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- PDB-5klv: Structure of bos taurus cytochrome bc1 with fenamidone inhibited -

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基本情報

登録情報
データベース: PDB / ID: 5klv
タイトルStructure of bos taurus cytochrome bc1 with fenamidone inhibited
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 / cytochrome bc1 complex / fenamidone / 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 / hippocampus development / respiratory electron transport chain / 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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / 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 / Cytochrome b-c1 complex subunit 8 / UcrQ family / 3-layer Sandwich / 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 / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / 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 / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / 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 / Chem-FNM / HEME C / PROTOPORPHYRIN IX CONTAINING FE / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 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 / Chem-FNM / HEME C / PROTOPORPHYRIN IX CONTAINING FE / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 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 / フーリエ合成 / 解像度: 2.652 Å
データ登録者Xia, D. / Esser, L. / Zhou, F. / Zhou, Y. / Xiao, Y. / Tang, W.K. / Yu, C.A. / Qin, Z.
引用ジャーナル: J.Biol.Chem. / 年: 2016
タイトル: Hydrogen Bonding to the Substrate Is Not Required for Rieske Iron-Sulfur Protein Docking to the Quinol Oxidation Site of Complex III.
著者: Esser, L. / Zhou, F. / Zhou, Y. / Xiao, Y. / Tang, W.K. / Yu, C.A. / Qin, Z. / Xia, D.
履歴
登録2016年6月25日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年10月12日Provider: repository / タイプ: Initial release
改定 1.12016年11月2日Group: Database references
改定 1.22016年12月7日Group: Database references
改定 1.32023年9月27日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
改定 1.42024年10月30日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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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)251,05928
ポリマ－241,13311
非ポリマー9,92617
水90150
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)502,11956
ポリマ－482,26622
非ポリマー19,85334
水21612
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 area114340 Å2
ΔGint-764 kcal/mol
Surface area159580 Å2
手法PISA
単位格子
Length a, b, c (Å)153.986, 153.986, 592.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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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 / 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: 6396.408 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 , 12種, 67分子

#12: 化合物 ChemComp-6PE / 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / [O-(1-O,2-O-ジヘキサノイル-L-グリセロ-3-ホスホ)-2-アミノエタノ-ル]アニオン


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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C3H8O3
#15: 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
#16: 化合物 ChemComp-FNM / (5S)-5-methyl-2-(methylsulfanyl)-5-phenyl-3-(phenylamino)-3,5-dihydro-4H-imidazol-4-one / フェナミドン


分子量: 311.401 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C17H17N3OS / コメント: 阻害剤*YM
#17: 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
#18: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


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-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL / DPPE


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
#21: 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
#22: 化合物 ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / O-(1-O,2-O-ジミリストイル-L-グリセロ-3-ホスホ)コリン


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
#23: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 50 / 由来タイプ: 天然 / 式: H2O

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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: 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: 3.64 Å3/Da / 溶媒含有率: 66.23 %
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 / pH: 7.2
詳細: 50 mM MOPS 7.2 pH, 20 mM Ammonium acetate, 20% glycerol. Incubation with 2-5 mol excess of Fenamidone. Precipitant 12% PEG4000, 0.5 M KCl, 0.1% DHPC; Protein:PPT ratio 1:0.57

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データ収集

回折平均測定温度: 100 K
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 Å
検出器タイプ: MARRESEARCH / 検出器: AREA DETECTOR / 日付: 2012年8月21日
放射プロトコル: 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 Å / 相対比: 1
反射解像度: 2.65→50 Å / Num. obs: 103188 / % possible obs: 99.9 % / 冗長度: 14.1 % / Biso Wilson estimate: 64.97 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 7.6
反射 シェル解像度: 2.65→2.7 Å / 冗長度: 11.6 % / Rmerge(I) obs: 1.684 / % possible all: 99.9

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.11rc1_2513: ???)精密化
DENZOデータ削減
SCALEPACKデータスケーリング
PDB_EXTRACT3.2データ抽出
HKL-2000データ削減
PHENIX位相決定
精密化構造決定の手法: フーリエ合成
開始モデル: 1SQX

1sqx


解像度: 2.652→34.676 Å / SU ML: 0.39 / 交差検証法: THROUGHOUT / σ(F): 1.37 / 位相誤差: 29.19 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.269 1687 1.65 %
Rwork0.2283 --
obs0.229 102445 99.19 %
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
精密化ステップサイクル: LAST / 解像度: 2.652→34.676 Å
タンパク質核酸リガンド溶媒全体
原子数16315 0 548 50 16913
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00517283
X-RAY DIFFRACTIONf_angle_d0.74723429
X-RAY DIFFRACTIONf_dihedral_angle_d15.59810222
X-RAY DIFFRACTIONf_chiral_restr0.0432523
X-RAY DIFFRACTIONf_plane_restr0.0052951
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6517-2.72970.3471360.33948088X-RAY DIFFRACTION97
2.7297-2.81780.36211380.31798292X-RAY DIFFRACTION99
2.8178-2.91850.35131390.3048303X-RAY DIFFRACTION99
2.9185-3.03520.35181400.28728337X-RAY DIFFRACTION100
3.0352-3.17330.30371380.27448325X-RAY DIFFRACTION99
3.1733-3.34050.30111410.2528392X-RAY DIFFRACTION100
3.3405-3.54960.29371400.23638356X-RAY DIFFRACTION99
3.5496-3.82330.29261390.22138361X-RAY DIFFRACTION99
3.8233-4.20750.25391410.2048418X-RAY DIFFRACTION99
4.2075-4.81490.20481420.18098418X-RAY DIFFRACTION99
4.8149-6.0610.25761430.2098574X-RAY DIFFRACTION100
6.061-34.67940.23311500.20748894X-RAY DIFFRACTION100
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)
11.1458-0.2274-0.32581.3172-0.77492.20570.03570.0123-0.05780.08070.01360.46720.1154-0.7417-0.08020.3076-0.1255-0.00620.48180.0160.717532.462392.430289.8946
20.8539-0.38410.27550.79090.71791.23450.10220.1357-0.0979-0.1226-0.0270.29790.0296-0.150.010.6074-0.31210.11380.453-0.02620.709539.439174.8076100.4148
32.55270.9302-0.29033.62250.12221.87890.05110.0748-0.20750.04060.30621.21360.3151-1.0072-0.36090.4104-0.1312-0.0420.75940.06140.800225.538787.209792.2189
40.22750.4212-0.54182.0854-0.18521.8419-0.10770.00920.13850.24150.0190.4662-0.0839-0.5074-0.28650.5161-0.36210.23760.34860.01350.6437.338786.9563111.215
50.20310.20180.3121.1278-0.66711.63320.0057-0.22380.05590.4387-0.1190.0624-0.3001-0.4194-0.17840.6741-0.2390.24070.2489-0.04970.667149.609195.0186115.242
60.1424-0.0052-0.04260.2572-0.02010.09470.1671-0.03850.12390.2502-0.0999-0.0984-0.1823-0.14420.00610.6388-0.30680.0499-0.35020.02850.527868.0417104.21292.7521
70.4038-0.1216-0.47430.03970.14730.56480.0032-0.08520.0659-0.04350.0953-0.1779-0.16260.2212-0.00990.7425-0.0922-0.04820.18080.00340.649670.546789.932378.398
80.0690.119901.71880.53020.23860.09760.1948-0.091-0.2222-0.02260.3887-0.161-0.14190.12010.5628-0.2129-0.20130.0570.02320.67353.240588.949872.8448
90.29340.07380.17481.28920.51820.2803-0.16190.0884-0.1559-0.1980.0167-0.01430.1324-0.04180.16080.6023-0.1391-0.07920.0969-0.02260.625767.74573.015774.1363
101.7380.97870.38681.04920.37760.13820.276-0.41380.63810.5659-0.32540.2408-0.10560.08830.07371.0751-0.46460.06290.5343-0.02870.816363.209375.5467136.0252
110.27760.1868-0.10060.7666-0.36150.25890.1219-0.38880.06130.6026-0.1380.0809-0.1557-0.0725-0.06691.2513-0.55490.16330.48060.01090.479165.690467.7567160.6939
120.0395-0.23110.1281.4799-0.580.67070.2997-0.2941-0.01270.2138-0.1785-0.1778-0.31640.0167-0.15431.6082-0.5413-0.00580.8540.17510.683274.724656.924173.8332
130.47120.404-0.51720.4576-0.70381.20380.3066-0.5333-0.1960.6419-0.3876-0.320.20990.21810.18911.2126-0.4916-0.07470.55670.1210.5379.530764.0902162.8481
140.2976-0.0101-0.04090.5370.03640.41860.1048-0.3841-0.18810.4927-0.0571-0.02080.03090.00690.59521.1813-0.54920.25030.54590.12430.466660.42261.518157.3498
150.0512-0.00030.02110.09-0.01880.0130.068-0.0587-0.03290.0820.0150.28280.0815-0.07360.01080.9613-0.57550.08040.34670.16020.551264.777146.641149.0473
160.49040.2917-0.12540.7222-0.26750.09930.0989-0.2664-0.10440.3934-0.0862-0.0381-0.06420.03320.00870.8346-0.41470.05250.41110.18490.623363.347839.3176150.8211
170.25610.57250.2013.1217-1.04211.35490.2304-0.4856-0.0956-0.4294-0.1601-0.35130.0471-0.23130.04991.6739-0.45760.41311.30350.12310.771544.722559.438181.1954
180.645-0.2893-0.35020.5568-0.08261.46260.0222-0.53660.02950.51450.11590.0546-0.10070.0342-0.1071.9788-0.6520.31471.38420.02250.561657.738973.7213194.2337
191.54890.4726-1.22444.0468-2.36451.9820.0492-0.6435-0.16210.6421-0.4212-0.2136-0.20440.76770.40091.9402-0.57840.17211.41380.39690.865352.640246.7289199.2017
200.429-0.0893-0.09760.03760.08580.32450.0124-0.5134-0.19580.4761-0.05830.1409-0.04720.0481-0.35321.508-0.46460.54410.99920.14870.548745.667169.4286175.6449
215.673-0.0805-2.44259.6159-2.14413.7926-0.13860.5087-0.6426-0.3531-0.15170.55340.6402-0.91890.33320.5029-0.30920.06050.4889-0.06640.574547.182263.4422115.6224
220.9505-0.1236-0.30540.53440.04691.04610.1257-0.3487-0.08320.3465-0.1203-0.29210.34030.7004-0.08960.9568-0.3574-0.31220.79730.01270.7019110.281871.6266143.5616
233.3812-0.5406-1.29014.9127-2.10674.01550.0883-1.2389-0.49520.347-0.2240.15790.22550.45550.06361.5658-0.1621-0.0831.54990.41070.819282.130241.0578191.8006
245.0634-1.6566-0.24853.8051-2.09175.8064-0.8308-0.8439-0.45960.67480.5456-0.02530.08230.43270.29472.074-0.249-0.09791.28950.3780.949282.054842.1196186.5575
252.23761.0138-0.87072.3013-1.6191.1524-0.38590.4859-0.1834-0.89480.29210.09250.6204-0.2611-0.03361.2271-0.58360.08830.68440.08480.710150.917832.4419127.8968
260.249-0.04930.04510.2466-0.11550.0836-0.0009-0.05-0.0784-0.04950.09420.18790.0601-0.0713-0.05860.7534-0.39210.21590.45020.09160.657952.666848.4811125.4343
270.0582-0.0053-0.02340.2782-0.08640.160.1329-0.12130.10420.2577-0.01080.10810.0263-0.07120.1010.702-0.36380.10690.29280.02040.507960.191955.6247120.758
280.73570.1519-0.36280.281-0.25620.30860.1491-0.3029-0.04060.2637-0.12880.35890.0033-0.1109-0.10140.9222-0.5380.19290.68690.00860.761747.258548.2984123.7808
295.535-1.1931.66081.3559-0.46972.03110.0858-0.5296-0.87090.4460.04030.06290.4138-0.0275-0.08711.0244-0.1553-0.01580.41250.16360.672678.337243.4854118.4077
304.85222.67180.04959.4808-0.80895.58770.3686-0.01870.07230.4190.0864-1.0256-0.27570.3091-0.32320.5684-0.16250.21050.34250.0550.649664.798369.3935122.6712
311.929-0.0247-1.04161.4858-0.88191.19360.3567-0.7853-0.12450.6135-0.10040.4785-0.35170.0209-0.29230.81-0.41950.26170.73140.01990.839941.51971.0474128.532
321.01350.3194-0.25872.7736-1.53521.54360.16050.0047-0.12540.29460.17950.04260.033-0.4531-0.23321.0984-0.42850.27640.65350.09990.63646.397345.4283153.7471
336.3313-3.64520.65482.25080.63586.786-0.3492-0.4926-0.6482-0.77690.2080.21171.8647-0.1480.1831.57-0.47130.47821.32270.19940.90653.111431.8366183.6952
343.4864-0.32150.8030.9956-1.1644.4162-0.30830.4703-0.43890.3942-0.4386-0.16480.0331-0.33860.68382.2854-0.510.59141.50420.10390.989732.480953.1123195.8677
351.6850.3019-1.60841.99991.4563.177-0.3076-0.5527-0.51470.6773-0.17040.1186-0.03250.28750.47911.9705-0.63550.29841.27130.16750.930539.57634.3831192.7736
362.35640.146-0.27160.06270.32382.1494-0.2011-0.5509-0.68660.32850.25430.64290.7686-0.167-0.10391.5605-0.50020.32271.43120.3710.855642.63745.4723190.058
374.34692.6974-0.21744.7346-0.05121.80.16270.06260.3498-0.187-0.42450.43750.2374-0.74230.21491.2356-0.16020.26050.969-0.21910.822534.879993.8157138.0032
382.3062-1.4251.21564.183-0.47560.66520.1208-0.56010.41980.35520.37140.09590.2112-0.7069-0.54591.1547-0.35130.36250.7752-0.14830.725140.826788.6222159.4434
391.3279-0.6176-1.14230.8048-0.25742.1823-0.2363-0.0313-0.38740.4102-0.21040.24510.2746-0.3020.42071.5584-0.29730.57961.50390.17331.073537.529281.0121181.8115
409.66741.4329-1.85823.8857-4.69495.6741-0.3153-0.4660.58980.9443-0.10170.2510.2454-0.04950.3281.7040.27440.40871.8664-0.50790.949237.867288.4408190.7928
410.9238-0.3664-0.39372.1531-1.98998.10510.1405-0.24810.18130.6527-0.312-0.0131-1.0518-0.24150.22981.3652-0.30650.2260.645-0.24740.806254.9116105.2514143.5246
425.1541.23660.35655.33194.80934.4868-0.1763-0.64320.2978-0.12380.121-0.0995-0.36110.04230.04181.5927-0.32310.32791.6257-0.36760.916940.2665100.6123164.701
432.99680.09081.07629.29076.14194.4051-0.31130.0744-0.0958-0.32630.27020.27520.34630.01060.03271.2453-0.40480.0970.9667-0.09010.580268.078570.4779166.171
440.7997-0.03860.71280.151-0.43361.7038-0.01680.010.18940.2425-0.01730.1849-0.29270.1397-0.0061.0262-0.44870.10280.61360.01080.52666.217363.2738145.1502
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 119 )
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 170 )
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 215 )
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 277 )
5X-RAY DIFFRACTION5chain 'A' and (resid 278 through 446 )
6X-RAY DIFFRACTION6chain 'B' and (resid 15 through 223 )
7X-RAY DIFFRACTION7chain 'B' and (resid 224 through 266 )
8X-RAY DIFFRACTION8chain 'B' and (resid 267 through 419 )
9X-RAY DIFFRACTION9chain 'B' and (resid 420 through 439 )
10X-RAY DIFFRACTION10chain 'C' and (resid 3 through 32 )
11X-RAY DIFFRACTION11chain 'C' and (resid 33 through 133 )
12X-RAY DIFFRACTION12chain 'C' and (resid 134 through 152 )
13X-RAY DIFFRACTION13chain 'C' and (resid 153 through 201 or resid 1101)
14X-RAY DIFFRACTION14chain 'C' and (resid 202 through 286 )
15X-RAY DIFFRACTION15chain 'C' and (resid 287 through 340 )
16X-RAY DIFFRACTION16chain 'C' and (resid 341 through 379 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 22 )
18X-RAY DIFFRACTION18chain 'D' and (resid 23 through 131 or resid 1001)
19X-RAY DIFFRACTION19chain 'D' and (resid 132 through 151 )
20X-RAY DIFFRACTION20chain 'D' and (resid 152 through 231 )
21X-RAY DIFFRACTION21chain 'D' and (resid 232 through 241 )
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 73 )
23X-RAY DIFFRACTION23chain 'E' and (resid 74 through 122 )
24X-RAY DIFFRACTION24chain 'E' and (resid 123 through 196 or resid 1001)
25X-RAY DIFFRACTION25chain 'F' and (resid 6 through 24 )
26X-RAY DIFFRACTION26chain 'F' and (resid 25 through 35 )
27X-RAY DIFFRACTION27chain 'F' and (resid 36 through 70 )
28X-RAY DIFFRACTION28chain 'F' and (resid 71 through 90 )
29X-RAY DIFFRACTION29chain 'F' and (resid 91 through 110 )
30X-RAY DIFFRACTION30chain 'G' and (resid 1 through 10 )
31X-RAY DIFFRACTION31chain 'G' and (resid 11 through 30 )
32X-RAY DIFFRACTION32chain 'G' and (resid 31 through 68 )
33X-RAY DIFFRACTION33chain 'G' and (resid 69 through 75 )
34X-RAY DIFFRACTION34chain 'H' and (resid 12 through 27 )
35X-RAY DIFFRACTION35chain 'H' and (resid 28 through 46 )
36X-RAY DIFFRACTION36chain 'H' and (resid 47 through 78 )
37X-RAY DIFFRACTION37chain 'J' and (resid 1 through 16 )
38X-RAY DIFFRACTION38chain 'J' and (resid 17 through 46 )
39X-RAY DIFFRACTION39chain 'J' and (resid 47 through 55 )
40X-RAY DIFFRACTION40chain 'J' and (resid 56 through 61 )
41X-RAY DIFFRACTION41chain 'K' and (resid 2 through 42 )
42X-RAY DIFFRACTION42chain 'K' and (resid 43 through 51 )
43X-RAY DIFFRACTION43chain 'C' and resid 1001
44X-RAY DIFFRACTION44chain 'C' and resid 1002

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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