゴリ: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.name / _em_software.version
改定 1.22017年8月23日Group: Source and taxonomy / Structure summary / カテゴリ: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
改定 1.32019年12月11日Group: Other / カテゴリ: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
改定 1.42024年10月23日Group: Data collection / Database references / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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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-4032
  • 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

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集合体

登録構造単位
A: NADH-ubiquinone oxidoreductase chain 3
B: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
C: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
D: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
E: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
F: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
G: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, NDUFS1
H: NADH-ubiquinone oxidoreductase chain 1
I: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
J: NADH-ubiquinone oxidoreductase chain 6
K: NADH-ubiquinone oxidoreductase chain 4L
L: NADH-ubiquinone oxidoreductase chain 5
M: NADH-ubiquinone oxidoreductase chain 4
N: NADH-ubiquinone oxidoreductase chain 2
O: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, NDUFA10,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
P: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
Q: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
R: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
S: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
T: Acyl carrier protein, mitochondrial
U: Acyl carrier protein, mitochondrial
V: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
X: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Y: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Z: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
a: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
b: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
c: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
d: NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2
e: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
f: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
g: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
h: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
i: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
j: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, NDUFB2
k: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3, NDUFB3
l: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, NDUFB8
m: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
p: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10
q: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
r: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7, NDUFA7
s: NADH dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)885,28556
ポリマ－881,55845
非ポリマー3,72711
水00
1


  • 登録構造と同一
  • ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_5551
Buried area189940 Å2
ΔGint-1625 kcal/mol
Surface area326800 Å2
手法PISA

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要素

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NADH-ubiquinone oxidoreductase chain ... , 7種, 7分子 AHJKLMN

#1: タンパク質 NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


分子量: 12510.898 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
参照: UniProt: P03898, NADH:ubiquinone reductase (H+-translocating)
#8: タンパク質 NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


分子量: 35084.062 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
参照: UniProt: P03887, NADH:ubiquinone reductase (H+-translocating)
#10: タンパク質 NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


分子量: 18622.936 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
参照: UniProt: P03924, NADH:ubiquinone reductase (H+-translocating)
#11: タンパク質 NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


分子量: 10437.718 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
参照: UniProt: P03902, NADH:ubiquinone reductase (H+-translocating)
#12: タンパク質 NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


分子量: 68067.609 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
参照: UniProt: P03920, NADH:ubiquinone reductase (H+-translocating)
#13: タンパク質 NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


分子量: 51886.402 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
参照: UniProt: P03910, NADH:ubiquinone reductase (H+-translocating)
#14: タンパク質 NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


分子量: 38901.461 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
参照: UniProt: P03892, NADH:ubiquinone reductase (H+-translocating)

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7種, 7分子 BCDIQRe

#2: タンパク質 NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / Complex I-20kD / CI-20kD / NADH-ubiquinone oxidoreductase 20 kDa subunit / PSST subunit


分子量: 16625.518 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: This chain coordinates Iron-sulphur cluster. / 由来: (天然) Bos taurus (ウシ)
参照: UniProt: P42026, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#3: タンパク質 NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / Complex I-30kD / CI-30kD / NADH-ubiquinone oxidoreductase 30 kDa subunit


分子量: 24202.396 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
参照: UniProt: P23709, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#4: タンパク質 NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / Complex I-49kD / CI-49kD / NADH-ubiquinone oxidoreductase 49 kDa subunit


分子量: 48693.758 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
参照: UniProt: P17694, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#9: タンパク質 NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / Complex I-23kD / CI-23kD / NADH-ubiquinone oxidoreductase 23 kDa subunit / TYKY subunit


分子量: 20219.947 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: This chain coordinates two SF4. / 由来: (天然) Bos taurus (ウシ)
参照: UniProt: P42028, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#17: タンパク質 NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-18 kDa / CI-18 kDa / Complex I-AQDQ / CI-AQDQ / NADH-ubiquinone oxidoreductase 18 kDa subunit


分子量: 9634.868 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
#18: タンパク質 NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Complex I-13kD-A / CI-13kD-A / NADH-ubiquinone oxidoreductase 13 kDa-A subunit


分子量: 8316.853 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: This chain coordinates a Zinc ion. / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P23934
#31: タンパク質 NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Complex I-15 kDa / CI-15 kDa / NADH-ubiquinone oxidoreductase 15 kDa subunit


分子量: 12694.671 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q02379

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NADH dehydrogenase [ubiquinone] flavoprotein ... , 3種, 3分子 EFs

#5: タンパク質 NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase subunit II / NADH-ubiquinone oxidoreductase 24 kDa subunit


分子量: 27341.496 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: This chain coordinates one FES. / 由来: (天然) Bos taurus (ウシ)
参照: UniProt: P04394, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#6: タンパク質 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Complex I-51kD / CI-51kD / NADH dehydrogenase flavoprotein 1 / NADH-ubiquinone oxidoreductase 51 kDa subunit


分子量: 50718.777 Da / 分子数: 1 / 由来タイプ: 天然
詳細: This chain coordinates two iron-sulfur clusters and also binds Flavin mono nucleotide.
由来: (天然) Bos taurus (ウシ)
参照: UniProt: P25708, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#45: タンパク質・ペプチド NADH dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3


分子量: 2996.685 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)

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タンパク質 , 1種, 1分子 G

#7: タンパク質 NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, NDUFS1 / Complex I-75kD / CI-75kD


分子量: 66442.281 Da / 分子数: 1 / 由来タイプ: 天然
詳細: This chain coordinates one binuclear FES and two SF4.
由来: (天然) Bos taurus (ウシ)
参照: UniProt: P15690, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12種, 12分子 OPSVWXYZabqr

#15: タンパク質 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, NDUFA10,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Complex I-42kD / CI-42kD / NADH-ubiquinone oxidoreductase 42 kDa subunit


分子量: 34014.227 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P34942
#16: タンパク質 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / Complex I-39kD / CI-39kD / NADH-ubiquinone oxidoreductase 39 kDa subunit


分子量: 28528.021 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
#19: タンパク質 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / Complex I-B8 / CI-B8 / NADH-ubiquinone oxidoreductase B8 subunit


分子量: 9270.575 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q02370
#22: タンパク質 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / Complex I subunit B13 / Complex I-13kD-B / CI-13kD-B / NADH-ubiquinone oxidoreductase 13 kDa-B subunit


分子量: 13334.608 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P23935
#23: タンパク質 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / Complex I-B14 / CI-B14 / NADH-ubiquinone oxidoreductase B14 subunit


分子量: 15083.544 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q02366
#24: タンパク質 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / Complex I-19kD / CI-19kD / Complex I-PGIV / CI-PGIV / NADH-ubiquinone oxidoreductase 19 kDa subunit


分子量: 18115.223 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P42029
#25: タンパク質 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / Complex I-B14.7 / CI-B14.7 / NADH-ubiquinone oxidoreductase subunit B14.7


分子量: 14412.514 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q8HXG6
#26: タンパク質 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Cell death regulatory protein GRIM-19 / Complex I-B16.6 / CI-B16.6 / Gene associated with retinoic- ...Cell death regulatory protein GRIM-19 / Complex I-B16.6 / CI-B16.6 / Gene associated with retinoic-interferon-induced mortality 19 protein / GRIM-19 / NADH-ubiquinone oxidoreductase B16.6 subunit


分子量: 14135.900 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q95KV7
#27: タンパク質 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Complex I-MWFE / CI-MWFE / NADH-ubiquinone oxidoreductase MWFE subunit


分子量: 8117.445 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q02377
#28: タンパク質 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Complex I-B9 / CI-B9 / NADH-ubiquinone oxidoreductase B9 subunit


分子量: 7860.488 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q02371
#43: タンパク質 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Complex I-B17.2 / CIB17.2 / NADH-ubiquinone oxidoreductase subunit B17.2


分子量: 16309.545 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: O97725
#44: タンパク質 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7, NDUFA7


分子量: 7422.140 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)

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Acyl carrier protein, ... , 2種, 2分子 TU

#20: タンパク質 Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


分子量: 8672.939 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P52505
#21: タンパク質 Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


分子量: 9846.298 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P52505

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NADH dehydrogenase [ubiquinone] 1 subunit ... , 2種, 2分子 cd

#29: タンパク質 NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / Complex I-KFYI / CI-KFYI / NADH-ubiquinone oxidoreductase KFYI subunit


分子量: 8796.211 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q02376
#30: タンパク質 NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2 / Complex I-B14.5b / CI-B14.5b / NADH-ubiquinone oxidoreductase subunit B14.5b


分子量: 11988.300 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q02827

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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11種, 11分子 fghijklmnop

#32: タンパク質 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / Complex I-MNLL / CI-MNLL / NADH-ubiquinone oxidoreductase MNLL subunit


分子量: 6978.148 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q02378
#33: タンパク質 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / Complex I-ESSS / CI-ESSS / NADH-ubiquinone oxidoreductase ESSS subunit


分子量: 17594.945 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q8HXG5
#34: タンパク質 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / Complex I-SGDH / CI-SGDH / NADH-ubiquinone oxidoreductase SGDH subunit


分子量: 18069.865 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q02380
#35: タンパク質 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Complex I-B17 / CI-B17 / NADH-ubiquinone oxidoreductase B17 subunit


分子量: 11636.995 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q02367
#36: タンパク質 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, NDUFB2


分子量: 4443.468 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
#37: タンパク質 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3, NDUFB3


分子量: 6315.777 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
#38: タンパク質 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, NDUFB8


分子量: 10060.393 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
#39: タンパク質 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / Complex I-B15 / CI-B15 / NADH-ubiquinone oxidoreductase B15 subunit


分子量: 13415.493 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P48305
#40: タンパク質 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Complex I-B22 / CI-B22 / NADH-ubiquinone oxidoreductase B22 subunit


分子量: 19246.094 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q02369
#41: タンパク質 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Complex I-B18 / CI-B18 / NADH-ubiquinone oxidoreductase B18 subunit


分子量: 7583.900 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q02368
#42: タンパク質 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10, NDUFB10 / Complex I-PDSW / CI-PDSW / NADH-ubiquinone oxidoreductase PDSW subunit


分子量: 16906.949 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q02373

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非ポリマー , 5種, 11分子

#46: 化合物
ChemComp-SF4 / IRON/SULFUR CLUSTER


分子量: 351.640 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Fe4S4
#47: 化合物 ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


分子量: 175.820 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Fe2S2
#48: 化合物 ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / FMN


分子量: 456.344 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C17H21N4O9P
#49: 化合物 ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


分子量: 743.405 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C21H28N7O17P3
#50: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Zn

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詳細

Has protein modificationY

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: Bovine respiratory Complex I / タイプ: COMPLEX
詳細: Complex I is the first enzyme in the electron transport chain located in the inner membrane of mitochondria and in higher eukaryotes, it is a multi-subunit membrane protein complex, consisting of >40 subunits.
Entity ID: #1-#45 / 由来: NATURAL
分子量値: 1 MDa / 実験値: NO
由来(天然)生物種: Bos taurus (ウシ) / 細胞内の位置: Mitochondria / 器官: Heart / Organelle: Mitochondria
緩衝液pH: 8
緩衝液成分濃度: 150 mM / 名称: sodium chloride / 式: NaCl
試料濃度: 3.5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
詳細: Enzyme was purified from bovine heart mitochondria. The detergent used for the final step is cymal-7.
試料支持グリッドの材料: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil
急速凍結装置: HOMEMADE PLUNGER / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277.15 K
詳細: The specimen was vitrified in an environmental plunge-freeze apparatus, blot for 12-15 seconds after the diameter of the blotted meniscus ceases to spread and plunged.

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: FEI TITAN KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD / 倍率（公称値）: 59000 X / 倍率（補正後）: 105263 X / Calibrated defocus min: 1800 nm / 最大 デフォーカス（補正後）: 5500 nm / Cs: 2.7 mm / C2レンズ絞り径: 70 µm / アライメント法: COMA FREE
試料ホルダ凍結剤: NITROGEN
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
最高温度: 85 K / 最低温度: 85 K
撮影平均露光時間: 2 sec. / 電子線照射量: 35 e/Å2 / 検出モード: INTEGRATING
フィルム・検出器のモデル: FEI FALCON II (4k x 4k)
詳細: Images were collected in movie mode at 17 frames per second. Thus each frame has ~1.0 e/A2s
画像スキャンサンプリングサイズ: 14 µm / 横: 4096 / 縦: 4096 / 動画フレーム数/画像: 34 / 利用したフレーム数/画像: 1-34

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解析

ソフトウェア名称: REFMAC / バージョン: 5.8.0134 / 分類: 精密化
EMソフトウェア
ID名称バージョンカテゴリ詳細
2EPU画像取得
4CTFFIND4CTF補正CTF was estimated on the full image
7Coot0.8.3モデルフィッティングCoot was used for manual model building and fixing geometry related issues
9REFMAC5.8.0134モデル精密化
11RELION1.4最終オイラー角割当Maximum Likelihood
12RELION1.4分類Maximum Likelihood
13RELION1.4３次元再構成Maximum Likelihood
画像処理詳細: Each image was exposed for 2 seconds resulting in a total dose of ~35 e/A2s. The frames were captures with a in-house protocol at 17 frames/second.
CTF補正詳細: Ctf was estimated from the whole micrograph. Ctf was corrected per particle.
タイプ: NONE
粒子像の選択選択した粒子像数: 139456 / 詳細: All particles were picked manually
対称性点対称性: C1 (非対称)
3次元再構成解像度: 4.35 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 33301 / クラス平均像の数: 1 / 対称性のタイプ: POINT
原子モデル構築B value: 86.75 / プロトコル: OTHER / 空間: RECIPROCAL / Target criteria: Maximum likelihood
精密化解像度: 4.35→478.8 Å / Cor.coef. Fo:Fc: 0.945 / SU B: 23.477 / SU ML: 0.274 / ESU R: 0.224
立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES
Rfactor反射数%反射
Rwork0.36429 --
obs0.36429 2793924 100 %
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 86.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.15 Å2-0.2 Å2
2---0.17 Å2-0.3 Å2
3---0.47 Å2
精密化ステップサイクル: 1 / 合計: 51652
拘束条件
Refine-IDタイプDev idealDev ideal target数
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01952567
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.2812.05372251
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.04457844
ELECTRON MICROSCOPYr_dihedral_angle_2_deg38.4522.7781314
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.653155751
ELECTRON MICROSCOPYr_dihedral_angle_4_deg8.19615201
ELECTRON MICROSCOPYr_chiral_restr0.090.28877
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.02139887
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it0.669.83631523
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it1.2314.75439318
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it0.4469.64421044
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined4.12383.56275712
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS精密化 シェル解像度: 4.35→4.463 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rwork0.518 206837 -
Rfree-0 -
obs--100 %

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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

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