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- PDB-7tay: Bos Taurus Mitochondrial BC1 in complex with Pyramoxadone -

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基本情報

登録情報
データベース: PDB / ID: 7tay
タイトルBos Taurus Mitochondrial BC1 in complex with Pyramoxadone
要素
  • (Cytochrome b-c1 complex subunit ...) x 9
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
キーワードOXIDOREDUCTASE / Mitochondrial respiratory chain complex / cytochrome bc1 / inhibitors / electron transfer
機能・相同性
機能・相同性情報


Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / Respiratory electron transport / thalamus development / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity ...Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / Respiratory electron transport / thalamus development / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / hypothalamus development / midbrain development / ubiquinone binding / respiratory electron transport chain / hippocampus development / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / heme binding / mitochondrion / proteolysis / metal ion binding / membrane
類似検索 - 分子機能
Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Rieske Iron-sulfur Protein ...Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Chem-8PE / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PQU / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Cytochrome c1, heme protein, mitochondrial ...1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Chem-8PE / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PQU / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 9 / Cytochrome b / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial
類似検索 - 構成要素
生物種Bos taurus (ウシ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.95 Å
データ登録者Xia, D. / Zhou, F. / Esser, L.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Cancer Institute (NIH/NCI) 米国
引用ジャーナル: to be published
タイトル: Conformation Switch of Rieske ISP subunit is revealed by the Crystal Structure of Bacterial Cytochrome bc1 in Complex with Azoxystrobin
著者: Xia, D. / Esser, L. / Zhou, F.
履歴
登録2021年12月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年1月18日Provider: repository / タイプ: Initial release
改定 1.12023年10月25日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

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: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6, mitochondrial
I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
J: Cytochrome b-c1 complex subunit 9
K: Cytochrome b-c1 complex subunit 10
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)250,97825
ポリマ－241,26411
非ポリマー9,71414
水181
1
A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6, mitochondrial
I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
J: Cytochrome b-c1 complex subunit 9
K: Cytochrome b-c1 complex subunit 10
ヘテロ分子

A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6, mitochondrial
I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
J: Cytochrome b-c1 complex subunit 9
K: Cytochrome b-c1 complex subunit 10
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)501,95750
ポリマ－482,52922
非ポリマー19,42828
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area112200 Å2
ΔGint-770 kcal/mol
Surface area158180 Å2
手法PISA
単位格子
Length a, b, c (Å)153.392, 153.392, 590.928
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw

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要素

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Cytochrome b-c1 complex subunit ... , 9種, 9分子 ABEFGHIJK

#1: タンパク質 Cytochrome b-c1 complex subunit 1, mitochondrial / Complex III subunit 1 / Core protein I / Ubiquinol-cytochrome-c reductase complex core protein 1


分子量: 49266.254 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P31800
#2: タンパク質 Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome-c reductase complex core protein 2


分子量: 46575.469 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P23004
#5: タンパク質 Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / ...Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


分子量: 21640.580 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P13272, quinol-cytochrome-c reductase
#6: タンパク質 Cytochrome b-c1 complex subunit 7 / Complex III subunit 7 / Complex III subunit VII / QP-C / Ubiquinol-cytochrome c reductase complex ...Complex III subunit 7 / Complex III subunit VII / QP-C / Ubiquinol-cytochrome c reductase complex 14 kDa protein


分子量: 13370.206 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00129
#7: タンパク質 Cytochrome b-c1 complex subunit 8 / Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa ...Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa protein / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C


分子量: 9448.833 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P13271
#8: タンパク質 Cytochrome b-c1 complex subunit 6, mitochondrial / Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / ...Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / Mitochondrial hinge protein / Ubiquinol-cytochrome c reductase complex 11 kDa protein


分子量: 9189.116 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00126
#9: タンパク質 Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / ...Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Rieske protein UQCRFS1 / Ubiquinol-cytochrome c reductase iron-sulfur subunit


分子量: 7964.259 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P13272, quinol-cytochrome-c reductase
#10: タンパク質 Cytochrome b-c1 complex subunit 9 / Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol- ...Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol-cytochrome c reductase complex 7.2 kDa protein


分子量: 7338.425 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00130
#11: タンパク質 Cytochrome b-c1 complex subunit 10 / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c reductase complex 6.4 kDa protein


分子量: 6527.604 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P07552

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タンパク質 , 2種, 2分子 CD

#3: タンパク質 Cytochrome b / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol- ...Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


分子量: 42620.340 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00157
#4: タンパク質 Cytochrome c1, heme protein, mitochondrial / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol- ...Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit / Cytochrome c-1


分子量: 27323.277 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00125

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非ポリマー , 11種, 15分子

#12: 化合物 ChemComp-6PE / 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


分子量: 410.420 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C17H33NO8P
#13: 化合物 ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


分子量: 1464.043 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C81H156O17P2 / コメント: リン脂質*YM
#14: 化合物 ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


分子量: 616.487 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C34H32FeN4O4
#15: 化合物 ChemComp-PQU / (5S)-3-anilino-5-methyl-5-(6-phenoxypyridin-3-yl)-1,3-oxazolidine-2,4-dione


分子量: 375.377 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C21H17N3O4 / タイプ: SUBJECT OF INVESTIGATION
#16: 化合物 ChemComp-8PE / (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate / 3-SN-PHOSPHATIDYLETHANOLAMINE


分子量: 691.959 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C37H74NO8P / コメント: リン脂質*YM
#17: 化合物 ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


分子量: 691.959 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C37H74NO8P / コメント: リン脂質*YM
#18: 化合物 ChemComp-CL / CHLORIDE ION


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#19: 化合物 ChemComp-HEC / HEME C


分子量: 618.503 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C34H34FeN4O4
#20: 化合物 ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


分子量: 175.820 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Fe2S2
#21: 化合物 ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


分子量: 678.940 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C36H73NO8P / コメント: DMPC, リン脂質*YM
#22: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.6 Å3/Da / 溶媒含有率: 65.85 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 50 mM MOPS 7.2 pH, 20 mM Ammonium acetate, 20% glycerol. Incubation with 5 molar excess of pyramoxadone. Precipitant 12% PEG4000, 0.5 M KCL, 0.1% DHPC.

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 22-ID / 波長: 1.00116 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2012年7月20日
放射モノクロメーター: Si(111) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.00116 Å / 相対比: 1
反射解像度: 2.95→50 Å / Num. obs: 75442 / % possible obs: 99.8 % / 冗長度: 13.7 % / Biso Wilson estimate: 75.45 Å2 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.055 / Rrim(I) all: 0.207 / Χ2: 0.987 / Net I/σ(I): 7.8 / Num. measured all: 1030646
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-3.0212.31.57349610.5810.4551.6390.755100
3.02-3.0912.41.44149340.6740.4151.5010.806100
3.09-3.1812.81.19949720.7560.3391.2480.82299.9
3.18-3.2712.91.0449720.8250.2921.0810.847100
3.27-3.3813.30.79649400.9180.2210.8270.92299.9
3.38-3.513.40.68250170.9410.1880.7080.999100
3.5-3.6413.30.50849550.9660.140.5281.02999.9
3.64-3.811.90.44549980.9460.1270.4631.25399.9
3.8-413.60.350150.9770.0810.3111.10999.9
4-4.2514.30.19450060.9860.0520.2011.08299.9
4.25-4.5814.70.13450370.9960.0350.1391.05299.8
4.58-5.0414.90.10650480.9970.0280.1091.034100
5.04-5.77150.09750880.9980.0250.11.03100
5.77-7.2715.10.07851690.9980.020.081.02599.9
7.27-5014.40.0553300.9980.0130.0520.98798.5

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20_4444精密化
DENZOデータ削減
SCALEPACKデータスケーリング
PDB_EXTRACT3.27データ抽出
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1SQX

1sqx


解像度: 2.95→41.58 Å / SU ML: 0.3967 / 交差検証法: FREE R-VALUE / σ(F): 0.77 / 位相誤差: 26.1418
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2581 1975 2.65 %
Rwork0.2272 72516 -
obs0.228 74491 99.85 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 99.71 Å2
精密化ステップサイクル: LAST / 解像度: 2.95→41.58 Å
タンパク質核酸リガンド溶媒全体
原子数16306 0 536 1 16843
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00617251
X-RAY DIFFRACTIONf_angle_d0.858523395
X-RAY DIFFRACTIONf_chiral_restr0.05032522
X-RAY DIFFRACTIONf_plane_restr0.00622960
X-RAY DIFFRACTIONf_dihedral_angle_d14.47846332
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.020.33461390.30555080X-RAY DIFFRACTION99.9
3.02-3.110.33431390.30045123X-RAY DIFFRACTION99.91
3.11-3.20.28351390.28545106X-RAY DIFFRACTION99.9
3.2-3.30.29671390.2675109X-RAY DIFFRACTION99.96
3.3-3.420.27381400.25465125X-RAY DIFFRACTION99.92
3.42-3.550.25051390.25025117X-RAY DIFFRACTION99.96
3.55-3.720.34641410.29665141X-RAY DIFFRACTION99.85
3.72-3.910.28221390.23135143X-RAY DIFFRACTION99.92
3.91-4.160.2521420.21365187X-RAY DIFFRACTION99.98
4.16-4.480.21961410.19775151X-RAY DIFFRACTION99.89
4.48-4.930.19241410.18025218X-RAY DIFFRACTION99.91
4.93-5.640.20491430.2035239X-RAY DIFFRACTION99.94
5.64-7.10.28231440.24135292X-RAY DIFFRACTION99.96
7.1-41.580.25961490.20225485X-RAY DIFFRACTION99
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.839644321492-0.2045022269120.1131209884191.07790984035-0.4988831591082.273616649960.011487446334-0.00212454875435-0.1880998944490.2185978319460.0625973682750.5235464807830.236938728991-0.735771056226-0.08901523167020.500912121056-0.1429092212890.1046156852970.621523346117-0.005600670521160.97935242648432.43486.63592.667
20.138163870269-0.1282168972310.594475294932.53592689159-0.4695376404982.330059538910.0508541491458-0.607618300453-0.2735147831760.266706955299-0.009362013266530.6290141015430.204620177434-0.814528641008-0.09578080048080.718223420781-0.2880144524220.2263975041230.629816609028-0.07127485914520.86057771999535.2683.236110.097
30.565308536416-0.2562424178460.6997919778261.724696970440.01259893213231.52875196425-0.00968409555627-0.2357814625750.04050573652380.556056434219-0.04526937861960.14211779667-0.156394831387-0.381341768910.06431042172170.879461158206-0.1176201130380.2511873075320.4326118469660.00409834982790.80953018154349.10994.902114.958
41.62288826598-0.202880087769-0.3847907430271.22499946495-0.04083070608351.762527915650.102380987311-0.06460861664760.1593711624610.134546202527-0.0224422905042-0.0191852651893-0.174059699524-0.0251091028963-0.05296897984250.766095137998-0.1555677162260.02673418951810.1898882095920.02758961983180.68072670323267.651103.70492.467
51.44284569932-0.4330801955630.2210629231580.6077611488870.5384272827411.50748331097-0.0724823734526-0.02849336853250.0484870768375-0.4027959579280.101634188967-0.0127391450123-0.1878143784330.0270139751532-0.0688765934520.764594430052-0.03713414533420.002546650135210.3112451167870.03174022845660.64231467404870.13190.5678.787
62.38660871798-0.705132268528-1.594422655080.2360776006870.2508398539533.705206146560.1329017983750.125863470198-0.2878989967150.300384014122-0.1917960687580.616216809078-0.00821870799155-0.506480755820.07954494740490.675178866776-0.0948475448543-0.1637362914970.3679931439650.005185559823190.88607546375150.23382.19974.788
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91.294062174060.2387447708170.4402758516630.7454548508510.07036100810950.6967558865340.107503850494-0.502950696722-0.1653344893650.664090430108-0.05452761555610.01291290776070.378031346947-0.122207653625-0.06005029007061.67907927974-0.3469730272190.1785799017950.6559935022110.03736535034360.68640221837167.78365.907158.165
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184.14815937308-1.236302278681.678761654891.190107030710.7527622156972.59341732535-0.22178200203-0.333738978212-0.3750196138980.138183323230.1550436705770.2819026849810.263437504484-0.3002361701250.04399034804512.91228222534-0.4453634211761.014971422991.119439990160.1437889557690.80307805296646.94268.697187.235
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210.2236099829130.0923554910422-0.9219579696550.777223850083-0.4467399600143.559351984330.421731371092-0.2966059452580.008400079530470.3790109386620.0552449875521-0.0103065472730.3616370987770.841568112977-0.5153066978951.02957427821-0.333266788727-0.362524354820.869051931926-0.07520108460180.970954502293113.59872.904135.95
226.77844434434-0.8340061745393.514939051521.175403749121.055586339479.1496030038-0.225076503177-1.37167937711-0.1494077972760.0470827507760.9759408846060.0933612527664-0.134157808528-0.104293313171-0.5614622175492.36677842548-0.103386839901-0.1748615929291.483253249710.05381185767620.57275181371990.99963.994180.452
231.57651159841-0.75194036037-0.4682408766222.18170796595-0.08489320952131.521697383180.25743591999-0.552280078159-0.324327062782-0.21087908702-0.120300545997-0.190606375078-0.3704114295140.123498996167-0.1044561944321.971167417160.01997899490910.009878269225461.301058559580.3727197471181.0861974158682.03441.051191.343
241.60245384707-1.23103451735-1.498150319193.14684278953-0.6828862590533.13595553275-0.929027293-1.05935265237-0.8153290612780.7415293756670.8411331320650.323808283935-0.1248577705670.5832896258470.1087462012352.454470358680.00347847584063-0.04938291042091.362883762540.4101114544091.0715679212180.60741.223184.522
258.16186051386-1.88949771249-2.113154432843.917202403244.383168890594.90383941475-0.643297632772-0.469728832116-0.673238171186-0.1746617814090.186798631536-0.210525632160.6341044321870.3164936827160.3988398806761.99173169571-0.1429261444410.1320049971391.466782886570.2257114306051.454419376191.26349.615200.607
262.909195707241.03868370321-0.7074818099932.02834110273-1.938877622241.883578939380.007681166335830.1160817622240.00804940589524-0.7238646923020.01936908041050.2353077631831.23600537297-0.2392882382570.0003774362712192.0725529926-0.7066886971530.1022395150520.8281025916060.1286830454860.90674594540151.04632.274127.611
270.548206625688-0.161772814924-0.3585105633891.89504307289-0.3718428305361.580330324610.0836225901649-0.1394251857160.06630841408980.544914362206-0.0001546503840180.4340037603810.403535947741-0.389289029454-0.1062220008241.18793913554-0.3611899916770.2163115470970.5116394895290.002517219946040.80522522103854.85753.205122.707
283.157996124660.3974309354680.3926834988010.453583601393-0.02799894014670.062560327181-0.4321737174430.44187106671-0.681906356889-0.5665001993330.5658902533520.9110763871880.375140343181-0.497497272103-0.1866836949221.39255347616-0.7344233984060.1739079159020.9344994680340.05986914328040.9100190475553.86642.937118.358
294.95498777296-1.152458237930.8024698157522.70577804467-0.504028218373.167608741750.0514215146232-0.379249926848-0.8039270230421.10488529699-0.1266643910450.3525974170320.648167845090.09230693216950.1032267766421.3284508111-0.1541891120580.01814326178890.4742731316950.07888963558240.77769291032278.14943.299118.023
302.49252937712-1.00193541627-1.194629445982.364608506481.335165714381.47022039621-0.2399941413020.2068264244510.3833438106640.425909699290.2413952991690.3012938170770.130731231617-0.199260945855-0.003912664949681.02383448248-0.263335905310.1996029286790.6114886806020.1571040794040.86850652991554.11170.608121.79
310.7652329107950.670509970557-0.9731128106110.588000992709-0.8508627604541.236352522580.312078054788-0.443594362682-0.371247165020.873987325666-0.2726153332470.9924885959870.249410744155-0.832765239727-0.05313151502921.64847584922-0.5075690116840.6417752330441.461474156760.03189420730771.4954740379934.69767.615137.103
324.53030556967-0.0357369391259-1.175259610081.836856606582.066605343452.602859410110.1146368266-0.347378174409-0.1472413400880.0691922891840.5383157650940.3666731547260.149737233152-0.0448170886627-0.497545382581.62714806796-0.2785277472190.5107163324061.424640082490.3843069741571.1224346970739.94652.499140.183
331.092751587770.315875382886-0.3371698118460.818236440605-0.325327697451.300237335430.080865227128-0.467147229723-0.3547121598970.559725525888-0.274853792913-0.157004578652-0.0371188673136-0.1312908605820.04585252767831.83475054328-0.4687035942530.3113122356040.7905894599330.08931407859440.98685762533850.34940.034161.259
348.67685200036-1.473184891120.7752703472333.738929579974.527819837646.40508749282-0.224805352742-0.363966056986-0.568675817810.780767021660.1289688550990.2264610069690.809368787346-0.1872679521930.04415901905942.22297452786-0.6189190230250.4492241634181.21518674215-0.003264783794551.1818923263752.4731.371183.92
352.890047860650.400895451555-0.4056425051971.63706186294-1.264634405390.988884950793-0.4184899406330.725590688164-0.133292342379-1.272174243880.43475919398-0.1739255303-0.0886104698445-0.02616492504530.05989360836552.02002137505-0.3477060293480.6354022989841.406334268420.1163245621441.2168835908432.11753.191195.465
363.37980676641.47258977064-1.466849559283.211742119011.620237552712.65153478902-0.05525298071450.271847458079-0.06398951293860.491840139226-0.146157201096-0.389610344055-0.388976349399-0.1648551335040.1807656795782.23913713494-0.4884352244240.4896149380591.311940247670.2067389092721.1998994714638.91435.081191.85
370.844765538875-0.238806928486-0.05718964179241.933238990980.8556623991780.361290930904-0.1098362349710.176257728368-0.01135852398860.1744063735830.0876944643477-0.3820909704680.808354675098-0.9576278659460.002195954444011.93268316945-0.3965602466390.387648220981.443788349440.2878651927741.034107475542.84744.538190.363
380.580390925060.516522134719-0.1629837033833.885303167094.188180404785.528051839750.7251228992351.492838699990.0790081506916-1.2224678882-0.8339372484540.341637503506-1.92558410468-3.63290632078-0.04253463451021.66532046631-0.315271891970.6173496613371.79127930485-0.4576999186950.99362061662227.96590.65138.398
392.63884943512-0.790662753480.7613538564433.64132140401-0.03066933764951.09910409329-0.0644674143878-0.6356166334580.3956695190890.3239541259850.1937036604080.02016762295680.513934704459-0.836309961146-0.1544964352391.28786897787-0.1799920896640.4400125665330.889770202739-0.1606319045540.91522415317939.95189.884153.243
401.204192091890.4496982106560.5491703460570.755658072826-0.6375105765381.458425778970.3820981886730.4260012205330.489857206437-0.134437033867-0.02771785631140.170334095024-0.692636154206-1.33229779024-0.3511528884032.27255453378-0.292077085741.019293679051.47469634123-0.175262018571.3393078728535.97177.68179.361
414.661126863690.8151206984110.1724096641945.787295644240.2345356849280.24490580248-0.929308189162-0.6207766643120.2060750984990.659666609397-0.7150240701150.3785241054560.706034498313-0.2251062862331.375653740571.868845656620.0308760853620.3572189459221.22764802753-0.01925680220710.74240765033338.486.45187.429
421.842783492840.340797973029-1.266959298964.74321890657-2.336533694246.041297394720.380927922892-0.1188633373550.47983832303-0.1303895802770.2000725940060.411638936034-1.303152729220.004960814981-0.3858333190031.40565314718-0.2211152726340.2939714560580.623502983513-0.1685980313840.80883670202855.899105.404138.896
438.462526817120.816643925993-1.694707400361.6166631495-2.063441857414.99428512886-0.006679693100480.1329593028660.5969446122530.0967210680753-0.293840862493-0.00466517532916-0.271210588558-0.2499123953230.279553177022.0153740321-0.2667946208750.2829366523221.15441269661-0.179802845910.98048900468444.383101.218163.927
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:215 )A1 - 215
2X-RAY DIFFRACTION2( CHAIN A AND RESID 216:265 )A216 - 265
3X-RAY DIFFRACTION3( CHAIN A AND RESID 266:446 )A266 - 446
4X-RAY DIFFRACTION4( CHAIN B AND RESID 15:222 )B15 - 222
5X-RAY DIFFRACTION5( CHAIN B AND RESID 223:266 )B223 - 266
6X-RAY DIFFRACTION6( CHAIN B AND RESID 267:315 )B267 - 315
7X-RAY DIFFRACTION7( CHAIN B AND RESID 316:439 )B316 - 439
8X-RAY DIFFRACTION8( CHAIN C AND RESID 3:32 )C3 - 32
9X-RAY DIFFRACTION9( CHAIN C AND ( RESID 33:244 OR RESID 1001:1002 ) )C33 - 244
10X-RAY DIFFRACTION9( CHAIN C AND ( RESID 33:244 OR RESID 1001:1002 ) )C1001 - 1002
11X-RAY DIFFRACTION10( CHAIN C AND RESID 245:271 )C245 - 271
12X-RAY DIFFRACTION11( CHAIN C AND RESID 272:379 )C272 - 379
13X-RAY DIFFRACTION12( CHAIN C AND RESID 1003:1003 )C1003
14X-RAY DIFFRACTION13( CHAIN D AND ( RESID 1:84 OR RESID 1001:1001 ) )D1 - 84
15X-RAY DIFFRACTION13( CHAIN D AND ( RESID 1:84 OR RESID 1001:1001 ) )D1001
16X-RAY DIFFRACTION14( CHAIN D AND RESID 85:97 )D85 - 97
17X-RAY DIFFRACTION15( CHAIN D AND RESID 98:131 )D98 - 131
18X-RAY DIFFRACTION16( CHAIN D AND RESID 132:151 )D132 - 151
19X-RAY DIFFRACTION17( CHAIN D AND RESID 152:178 )D152 - 178
20X-RAY DIFFRACTION18( CHAIN D AND RESID 179:197 )D179 - 197
21X-RAY DIFFRACTION19( CHAIN D AND RESID 198:231 )D198 - 231
22X-RAY DIFFRACTION20( CHAIN D AND RESID 232:241 )D232 - 241
23X-RAY DIFFRACTION21( CHAIN E AND RESID 1:60 )E1 - 60
24X-RAY DIFFRACTION22( CHAIN E AND RESID 61:73 )E61 - 73
25X-RAY DIFFRACTION23( CHAIN E AND RESID 74:122 )E74 - 122
26X-RAY DIFFRACTION24( CHAIN E AND ( RESID 123:187 OR RESID 1001:1001 ) )E123 - 187
27X-RAY DIFFRACTION24( CHAIN E AND ( RESID 123:187 OR RESID 1001:1001 ) )E1001
28X-RAY DIFFRACTION25( CHAIN E AND RESID 188:196 )E188 - 196
29X-RAY DIFFRACTION26( CHAIN F AND RESID 6:24 )F6 - 24
30X-RAY DIFFRACTION27( CHAIN F AND RESID 25:82 )F25 - 82
31X-RAY DIFFRACTION28( CHAIN F AND RESID 83:90 )F83 - 90
32X-RAY DIFFRACTION29( CHAIN F AND RESID 91:110 )F91 - 110
33X-RAY DIFFRACTION30( CHAIN G AND RESID 1:22 )G1 - 22
34X-RAY DIFFRACTION31( CHAIN G AND RESID 23:32 )G23 - 32
35X-RAY DIFFRACTION32( CHAIN G AND RESID 33:44 )G33 - 44
36X-RAY DIFFRACTION33( CHAIN G AND RESID 45:69 )G45 - 69
37X-RAY DIFFRACTION34( CHAIN G AND RESID 70:75 )G70 - 75
38X-RAY DIFFRACTION35( CHAIN H AND RESID 12:27 )H12 - 27
39X-RAY DIFFRACTION36( CHAIN H AND RESID 28:44 )H28 - 44
40X-RAY DIFFRACTION37( CHAIN H AND RESID 45:78 )H45 - 78
41X-RAY DIFFRACTION38( CHAIN J AND RESID 2:6 )J2 - 6
42X-RAY DIFFRACTION39( CHAIN J AND RESID 7:46 )J7 - 46
43X-RAY DIFFRACTION40( CHAIN J AND RESID 47:51 )J47 - 51
44X-RAY DIFFRACTION41( CHAIN J AND RESID 52:61 )J52 - 61
45X-RAY DIFFRACTION42( CHAIN K AND RESID 2:36 )K2 - 36
46X-RAY DIFFRACTION43( CHAIN K AND RESID 37:50 )K37 - 50

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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