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- PDB-5nhg: Crystal structure of the human dihydrolipoamide dehydrogenase -

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基本情報

登録情報
データベース: PDB / ID: 5nhg
タイトルCrystal structure of the human dihydrolipoamide dehydrogenase
要素Dihydrolipoyl dehydrogenase, mitochondrial
キーワードOXIDOREDUCTASE / dihydrolipoamide dehydrogenase / E3 subunit / pyruvate dehydrogenase complex / alpha-ketoglutarate dehydrogenase complex
機能・相同性
機能・相同性情報


acetyltransferase complex / acrosomal matrix / OGDH complex synthesizes succinyl-CoA from 2-OG / OADH complex synthesizes glutaryl-CoA from 2-OA / oxoadipate dehydrogenase complex / Glycine degradation / branched-chain alpha-ketoacid dehydrogenase complex / BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV / Loss-of-function mutations in DBT cause MSUD2 / Loss-of-function mutations in DLD cause MSUD3/DLDD ...acetyltransferase complex / acrosomal matrix / OGDH complex synthesizes succinyl-CoA from 2-OG / OADH complex synthesizes glutaryl-CoA from 2-OA / oxoadipate dehydrogenase complex / Glycine degradation / branched-chain alpha-ketoacid dehydrogenase complex / BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV / Loss-of-function mutations in DBT cause MSUD2 / Loss-of-function mutations in DLD cause MSUD3/DLDD / H139Hfs13* PPM1K causes a mild variant of MSUD / PDH complex synthesizes acetyl-CoA from PYR / Branched-chain ketoacid dehydrogenase kinase deficiency / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / Regulation of pyruvate dehydrogenase (PDH) complex / pyruvate decarboxylation to acetyl-CoA / oxoglutarate dehydrogenase complex / branched-chain amino acid catabolic process / pyruvate dehydrogenase complex / Branched-chain amino acid catabolism / 2-oxoglutarate metabolic process / motile cilium / Signaling by Retinoic Acid / pyruvate metabolic process / sperm capacitation / mitochondrial electron transport, NADH to ubiquinone / gastrulation / Mitochondrial protein degradation / regulation of membrane potential / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / proteolysis / nucleus
類似検索 - 分子機能
: / Dihydrolipoamide dehydrogenase / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain ...: / Dihydrolipoamide dehydrogenase / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
FLAVIN-ADENINE DINUCLEOTIDE / Dihydrolipoyl dehydrogenase, mitochondrial
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.27 Å
データ登録者Szabo, E. / Mizsei, R. / Wilk, P. / Zambo, Z. / Torocsik, B. / Weiss, M.S. / Adam-Vizi, V. / Ambrus, A.
資金援助 ハンガリー, ドイツ, 6件
組織認可番号国
Hungarian Academy of Sciences02001 ハンガリー
Hungarian Scientific Research Fund112230 ハンガリー
Hungarian Brain Research ProgramKTIA_13_NAP-A-III/6 ハンガリー
Hungarian Academy of SciencesBolyai Fellowship [to A.A.] ハンガリー
European Molecular Biology OrganizationShort-term Fellowship [to A.A.] ハンガリー
Helmholtz-Zentrum Berlin16204087-ST, BESSY: 362 [to E.Sz., A.A.] ドイツ
引用ジャーナル: Free Radic. Biol. Med. / 年: 2018
タイトル: Crystal structures of the disease-causing D444V mutant and the relevant wild type human dihydrolipoamide dehydrogenase.
著者: Szabo, E. / Mizsei, R. / Wilk, P. / Zambo, Z. / Torocsik, B. / Weiss, M.S. / Adam-Vizi, V. / Ambrus, A.
履歴
登録2017年3月21日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02018年5月16日Provider: repository / タイプ: Initial release
改定 1.12018年7月4日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
改定 1.22024年1月17日Group: Data collection / Database references / 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_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.32024年11月13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

ダウンロードとリンク

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集合体

登録構造単位
A: Dihydrolipoyl dehydrogenase, mitochondrial
B: Dihydrolipoyl dehydrogenase, mitochondrial
C: Dihydrolipoyl dehydrogenase, mitochondrial
D: Dihydrolipoyl dehydrogenase, mitochondrial
E: Dihydrolipoyl dehydrogenase, mitochondrial
F: Dihydrolipoyl dehydrogenase, mitochondrial
G: Dihydrolipoyl dehydrogenase, mitochondrial
H: Dihydrolipoyl dehydrogenase, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)427,39624
ポリマ－420,0488
非ポリマー7,34916
水4,954275
1
A: Dihydrolipoyl dehydrogenase, mitochondrial
B: Dihydrolipoyl dehydrogenase, mitochondrial
ヘテロ分子


  • ソフトウェアが定義した集合体
  • 根拠: gel filtration, Ambrus A et al., Hum. Mol. Genet., 20:2984-2995, 2011., mass spectrometry, Ambrus A et al., Hum. Mol. Genet., 20:2984-2995, 2011; Ambrus A et al., Biochim. Biophys. Acta., ...根拠: gel filtration, Ambrus A et al., Hum. Mol. Genet., 20:2984-2995, 2011., mass spectrometry, Ambrus A et al., Hum. Mol. Genet., 20:2984-2995, 2011; Ambrus A et al., Biochim. Biophys. Acta., 1862(11):2098-2109, 2016.
  • 107 kDa, 2 ポリマー
  • Omokage検索でこの集合体の類似形状データを探す (詳細)
分子量 (理論値)分子数
合計 (水以外)106,8276
ポリマ－105,0122
非ポリマー1,8154
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint-51 kcal/mol
Surface area34500 Å2
手法PISA
2
C: Dihydrolipoyl dehydrogenase, mitochondrial
D: Dihydrolipoyl dehydrogenase, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,9146
ポリマ－105,0122
非ポリマー1,9024
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11400 Å2
ΔGint-47 kcal/mol
Surface area34910 Å2
手法PISA
3
E: Dihydrolipoyl dehydrogenase, mitochondrial
F: Dihydrolipoyl dehydrogenase, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,9497
ポリマ－105,0122
非ポリマー1,9385
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-44 kcal/mol
Surface area34570 Å2
手法PISA
4
G: Dihydrolipoyl dehydrogenase, mitochondrial
H: Dihydrolipoyl dehydrogenase, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,7055
ポリマ－105,0122
非ポリマー1,6933
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11140 Å2
ΔGint-52 kcal/mol
Surface area34630 Å2
手法PISA
単位格子
Length a, b, c (Å)60.060, 113.540, 136.880
Angle α, β, γ (deg.)83.180, 84.750, 81.090
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A
21(chain B and resid 4 through 474)
31(chain C and resid 4 through 474)
41(chain D and resid 4 through 474)
51chain E
61chain F
71chain G
81chain H

NCSドメイン領域:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 4 - 474 / Label seq-ID: 25 - 495

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2(chain B and resid 4 through 474)BB
3(chain C and resid 4 through 474)CC
4(chain D and resid 4 through 474)DD
5chain EEE
6chain FFF
7chain GGG
8chain HHH

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要素

#1: タンパク質
Dihydrolipoyl dehydrogenase, mitochondrial / Dihydrolipoamide dehydrogenase / Glycine cleavage system L protein


分子量: 52505.980 Da / 分子数: 8 / 由来タイプ: 組換発現
詳細: sequence of the Strep-tag with linker amino acids: ASWSHPQFEKGALEVLFQGPG
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DLD, GCSL, LAD, PHE3 / プラスミド: pET52b+ / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P09622, dihydrolipoyl dehydrogenase
#2: 化合物
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / FAD


分子量: 785.550 Da / 分子数: 8 / 由来タイプ: 組換発現 / 式: C27H33N9O15P2 / コメント: FAD*YM
#3: 化合物
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / トリス(ヒドロキシメチル)メチルアンモニウム


分子量: 122.143 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C4H12NO3 / コメント: pH緩衝剤*YM
#4: 化合物 ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / ビストリス


分子量: 209.240 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C8H19NO5 / コメント: pH緩衝剤*YM
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 275 / 由来タイプ: 天然 / 式: H2O
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: 2.28 Å3/Da / 溶媒含有率: 46.06 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.45
詳細: 0.1 M Bis-Tris (pH 7.45), 0.2 M MgCl2, 25 (w/v)% PEG 3350

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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: BESSY / ビームライン: 14.1 / 波長: 0.9184 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2016年9月23日
放射モノクロメーター: Si-111 crystal / 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: 0.9184 Å / 相対比: 1
反射解像度: 2.27→46.622 Å / Num. obs: 160435 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / 冗長度: 3.756 % / Biso Wilson estimate: 48.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.068 / Χ2: 1.022 / Net I/σ(I): 13.68 / Num. measured all: 602581 / Scaling rejects: 501
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.27-2.332.1060.5411.46110680.660.73391.9
2.33-2.393.7580.5942.19116730.7830.69298.5
2.39-2.463.9950.4862.8112880.8490.56299
2.46-2.543.9210.3883.42111130.8970.4599.2
2.54-2.623.8690.3184.14107410.9180.36999.3
2.62-2.713.7750.2265.51103130.9560.26499
2.71-2.823.6740.1746.8297060.9720.20496.8
2.82-2.934.0280.1438.996270.9840.16599.2
2.93-3.064.0040.11610.9392320.9880.13499.5
3.06-3.213.9730.08814.1388360.9920.10199.3
3.21-3.383.9310.06617.9683930.9950.07799.1
3.38-3.593.710.05421.1778210.9960.06397.5
3.59-3.843.9110.04725.3473110.9970.05498
3.84-4.144.0340.04229.0369570.9980.04899.3
4.14-4.543.9570.03932.5864150.9980.04599.3
4.54-5.083.7780.03733.4257450.9980.04398.8
5.08-5.863.7050.03531.7249100.9980.04196.3
5.86-7.183.9610.03534.1443130.9980.0499.3
7.18-10.153.730.02838.6232700.9990.03397.7
10.15-46.6223.8240.02641.5117030.9990.03193.3

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解析

ソフトウェア
名称分類
PHENIX精密化
MxCuBEデータ収集
XDSデータスケーリング
XDSデータ削減
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1ZMD

1zmd


解像度: 2.27→46.622 Å / SU ML: 0.29 / 交差検証法: FREE R-VALUE / σ(F): 1.13 / 位相誤差: 25.27
詳細: torsion-angle NCS restraints were used during refinement in phenix.refine
Rfactor反射数%反射
Rfree0.2096 4531 1.49 %
Rwork0.1805 --
obs0.1809 304054 93.02 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 190.7 Å2 / Biso mean: 74.983 Å2 / Biso min: 28.16 Å2
精密化ステップサイクル: final / 解像度: 2.27→46.622 Å
タンパク質核酸リガンド溶媒全体
原子数28011 0 735 275 29021
Biso mean--60.07 48.39 -
残基数----3771
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00728985
X-RAY DIFFRACTIONf_angle_d0.94239238
X-RAY DIFFRACTIONf_chiral_restr0.0594515
X-RAY DIFFRACTIONf_plane_restr0.0064993
X-RAY DIFFRACTIONf_dihedral_angle_d14.88217166
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A21863X-RAY DIFFRACTION11.317TORSIONAL
12B21863X-RAY DIFFRACTION11.317TORSIONAL
13C21863X-RAY DIFFRACTION11.317TORSIONAL
14D21863X-RAY DIFFRACTION11.317TORSIONAL
15E21863X-RAY DIFFRACTION11.317TORSIONAL
16F21863X-RAY DIFFRACTION11.317TORSIONAL
17G21863X-RAY DIFFRACTION11.317TORSIONAL
18H21863X-RAY DIFFRACTION11.317TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2701-2.29590.3628810.33615095517648
2.2959-2.32290.34191100.32466755686562
2.3229-2.35130.31551010.30967911801274
2.3513-2.3810.31981560.29939370952688
2.381-2.41230.31081370.2916104781061596
2.4123-2.44540.28231710.2834103371050897
2.4454-2.48030.37051760.2687104211059797
2.4803-2.51730.33551160.2551104551057197
2.5173-2.55670.26111230.2544103561047997
2.5567-2.59860.26121910.2503105841077597
2.5986-2.64340.24991480.2461104081055697
2.6434-2.69150.27581370.2353103451048297
2.6915-2.74320.25631450.232102631040894
2.7432-2.79920.27321310.240199651009693
2.7992-2.86010.28741800.2527105931077398
2.8601-2.92660.32181360.2321103131044998
2.9266-2.99980.26381400.2316106371077798
2.9998-3.08090.27221470.214104521059998
3.0809-3.17150.23521870.2129105301071798
3.1715-3.27380.22121750.2129105021067798
3.2738-3.39080.22562140.2011103951060998
3.3908-3.52650.24411370.1868106201075797
3.5265-3.6870.21571520.171598481000092
3.687-3.88130.16961410.158105791072099
3.8813-4.12430.16751880.1411105561074498
4.1243-4.44250.15371650.1237105211068699
4.4425-4.88910.13011830.1197105321071598
4.8891-5.59560.21041690.1322100441021394
5.5956-7.04590.16551530.1586105461069998
7.0459-46.63140.15361410.1378101121025394
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)
14.10692.4963.65322.50933.10145.63060.2209-0.03620.03090.0623-0.0272-0.20650.23770.2203-0.20040.4391-0.0096-0.06530.29580.020.495612.83960.4713-3.0052
22.70730.03521.69540.95371.02792.54110.00190.4413-0.1736-0.12950.0566-0.04140.18410.1768-0.08610.5657-0.0082-0.010.41590.02560.48335.6287-5.4614-18.6461
31.5004-0.0712-0.06491.42550.17261.26990.1897-0.2401-0.4640.32-0.014-0.07990.5314-0.0763-0.20390.7009-0.0574-0.1120.38540.06770.5370.9699-11.23531.5698
42.14571.1799-0.34943.77850.54771.12460.3958-0.6274-0.24090.7649-0.2016-0.18320.58360.0133-0.20920.7238-0.1075-0.12680.52270.09450.40665.1571-4.641312.8745
53.5294-0.8833-0.35960.9862-0.91150.65740.0979-0.50420.53330.40030.0336-0.19870.2371-0.0568-0.09160.481-0.0888-0.03320.3712-0.010.4627-2.67459.44974.8938
62.8240.26850.1253.85811.65325.80480.1818-0.03610.1324-0.0378-0.12010.3357-0.0108-0.5249-0.05020.2828-0.0439-0.00830.34660.04490.362-15.020915.3716-7.4983
73.2054-0.8832-0.53474.38672.22964.22310.20410.02060.14990.0138-0.37740.6385-0.0577-0.93090.06160.4149-0.00660.01340.59540.02550.5458-29.234626.331-24.3594
85.9506-3.99752.46955.3312-4.29323.4127-0.04950.2559-0.270.33490.0581-0.570.69870.29270.01150.49130.0235-0.06650.3815-0.04480.4324-4.2602-1.2183-30.2223
96.9745-6.4153-6.09885.96596.32037.17080.01720.2949-0.85690.4695-0.49460.9680.5623-0.82530.69640.5246-0.106-0.05690.58490.02020.584-23.89799.8708-27.3873
101.8778-0.775-0.26612.6211.33712.47040.16520.35440.0228-0.4224-0.21130.4073-0.1831-0.43830.04020.4280.0277-0.0730.45270.10280.3607-19.502723.1171-36.9613
112.02780.31211.80961.82530.28185.34940.00130.4856-0.0088-0.294-0.0326-0.1946-0.05220.56530.03240.44140.02080.08110.46780.04480.4453.746618.535-40.6478
122.4469-1.0116-1.62422.47711.50513.79310.26790.15550.3308-0.5099-0.1173-0.0524-0.4425-0.1978-0.18450.47170.0097-0.01250.36450.11140.4185-14.90133.1045-31.1075
133.1978-0.8805-0.49030.1996-0.17832.24220.1416-0.03640.34620.2216-0.0572-0.1009-0.096-0.1834-0.08130.3911-0.00670.02420.39310.0530.4213-4.987924.9611-19.5086
142.35220.1782-0.48414.77760.26993.36410.1104-0.1090.18120.10540.002-0.34240.02190.2205-0.15030.2453-0.0262-0.01090.29690.02340.36376.413919.6808-11.5853
151.59280.32840.48122.68470.43821.44390.1210.0406-0.2243-0.0985-0.0774-0.31420.17230.1854-0.08250.43120.088-0.03410.29910.04690.477411.547243.852-67.8404
161.3625-0.0480.45794.256-1.42552.75250.1718-0.0519-0.3814-0.08690.11660.85830.3199-0.138-0.26080.4745-0.0406-0.10690.34430.0370.6185-12.118237.8988-69.1966
173.77911.39771.51714.92760.4122.12850.2169-0.5048-0.07390.8199-0.1196-0.06120.3314-0.1405-0.09340.48920.06670.00450.34490.03460.34282.912146.1321-52.7544
184.92522.7865.70422.36932.5426.3687-0.516-0.28310.73730.2493-0.15320.1751-0.6242-0.2410.74220.52650.0551-0.13920.39480.00330.54266.098161.6951-60.3224
192.3505-0.54990.37414.2189-0.00243.96950.0992-0.01830.0649-0.1007-0.16350.45330.0247-0.27880.06590.35160.0186-0.04330.29930.01220.5243-13.613760.9371-72.9226
203.5591-1.4226-0.69246.10692.46094.23630.03670.26310.5337-0.4232-0.15410.2072-0.5731-0.36630.11160.53740.0701-0.04560.33210.06310.4816-9.927269.1775-78.1563
210.48130.0558-0.08191.33761.69991.71830.26190.3264-0.2163-0.865-0.40290.5939-0.0416-0.25970.03360.97790.2055-0.09620.58490.0850.5435-15.46368.7336-96.8365
220.394-0.02550.96812.1729-0.72522.3180.36960.5247-0.1456-0.9994-0.20450.06220.4196-0.0928-0.13520.9210.089-0.13880.58260.01560.489-9.120750.9093-97.2682
230.73250.58121.3431.33220.57671.6480.25080.6890.3271-1.2103-0.50520.2823-0.4574-0.19470.24071.43040.3846-0.13290.83680.24710.6242-13.798973.3187-108.0034
241.632-0.37930.55270.1335-0.43963.04250.30720.71120.3126-1.0592-0.1901-0.521-0.04960.8262-0.08831.24280.19910.29120.81440.20010.630210.451863.7863-106.5135
251.09780.33840.04880.86261.11261.32540.11570.53540.4498-1.0287-0.2345-0.3507-0.55710.07110.15181.58180.21660.1140.74770.25910.749-2.363579.684-108.3897
262.4772-0.84070.4543.644-1.7990.9748-0.14390.31750.7287-0.5282-0.1752-0.0389-0.826-0.19070.29731.17120.2022-0.09950.51950.1180.7462-11.954583.713-93.3801
273.7033-1.3208-0.46851.44410.13683.10930.3930.10090.5501-0.7165-0.5236-0.3622-0.1355-0.18990.11570.75650.09980.01010.43040.08470.5470.427173.915-88.2748
284.23461.2436-0.11716.5356-0.48335.04960.03740.11280.7898-0.83750.0373-0.4534-0.57980.5207-0.03280.45330.00750.11630.40580.03990.587413.006269.1308-82.1133
294.93880.2119-0.14945.27380.13043.49830.0493-0.37470.49440.27370.0869-0.5548-0.21810.3562-0.12790.5681-0.012-0.04460.3812-0.01570.53867.816666.7643-74.1186
302.3460.0381-0.20862.18490.71422.65670.2229-0.00460.1610.1916-0.21450.5915-0.1753-0.703-0.00460.44470.03480.03660.68-0.1430.5884-33.806341.369432.1938
311.32810.2285-0.38851.86060.54333.57030.1405-0.51890.25180.48-0.0243-0.3263-0.03180.236-0.16870.5886-0.0665-0.02930.5888-0.13880.5256-13.144741.974843.0394
324.7799-0.49690.08254.9827-0.45866.2979-0.05010.089-0.72290.4648-0.18940.30951.1185-0.78430.19450.6119-0.1801-0.00670.5342-0.08960.704-30.585419.849931.0832
337.22114.13982.56843.82161.3132.5899-0.14371.0813-0.889-0.37540.2478-0.11010.4686-0.3667-0.1670.4929-0.1296-0.01440.6575-0.22270.6329-26.700528.341119.874
342.2727-0.11540.27472.17310.32023.59110.188-0.08540.0887-0.11110.0665-0.6038-0.26290.2711-0.2490.3341-0.05050.05180.3115-0.07730.5056-6.782939.556814.5156
350.5296-0.59170.00891.20560.89880.80840.3176-0.15750.4488-0.19580.0435-0.4102-0.57340.238-0.39530.9031-0.08690.21970.4092-0.08030.90371.028260.42614.6826
360.9818-0.5573-0.05791.58030.49011.10030.35570.13810.5281-0.5759-0.1524-0.0726-0.8788-0.2898-0.14691.15120.13640.23960.43540.07510.8513-14.576467.4541-3.428
372.5647-0.8424-1.39650.15350.44250.57150.3310.36410.0919-0.367-0.1728-0.3265-0.5587-0.0922-0.23960.70680.09930.06930.41520.02940.6841-16.211849.9839-0.1638
381.70350.05111.291.46050.97958.8485-0.05390.04860.3331-0.302-0.32120.3211-1.164-0.42240.410.54230.17290.03330.4702-0.0350.6591-30.774949.0886.5179
392.0493-0.3450.74923.70781.49347.08560.16170.09580.0162-0.1972-0.20160.3157-0.1688-0.68250.00090.35950.07840.02360.4161-0.00690.4794-26.707241.30037.6715
400.91290.5820.39383.05611.20111.27790.3684-0.64630.36890.3203-0.34480.21880.0084-0.2195-0.04020.6201-0.24360.13230.6198-0.14950.5459-31.703687.9366-38.9607
411.37721.3683-0.36552.823-0.72420.44550.2257-0.61760.63980.32640.054-0.081-0.56920.1635-0.18490.7296-0.21520.28730.7526-0.36120.9833-26.5541105.3131-37.4482
421.12120.35510.19231.21090.36121.99730.541-0.96010.18510.7581-0.41590.02960.24340.0433-0.13140.8178-0.29950.03490.7953-0.09890.5575-18.044887.7424-28.2085
432.51570.04830.01250.52231.1553.35750.4033-0.9051-0.15660.5727-0.314-0.2620.45120.1714-0.08751.0089-0.2619-0.12520.76590.10020.5289-18.534676.5356-28.0221
445.12252.07222.09343.39372.96322.71220.2642-0.2444-0.30430.6026-0.12510.24260.2682-0.2156-0.11950.6589-0.21950.02340.51760.02060.5311-27.705973.3695-43.4002
459.02221.65721.10530.5417-0.76471.48450.2409-0.2443-0.80640.3458-0.3637-0.48620.4715-0.26250.13350.5503-0.13120.0260.4325-0.00570.506-15.55783.8807-47.6273
463.9094-1.2568-0.10398.222-0.41794.53310.2359-0.42160.36580.5424-0.0082-0.5235-0.0530.3744-0.21380.3078-0.0697-0.03190.4355-0.08330.5328-2.25491.9315-51.9191
474.5247-0.6949-0.49934.42741.48874.66660.22460.16880.1139-0.31070.0417-0.35930.01840.3308-0.24020.3713-0.01460.05270.2553-0.00590.5081-6.965990.5453-59.2244
480.66890.48851.20872.64171.09632.29160.5943-0.33840.6047-0.64120.4397-0.7482-0.5910.8978-0.9130.9313-0.00450.47670.5539-0.19311.54633.7894108.2324-72.7971
490.31230.3912-0.09712.655-1.78381.28710.5448-0.6090.71870.224-0.2569-0.1737-0.59370.264-0.15820.81-0.14870.37970.583-0.31321.2891-19.2513116.9154-45.2647
500.7903-0.1303-0.17633.1531.38951.53850.3796-0.09460.5348-0.69360.1865-0.6886-0.80940.661-0.5020.9455-0.17130.40230.6885-0.23441.52675.0049114.4697-69.5988
511.24010.52440.62741.7221-0.05071.52290.6660.15520.9182-0.8822-0.0786-0.1804-0.9582-0.7823-0.35861.15260.31690.54060.35230.13231.3928-23.6655121.8565-66.3128
521.0347-0.06330.47434.1050.34320.64260.68810.92330.8247-1.371-0.1903-0.0254-1.1112-0.229-0.11751.49580.35720.50660.51880.34811.2197-15.8035118.1205-79.9375
532.73261.1156-2.15393.33220.07213.05660.40760.25920.4317-0.80720.1886-0.7501-0.3908-0.0235-0.61140.74780.08520.21850.37510.01330.908-11.0363101.9437-74.6592
543.52270.28640.15514.2641.68445.88540.18690.18280.24780.0303-0.1770.56890.0116-0.5033-0.03250.3122-0.02520.02590.36170.00930.5788-28.573792.7177-60.3294
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 67 )A4 - 67
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 110 )A68 - 110
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 260 )A111 - 260
4X-RAY DIFFRACTION4chain 'A' and (resid 261 through 327 )A261 - 327
5X-RAY DIFFRACTION5chain 'A' and (resid 328 through 380 )A328 - 380
6X-RAY DIFFRACTION6chain 'A' and (resid 381 through 474 )A381 - 474
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 49 )B3 - 49
8X-RAY DIFFRACTION8chain 'B' and (resid 50 through 84 )B50 - 84
9X-RAY DIFFRACTION9chain 'B' and (resid 85 through 110 )B85 - 110
10X-RAY DIFFRACTION10chain 'B' and (resid 111 through 199 )B111 - 199
11X-RAY DIFFRACTION11chain 'B' and (resid 200 through 260 )B200 - 260
12X-RAY DIFFRACTION12chain 'B' and (resid 261 through 343 )B261 - 343
13X-RAY DIFFRACTION13chain 'B' and (resid 344 through 370 )B344 - 370
14X-RAY DIFFRACTION14chain 'B' and (resid 371 through 474 )B371 - 474
15X-RAY DIFFRACTION15chain 'C' and (resid 3 through 187 )C3 - 187
16X-RAY DIFFRACTION16chain 'C' and (resid 188 through 260 )C188 - 260
17X-RAY DIFFRACTION17chain 'C' and (resid 261 through 327 )C261 - 327
18X-RAY DIFFRACTION18chain 'C' and (resid 328 through 358 )C328 - 358
19X-RAY DIFFRACTION19chain 'C' and (resid 359 through 424 )C359 - 424
20X-RAY DIFFRACTION20chain 'C' and (resid 425 through 474 )C425 - 474
21X-RAY DIFFRACTION21chain 'D' and (resid 4 through 67 )D4 - 67
22X-RAY DIFFRACTION22chain 'D' and (resid 68 through 109 )D68 - 109
23X-RAY DIFFRACTION23chain 'D' and (resid 110 through 187 )D110 - 187
24X-RAY DIFFRACTION24chain 'D' and (resid 188 through 260 )D188 - 260
25X-RAY DIFFRACTION25chain 'D' and (resid 261 through 307 )D261 - 307
26X-RAY DIFFRACTION26chain 'D' and (resid 308 through 342 )D308 - 342
27X-RAY DIFFRACTION27chain 'D' and (resid 343 through 370 )D343 - 370
28X-RAY DIFFRACTION28chain 'D' and (resid 371 through 424 )D371 - 424
29X-RAY DIFFRACTION29chain 'D' and (resid 425 through 474 )D425 - 474
30X-RAY DIFFRACTION30chain 'E' and (resid 4 through 167 )E4 - 167
31X-RAY DIFFRACTION31chain 'E' and (resid 168 through 288 )E168 - 288
32X-RAY DIFFRACTION32chain 'E' and (resid 289 through 327 )E289 - 327
33X-RAY DIFFRACTION33chain 'E' and (resid 328 through 358 )E328 - 358
34X-RAY DIFFRACTION34chain 'E' and (resid 359 through 474 )E359 - 474
35X-RAY DIFFRACTION35chain 'F' and (resid 4 through 152 )F4 - 152
36X-RAY DIFFRACTION36chain 'F' and (resid 153 through 342 )F153 - 342
37X-RAY DIFFRACTION37chain 'F' and (resid 343 through 370 )F343 - 370
38X-RAY DIFFRACTION38chain 'F' and (resid 371 through 402 )F371 - 402
39X-RAY DIFFRACTION39chain 'F' and (resid 403 through 474 )F403 - 474
40X-RAY DIFFRACTION40chain 'G' and (resid 4 through 67 )G4 - 67
41X-RAY DIFFRACTION41chain 'G' and (resid 68 through 110 )G68 - 110
42X-RAY DIFFRACTION42chain 'G' and (resid 111 through 260 )G111 - 260
43X-RAY DIFFRACTION43chain 'G' and (resid 261 through 307 )G261 - 307
44X-RAY DIFFRACTION44chain 'G' and (resid 308 through 342 )G308 - 342
45X-RAY DIFFRACTION45chain 'G' and (resid 343 through 370 )G343 - 370
46X-RAY DIFFRACTION46chain 'G' and (resid 371 through 402 )G371 - 402
47X-RAY DIFFRACTION47chain 'G' and (resid 403 through 474 )G403 - 474
48X-RAY DIFFRACTION48chain 'H' and (resid 4 through 49 )H4 - 49
49X-RAY DIFFRACTION49chain 'H' and (resid 50 through 84 )H50 - 84
50X-RAY DIFFRACTION50chain 'H' and (resid 85 through 141 )H85 - 141
51X-RAY DIFFRACTION51chain 'H' and (resid 142 through 260 )H142 - 260
52X-RAY DIFFRACTION52chain 'H' and (resid 261 through 307 )H261 - 307
53X-RAY DIFFRACTION53chain 'H' and (resid 308 through 368 )H308 - 368
54X-RAY DIFFRACTION54chain 'H' and (resid 369 through 474 )H369 - 474

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万見について

-
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