[日本語] English
万見
- PDB-4he8: Crystal structure of the membrane domain of respiratory complex I... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 4he8
タイトルCrystal structure of the membrane domain of respiratory complex I from Thermus thermophilus
要素(NADH-quinone oxidoreductase subunit ...) x 7
キーワードOXIDOREDUCTASE / NADH-quinone oxidoreductase / complex I / proton pump / membrane protein / NADH / menaquinone / cytoplasmic membrane
機能・相同性
機能・相同性情報


トランスロカーゼ; ヒドロンの輸送の触媒; 酸化還元酵素反応を伴う / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / electron transport coupled proton transport / NADH dehydrogenase activity / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport ...トランスロカーゼ; ヒドロンの輸送の触媒; 酸化還元酵素反応を伴う / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / electron transport coupled proton transport / NADH dehydrogenase activity / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / plasma membrane
類似検索 - 分子機能
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2700 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / Helix Hairpins - #3510 / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2700 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / Helix Hairpins - #3510 / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-plastoquinone oxidoreductase, chain 5 subgroup / 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 / NADH-quinone oxidoreductase, chain 5-like / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
NADH-quinone oxidoreductase subunit 7 / NADH-quinone oxidoreductase subunit 10 / NADH-quinone oxidoreductase subunit 11 / NADH-quinone oxidoreductase subunit 12 / NADH-quinone oxidoreductase subunit 13 / NADH-quinone oxidoreductase subunit 14 / NADH-quinone oxidoreductase subunit 8
類似検索 - 構成要素
生物種Thermus thermophilus (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.3 Å
データ登録者Baradaran, R. / Berrisford, J.M. / Minhas, G.S. / Sazanov, L.A.
引用ジャーナル: Nature / 年: 2013
タイトル: Crystal structure of the entire respiratory complex I.
著者: Baradaran, R. / Berrisford, J.M. / Minhas, G.S. / Sazanov, L.A.
履歴
登録2012年10月3日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年2月13日Provider: repository / タイプ: Initial release
改定 1.12013年3月13日Group: Database references
改定 1.22023年9月20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 / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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

-
集合体

登録構造単位
A: NADH-quinone oxidoreductase subunit 7
J: NADH-quinone oxidoreductase subunit 10
K: NADH-quinone oxidoreductase subunit 11
L: NADH-quinone oxidoreductase subunit 12
M: NADH-quinone oxidoreductase subunit 13
N: NADH-quinone oxidoreductase subunit 14
H: NADH-quinone oxidoreductase subunit 8
B: NADH-quinone oxidoreductase subunit 7
D: NADH-quinone oxidoreductase subunit 10
E: NADH-quinone oxidoreductase subunit 11
F: NADH-quinone oxidoreductase subunit 12
G: NADH-quinone oxidoreductase subunit 13
I: NADH-quinone oxidoreductase subunit 14
C: NADH-quinone oxidoreductase subunit 8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)485,29918
ポリマ－483,31214
非ポリマー1,9864
水00
1
A: NADH-quinone oxidoreductase subunit 7
J: NADH-quinone oxidoreductase subunit 10
K: NADH-quinone oxidoreductase subunit 11
L: NADH-quinone oxidoreductase subunit 12
M: NADH-quinone oxidoreductase subunit 13
N: NADH-quinone oxidoreductase subunit 14
H: NADH-quinone oxidoreductase subunit 8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)242,6499
ポリマ－241,6567
非ポリマー9932
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area36890 Å2
ΔGint-409 kcal/mol
Surface area67160 Å2
手法PISA
2
B: NADH-quinone oxidoreductase subunit 7
D: NADH-quinone oxidoreductase subunit 10
E: NADH-quinone oxidoreductase subunit 11
F: NADH-quinone oxidoreductase subunit 12
G: NADH-quinone oxidoreductase subunit 13
I: NADH-quinone oxidoreductase subunit 14
C: NADH-quinone oxidoreductase subunit 8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)242,6499
ポリマ－241,6567
非ポリマー9932
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area36780 Å2
ΔGint-407 kcal/mol
Surface area67240 Å2
手法PISA
単位格子
Length a, b, c (Å)85.260, 120.540, 176.660
Angle α, β, γ (deg.)91.91, 95.73, 101.41
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111chain L
211chain F
112chain M
212chain G
113chain N
213chain I
114chain A
214chain B
115chain J
215chain D
116chain K
216chain E
117chain H and resid 4:354
217chain C and resid 4:354

NCSアンサンブル:
ID
1
2
3
4
5
6
7

-
要素

-
NADH-quinone oxidoreductase subunit ... , 7種, 14分子 ABJDKELFMGNIHC

#1: タンパク質 NADH-quinone oxidoreductase subunit 7 / NADH dehydrogenase I chain 7 / NDH-1 subunit 7


分子量: 13154.656 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: cytoplasmic membrane / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8
参照: UniProt: Q56217, NADH:ubiquinone reductase (H+-translocating)
#2: タンパク質 NADH-quinone oxidoreductase subunit 10 / NADH dehydrogenase I chain 10 / NDH-1 subunit 10


分子量: 18563.330 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: cytoplasmic membrane / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8
参照: UniProt: Q56225, NADH:ubiquinone reductase (H+-translocating)
#3: タンパク質 NADH-quinone oxidoreductase subunit 11 / NADH dehydrogenase I chain 11 / NDH-1 subunit 11


分子量: 10002.788 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: cytoplasmic membrane / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8
参照: UniProt: Q56226, NADH:ubiquinone reductase (H+-translocating)
#4: タンパク質 NADH-quinone oxidoreductase subunit 12 / NADH dehydrogenase I chain 12 / NDH-1 subunit 12


分子量: 65189.930 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: cytoplasmic membrane / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8
参照: UniProt: Q56227, NADH:ubiquinone reductase (H+-translocating)
#5: タンパク質 NADH-quinone oxidoreductase subunit 13 / NADH dehydrogenase I chain 13 / NDH-1 subunit 13


分子量: 49247.117 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: cytoplasmic membrane / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8
参照: UniProt: Q56228, NADH:ubiquinone reductase (H+-translocating)
#6: タンパク質 NADH-quinone oxidoreductase subunit 14 / NADH dehydrogenase I chain 14 / NDH-1 subunit 14


分子量: 44463.895 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: cytoplasmic membrane / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8
参照: UniProt: Q56229, NADH:ubiquinone reductase (H+-translocating)
#7: タンパク質 NADH-quinone oxidoreductase subunit 8 / NADH dehydrogenase I subunit 8 / NDH-1 subunit 8


分子量: 41034.523 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: cytoplasmic membrane / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8
参照: UniProt: Q60019, NADH:ubiquinone reductase (H+-translocating)

-
非ポリマー , 1種, 4分子

#8: 化合物
ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE / ウンデシルβ-マルトシド


分子量: 496.589 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C23H44O11 / コメント: 可溶化剤*YM

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.66 Å3/Da / 溶媒含有率: 66.38 %
結晶化温度: 290 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.5
詳細: 100 mM phosphate-citrate pH 4.5, 26% (v/v) PEG300, 5 mM CHAPS, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
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: ESRF / ビームライン: ID29 / 波長: 0.973 Å
検出器タイプ: ADSC QUANTUM 210 / 検出器: CCD / 日付: 2009年10月24日 / 詳細: mirrors
放射モノクロメーター: Si(311) / 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: 0.973 Å / 相対比: 1
反射解像度: 3.3→40 Å / Num. all: 99359 / Num. obs: 99359 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 2 % / Biso Wilson estimate: 97 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 5.9
反射 シェル解像度: 3.3→3.48 Å / 冗長度: 1.9 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 0.9 / Num. unique all: 13892 / Rsym value: 0.737 / % possible all: 92.6

-
解析

ソフトウェア
名称バージョン分類
MOSFLMデータ削減
PHASER位相決定
PHENIX(phenix.refine: dev_1041)精密化
SCALAデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 3RKO

3rko


解像度: 3.3→25.725 Å / SU ML: 0.44 / Isotropic thermal model: TLS and isotropic / 交差検証法: THROUGHOUT / σ(F): 0 / 位相誤差: 28.51 / 立体化学のターゲット値: ML
詳細: The data set was anisotropically scaled and truncated to 3.6, 3.4 and 3.3 A resolution along the a*, b* and c* axes, respectively, using the Diffraction Anisotropy Server (http://services.mbi. ...詳細: The data set was anisotropically scaled and truncated to 3.6, 3.4 and 3.3 A resolution along the a*, b* and c* axes, respectively, using the Diffraction Anisotropy Server (http://services.mbi.ucla.edu/anisoscale/)
Rfactor反射数%反射Selection details
Rfree0.2634 1816 2.04 %RANDOM
Rwork0.2088 ---
all0.2099 89170 --
obs0.2099 89170 86.73 %-
溶媒の処理減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 84.3 Å2
精密化ステップサイクル: LAST / 解像度: 3.3→25.725 Å
タンパク質核酸リガンド溶媒全体
原子数32514 0 136 0 32650
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00533576
X-RAY DIFFRACTIONf_angle_d1.0645830
X-RAY DIFFRACTIONf_dihedral_angle_d15.39211248
X-RAY DIFFRACTIONf_chiral_restr0.0715404
X-RAY DIFFRACTIONf_plane_restr0.0065562
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11L4638X-RAY DIFFRACTIONPOSITIONAL
12F4638X-RAY DIFFRACTIONPOSITIONAL0.012
21M3489X-RAY DIFFRACTIONPOSITIONAL
22G3489X-RAY DIFFRACTIONPOSITIONAL0.018
31N3154X-RAY DIFFRACTIONPOSITIONAL
32I3154X-RAY DIFFRACTIONPOSITIONAL0.015
41A724X-RAY DIFFRACTIONPOSITIONAL
42B724X-RAY DIFFRACTIONPOSITIONAL0.012
51J1217X-RAY DIFFRACTIONPOSITIONAL
52D1217X-RAY DIFFRACTIONPOSITIONAL0.014
61K703X-RAY DIFFRACTIONPOSITIONAL
62E703X-RAY DIFFRACTIONPOSITIONAL0.013
71H2379X-RAY DIFFRACTIONPOSITIONAL
72C2379X-RAY DIFFRACTIONPOSITIONAL0.013
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.3890.3704530.32332172X-RAY DIFFRACTION28
3.389-3.48850.3631940.30454503X-RAY DIFFRACTION58
3.4885-3.60080.34311440.28626480X-RAY DIFFRACTION84
3.6008-3.72920.31671490.26847378X-RAY DIFFRACTION95
3.7292-3.8780.30641640.24487401X-RAY DIFFRACTION96
3.878-4.05390.29341360.21757492X-RAY DIFFRACTION96
4.0539-4.26670.25961600.19817490X-RAY DIFFRACTION97
4.2667-4.53260.22231470.17967514X-RAY DIFFRACTION97
4.5326-4.88040.26091500.16987510X-RAY DIFFRACTION97
4.8804-5.36750.25861490.18327563X-RAY DIFFRACTION97
5.3675-6.1350.24451650.2077393X-RAY DIFFRACTION96
6.135-7.6950.23631530.21087394X-RAY DIFFRACTION95
7.695-25.7260.21921520.18767064X-RAY DIFFRACTION91
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)
12.54090.51750.27910.86981.1271.78430.1205-0.7187-0.44940.31560.0818-0.27720.63450.2998-0.2640.8441-0.0107-0.2590.80030.07930.53132.02168.222356.9469
23.87591.6159-2.16419.84841.99652.0960.3494-0.57570.01720.7209-0.3998-0.39070.4175-0.3416-0.02930.3199-0.0449-0.07430.8521-0.06860.39989.84544.888952.6793
34.789-2.16740.48870.9809-0.16956.21890.00730.26260.96860.48860.3549-0.9710.16060.6974-0.2060.38260.1448-0.07860.848-0.10430.801247.4553.218842.8594
41.71410.3255-0.21540.64280.27731.31060.05880.04910.46120.08560.3782-0.58980.39041.04280.16250.2361-0.0907-0.56770.72490.00771.171137.07137.76547.497
52.5556-0.1765-3.34040.25441.0146.7864-0.5093-0.4013-0.5210.62410.3439-0.55381.08810.7610.17140.61490.1604-0.2550.78410.07410.888338.9566-10.456342.1877
62.7656-0.5061-0.53553.73571.86242.19670.23040.20880.35120.2278-0.1832-0.2732-0.54810.2138-0.0120.3540.025-0.14940.54290.0580.287322.64949.407339.9601
72.48030.64170.30721.20680.29053.38490.32860.0805-0.5666-0.03050.4245-0.6983-0.29921.24931.11490.20930.1991-0.5530.98660.01630.389941.1718-2.290335.5316
80.70380.1818-0.27681.86060.04590.13680.19560.07650.01560.68670.19590.52280.21140.3414-0.17740.72390.0934-0.28620.64280.03910.50333.63374.057837.4487
91.91040.06810.317.1152-2.56833.01580.2861-0.0326-0.4784-0.3067-0.2606-0.08010.2526-0.0071-0.06050.31860.0244-0.19070.61430.0730.58324.7751-0.651443.2144
106.37694.365-2.73943.2671-3.21327.57230.0429-0.5249-0.39770.3197-0.088-0.386-0.14910.42380.05791.5889-0.1314-0.04331.0444-0.08781.272228.8791-22.290450.1792
115.66153.05295.76476.35086.13639.02121.7151-0.1445-1.18170.69780.9708-0.75831.15760.3322-1.66810.79680.0446-0.34270.91160.05170.877929.168-25.76936.8967
121.64760.2310.06262.46970.8222.7446-0.05790.2544-0.1607-0.0375-0.05870.82970.3733-0.48320.10461.0082-0.5144-0.2041.2598-0.12090.8794-5.7476-54.0006-39.422
132.5571-0.0592-0.18170.94921.18631.42570.03180.0095-0.4471-0.38440.13930.41381.4191-0.3121-0.19311.1218-0.3341-0.23980.59690.11210.81649.4479-51.3446-31.2462
141.5110.3031-0.31622.03961.02332.8575-0.130.4072-0.6391-0.15360.25640.00241.0992-0.1835-0.0911.2499-0.1653-0.12960.7209-0.13890.677115.301-60.4994-46.6675
150.62310.32830.25071.48231.85412.62580.06910.2051-0.3735-0.01080.2167-0.2181.32360.0038-0.15581.3167-0.049-0.26130.7284-0.0510.939420.0982-55.8129-29.7698
163.0989-0.25890.87721.15951.15952.49690.0186-0.118-0.3196-0.1296-0.23610.39170.1328-1.07910.08840.2094-0.0676-0.15340.90180.06920.6464-1.1819-26.9072-3.5379
171.62250.5751.00593.41860.62692.2187-0.24910.19070.17590.37060.34550.2069-0.0501-0.0535-0.03110.28250.0961-0.04440.49760.08710.420112.3919-24.9226-8.127
182.19360.0069-0.32942.22280.96122.9186-0.0894-0.0174-0.39730.2024-0.02880.31360.6527-0.50540.09990.4819-0.1797-0.13790.57650.08060.56497.7552-41.0792-17.8853
192.43110.44990.31771.06811.35371.96280.05260.13310.07950.05460.13060.3568-0.1454-0.6486-0.13020.2590.0918-0.03690.63270.01110.48320.4515-1.139736.381
202.6442-0.42830.23691.3731.03651.39790.1779-0.1390.01090.12840.00790.12890.2867-0.0291-0.21050.37290.0363-0.19710.58620.09020.41517.5622-5.166232.1317
211.9702-0.0868-0.51772.0868-1.03041.839-0.032-0.2348-0.107-0.05860.162-0.05490.4310.3699-0.13890.3310.005-0.08010.33040.04190.369517.7591-12.63526.525
222.06870.007-0.42040.90180.19071.49110.07130.2055-0.0914-0.26940.1385-0.34420.357-0.0771-0.14480.28590.0426-0.17270.50420.08810.512320.3163-15.963516.9139
232.236-1.65650.86873.19770.30831.3671-0.2344-0.03950.04410.6472-0.5284-0.18920.3544-1.06380.25960.5237-0.0721-0.05250.5645-0.09170.2576.5137-17.649721.9561
243.809-1.14871.63453.0238-1.69478.3657-0.0198-0.6789-0.43850.20770.31170.30150.4833-0.5874-0.3520.5461-0.09840.02140.42430.0880.44525.0489-29.590821.0183
253.5850.6855-0.33563.62760.93152.1750.199-0.0766-0.11280.50490.04630.22010.5109-0.196-0.24080.41330.0596-0.08370.4514-0.04870.38711.7541-22.651813.5738
266.24721.67440.58026.9978-1.75415.34830.82210.35960.42130.74690.0450.1957-0.0811-0.8566-0.10880.07540.2255-0.20160.47910.15280.7632-2.9159-13.773617.2135
270.30630.0962-0.95462.1710.11214.03550.8711-0.83710.19211.2429-0.1051-0.5062-0.63940.46010.41410.9903-0.2219-0.94261.1697-0.09050.772542.676314.277768.6726
282.7606-0.7691-0.24711.21081.1282.8437-0.0333-0.6833-0.29341.01430.2879-0.392-0.07450.3089-0.21541.0858-0.0006-0.34010.80020.02760.634229.494314.27368.7927
294.3545-5.57590.50597.785-1.44276.6005-0.8482-0.3421-0.39350.58990.11710.09570.7744-0.54280.55960.5898-0.1086-0.08990.64510.18650.793912.365211.190962.1326
302.4494-0.65932.34442.3522-1.44257.9530.6821-0.0921-0.55870.36450.1980.4795-0.7943-0.6237-0.40371.22710.30290.18020.8081-0.13560.6566.239122.572868.8042
312.2346-0.2897-0.61170.60270.46641.33590.22460.65930.611-0.2934-0.2262-0.0391-0.6111-0.39040.00530.76720.19040.08890.61360.15450.494837.5807-75.395715.0988
324.0697-1.23790.91659.25580.71461.7276-0.15820.45250.0468-0.8657-0.0026-0.3428-0.0593-0.55920.16090.39650.1597-0.03150.835-0.10180.402715.3613-75.497120.3295
335.58272.5012-0.57021.19310.45737.3028-0.1368-0.1103-1.0301-1.14710.3508-0.51-0.42781.015-0.22680.554-0.22740.08880.663-0.0040.766552.6371-67.94928.5507
343.9388-0.61130.47941.11031.18752.43560.0566-0.2955-0.1332-0.75390.1993-0.1657-0.22660.2277-0.27340.5040.02590.11160.44040.09090.585242.9036-74.074324.339
352.46620.14383.25991.49111.89596.6175-0.00620.17110.7219-1.04140.4878-1.0375-1.50210.7327-0.03860.7865-0.12630.17710.6466-0.04790.857942.1567-55.754929.5961
362.52710.3599-0.52142.10391.22742.4141-0.1521-0.0556-0.09350.4703-0.1032-0.1340.0161-0.09680.31390.3997-0.1054-0.09770.38110.04750.243429.2328-77.898732.4651
376.0151-0.74620.7910.51350.98794.53740.6477-0.11660.4799-0.55710.0478-0.074-0.26520.1619-0.39480.78390.03590.07180.34720.08210.507345.8555-63.43136.148
380.9484-0.4880.01232.10560.11220.69480.05670.07160.0115-0.4788-0.1169-0.2660.33640.3288-0.10130.7776-0.12750.00410.41230.10470.441439.3197-70.8834.5398
392.6561-0.7965-0.33826.0669-1.89533.29340.35930.01860.3690.3094-0.18440.3216-0.0668-0.4059-0.07560.54930.0709-0.0120.56530.1440.473529.62-67.637129.1296
407.39-4.59543.70655.4361-1.70182.0095-0.08780.37110.2341-0.15210.1236-0.1868-0.42530.3523-0.01172.26480.1790.18630.9326-0.05430.976330.0555-45.666921.9994
416.588-1.5135-4.24483.69383.71674.96830.14820.6881.1285-1.14440.13880.1229-0.8840.1864-0.41021.54920.07170.06620.59980.30270.680830.3251-42.098135.2559
421.81230.2235-0.67412.60251.06842.91990.2660.18130.12380.0719-0.44770.6222-0.6403-1.0120.20310.92540.19750.12280.7957-0.14140.5963-5.32-18.8403112.787
433.45040.4581-0.82321.40050.65091.65480.33340.14020.79890.4251-0.28320.0103-1.71350.1545-0.02441.05980.0490.09240.4190.0160.61749.8035-19.3454104.0781
441.48130.3858-1.23472.39811.46793.52620.3702-0.27480.5198-0.16060.17380.0269-1.12660.4116-0.37881.4075-0.14040.1170.7121-0.24740.76513.6659-10.7759117.4968
450.3410.40570.13610.50650.28870.35610.6409-0.30150.85570.1263-0.30550.4638-1.16420.31490.12192.2512-0.6328-0.07550.8231-0.9540.938419.7113-3.4071126.7936
460.3452-0.3638-0.42151.21930.76482.5290.2638-0.35960.36930.03440.2543-0.1953-1.50320.2386-0.37341.2405-0.15560.2550.7586-0.20890.818219.6454-13.4066102.2209
472.8467-0.0257-1.75831.45471.33432.9849-0.10630.07230.0530.1053-0.11820.405-0.0113-0.78460.23190.22820.0138-0.09330.73880.05040.6181.8434-45.257576.8281
482.19640.2184-1.05562.88620.8012.2499-0.2005-0.3988-0.1019-0.3330.316-0.04970.2832-0.0899-0.06960.4474-0.1387-0.07370.41070.08460.375115.709-45.256580.9518
492.8935-0.7717-0.81052.66391.07344.04180.22840.0360.4581-0.0679-0.13340.146-0.772-0.1216-0.02590.5301-0.01980.00610.35930.04810.40819.1525-29.844690.8131
502.291-0.2202-0.28730.63710.94821.9419-0.18040.4449-0.2277-0.0755-0.34090.30590.1922-0.6857-0.08440.4272-0.118-0.24010.8206-0.06750.62155.8308-70.890736.9766
512.7905-0.0953-1.45411.41161.36242.35310.07910.27980.056-0.0779-0.06190.2814-0.2425-0.36230.00610.2856-0.063-0.02570.43350.06920.344722.2778-64.267140.5443
521.4828-0.28030.152.259-1.29812.21690.11290.4248-0.0027-0.53-0.08470.2775-0.08760.2014-0.00180.37930.0277-0.11970.316-0.01040.424221.5473-56.822846.1361
532.9814-0.26370.36911.2541.38652.6014-0.0531-0.1812-0.1838-0.18790.33070.0576-0.5047-0.1128-0.18380.3392-0.0537-0.00890.37220.07450.412623.9395-53.080955.6382
541.63961.5566-0.82133.9332-0.27040.577-0.2184-0.13150.1261-0.2775-0.1212-0.2797-0.3568-0.90610.18590.47670.0295-0.06150.6148-0.07680.3239.8537-53.55551.1455
553.89840.116-1.40313.4168-2.74617.04710.08030.6040.9068-0.97480.42060.66990.1638-0.875-0.43970.53330.1342-0.08610.51280.06020.61966.6199-41.970252.1371
564.2638-0.53490.14542.64391.84972.90070.18380.45090.26-0.0437-0.20050.1065-0.9052-0.203-0.04970.4851-0.0655-0.01150.3622-0.03210.343314.592-47.758759.3128
575.9704-1.771.25156.6615-2.61925.29110.6776-0.2003-0.2866-0.8213-0.5678-0.02390.4614-0.41070.1730.2527-0.01480.00590.7964-0.08420.76951.3232-58.794556.2573
581.5863-0.78460.89393.19950.19931.80510.41430.80660.1731-0.7407-0.3668-0.0775-0.45010.4280.06351.26750.1350.40180.73190.08710.717448.5731-79.79842.8798
592.96550.5365-0.17540.79080.59452.31410.12140.70290.2594-1.2888-0.10810.1216-0.1786-0.064-0.03611.16250.10190.01230.64860.06040.429135.4999-81.7553.3341
603.39423.2959-2.92485.3054-1.29893.9969-0.62430.69351.2096-0.3117-0.3135-0.4876-0.4263-0.54190.10230.37350.0756-0.27310.73030.13580.705918.4025-81.295610.7292
612.30560.8757-0.25571.9975-0.24648.07350.30510.425-0.4384-0.83330.4210.33040.5335-0.565-0.74061.0452-0.0809-0.24030.9216-0.21190.755613.7944-93.494.2758
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:88)
2X-RAY DIFFRACTION2chain 'A' and (resseq 89:116)
3X-RAY DIFFRACTION3chain 'J' and (resseq 1:24)
4X-RAY DIFFRACTION4chain 'J' and (resseq 25:57)
5X-RAY DIFFRACTION5chain 'J' and (resseq 58:107)
6X-RAY DIFFRACTION6chain 'J' and (resseq 108:160)
7X-RAY DIFFRACTION7chain 'K' and (resseq 1:23)
8X-RAY DIFFRACTION8chain 'K' and (resseq 24:51)
9X-RAY DIFFRACTION9chain 'K' and (resseq 52:78)
10X-RAY DIFFRACTION10chain 'K' and (resseq 79:86)
11X-RAY DIFFRACTION11chain 'K' and (resseq 87:95)
12X-RAY DIFFRACTION12chain 'L' and (resseq 1:119)
13X-RAY DIFFRACTION13chain 'L' and (resseq 120:178)
14X-RAY DIFFRACTION14chain 'L' and (resseq 179:425)
15X-RAY DIFFRACTION15chain 'L' and (resseq 426:605)
16X-RAY DIFFRACTION16chain 'M' and (resseq 1:170)
17X-RAY DIFFRACTION17chain 'M' and (resseq 171:244)
18X-RAY DIFFRACTION18chain 'M' and (resseq 245:467)
19X-RAY DIFFRACTION19chain 'N' and (resseq 1:56)
20X-RAY DIFFRACTION20chain 'N' and (resseq 57:187)
21X-RAY DIFFRACTION21chain 'N' and (resseq 188:229)
22X-RAY DIFFRACTION22chain 'N' and (resseq 230:279)
23X-RAY DIFFRACTION23chain 'N' and (resseq 280:302)
24X-RAY DIFFRACTION24chain 'N' and (resseq 303:339)
25X-RAY DIFFRACTION25chain 'N' and (resseq 340:395)
26X-RAY DIFFRACTION26chain 'N' and (resseq 396:427)
27X-RAY DIFFRACTION27chain 'H' and (resseq 2:96)
28X-RAY DIFFRACTION28chain 'H' and (resseq 97:304)
29X-RAY DIFFRACTION29chain 'H' and (resseq 305:329)
30X-RAY DIFFRACTION30chain 'H' and (resseq 330:354)
31X-RAY DIFFRACTION31chain 'B' and (resseq 1:88)
32X-RAY DIFFRACTION32chain 'B' and (resseq 89:116)
33X-RAY DIFFRACTION33chain 'D' and (resseq 1:24)
34X-RAY DIFFRACTION34chain 'D' and (resseq 25:57)
35X-RAY DIFFRACTION35chain 'D' and (resseq 58:107)
36X-RAY DIFFRACTION36chain 'D' and (resseq 108:160)
37X-RAY DIFFRACTION37chain 'E' and (resseq 1:23)
38X-RAY DIFFRACTION38chain 'E' and (resseq 24:51)
39X-RAY DIFFRACTION39chain 'E' and (resseq 52:78)
40X-RAY DIFFRACTION40chain 'E' and (resseq 79:86)
41X-RAY DIFFRACTION41chain 'E' and (resseq 87:95)
42X-RAY DIFFRACTION42chain 'F' and (resseq 1:119)
43X-RAY DIFFRACTION43chain 'F' and (resseq 120:178)
44X-RAY DIFFRACTION44chain 'F' and (resseq 179:379)
45X-RAY DIFFRACTION45chain 'F' and (resseq 380:425)
46X-RAY DIFFRACTION46chain 'F' and (resseq 426:605)
47X-RAY DIFFRACTION47chain 'G' and (resseq 1:170)
48X-RAY DIFFRACTION48chain 'G' and (resseq 171:244)
49X-RAY DIFFRACTION49chain 'G' and (resseq 245:467)
50X-RAY DIFFRACTION50chain 'I' and (resseq 1:56)
51X-RAY DIFFRACTION51chain 'I' and (resseq 57:187)
52X-RAY DIFFRACTION52chain 'I' and (resseq 188:229)
53X-RAY DIFFRACTION53chain 'I' and (resseq 230:279)
54X-RAY DIFFRACTION54chain 'I' and (resseq 280:302)
55X-RAY DIFFRACTION55chain 'I' and (resseq 303:339)
56X-RAY DIFFRACTION56chain 'I' and (resseq 340:395)
57X-RAY DIFFRACTION57chain 'I' and (resseq 396:427)
58X-RAY DIFFRACTION58chain 'C' and (resseq 2:96)
59X-RAY DIFFRACTION59chain 'C' and (resseq 97:304)
60X-RAY DIFFRACTION60chain 'C' and (resseq 305:329)
61X-RAY DIFFRACTION61chain 'C' and (resseq 330:354)

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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