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- PDB-6i4z: Crystal structure of the disease-causing P453L mutant of the huma... -

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基本情報

登録情報
データベース: PDB / ID: 6i4z
タイトルCrystal structure of the disease-causing P453L mutant of the human dihydrolipoamide dehydrogenase
要素Dihydrolipoyl dehydrogenase, mitochondrial
キーワードOXIDOREDUCTASE / Lipoamide dehydrogenase / Pathogenic mutation / E3 deficiency / Alpha-ketoglutarate dehydrogenase complex / 2-oxoglutarate dehydrogenase complex / Pyruvate 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: 2.342 Å
データ登録者Szabo, E. / Wilk, P. / Torocsik, B. / Weiss, M.S. / Adam-Vizi, V. / Ambrus, A.
資金援助 ハンガリー, 米国, ドイツ, 10件
組織認可番号国
Hungarian Academy of Sciences02001 [to A.-V.V.] ハンガリー
Hungarian Scientific Research Fund, grant#112230 [to A.-V.V.] ハンガリー
Hungarian Brain Research Program, grant#KTIA_13_NAP_III/6 and 2017-1.2.1-NKP-2017-00002 [to A.-V.V.] 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
Semmelweis University, Young Investigator Research Grant [to A.A.] ハンガリー
Gedeon Richter PIc., Young Investigator Research Grant [to A.A.] ハンガリー
Fulbright Commission, Fulbright Fellowship [to A.A.] 米国
European Union and Government of Hungary, grant#EFOP-3.6.3-VEKOP-16-2017-00009 [to S.E.] ハンガリー
European Union CALIPSOplus, grant#16204087-ST [to S.E. and A.A.] ドイツ
引用ジャーナル: Hum.Mol.Genet. / 年: 2019
タイトル: Underlying molecular alterations in human dihydrolipoamide dehydrogenase deficiency revealed by structural analyses of disease-causing enzyme variants.
著者: Szabo, E. / Wilk, P. / Nagy, B. / Zambo, Z. / Bui, D. / Weichsel, A. / Arjunan, P. / Torocsik, B. / Hubert, A. / Furey, W. / Montfort, W.R. / Jordan, F. / Weiss, M.S. / Adam-Vizi, V. / Ambrus, A.
履歴
登録2018年11月12日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年11月20日Provider: repository / タイプ: Initial release
改定 1.12019年12月11日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.22024年1月24日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.32024年11月6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: 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)430,10443
ポリマ－421,2268
非ポリマー8,87835
水8,143452
1
A: Dihydrolipoyl dehydrogenase, mitochondrial
B: Dihydrolipoyl dehydrogenase, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)107,55011
ポリマ－105,3062
非ポリマー2,2449
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11880 Å2
ΔGint-138 kcal/mol
Surface area35950 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)107,83814
ポリマ－105,3062
非ポリマー2,53212
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area12380 Å2
ΔGint-167 kcal/mol
Surface area35720 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)107,3589
ポリマ－105,3062
非ポリマー2,0517
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-124 kcal/mol
Surface area35780 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)107,3589
ポリマ－105,3062
非ポリマー2,0517
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-122 kcal/mol
Surface area35680 Å2
手法PISA
単位格子
Length a, b, c (Å)55.560, 123.390, 158.410
Angle α, β, γ (deg.)105.950, 91.310, 90.000
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
11(chain A and (resid 3 through 331 or resid 333 through 474 or resid 500))
21(chain B and (resid 3 through 331 or resid 333 through 474 or resid 500))
31(chain C and (resid 3 through 331 or resid 333 through 474 or resid 500))
41(chain D and (resid 3 through 331 or resid 333 through 474 or resid 500))
51(chain E and (resid 3 through 331 or resid 333 through 474 or resid 500))
61(chain F and (resid 3 through 331 or resid 333 through 474 or resid 500))
71(chain G and (resid 3 through 331 or resid 333 through 474 or resid 500))
81(chain H and (resid 3 through 331 or resid 333 through 474 or resid 500))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 331 or resid 333 through 474 or resid 500))A3 - 331
121(chain A and (resid 3 through 331 or resid 333 through 474 or resid 500))A333 - 474
131(chain A and (resid 3 through 331 or resid 333 through 474 or resid 500))A500
211(chain B and (resid 3 through 331 or resid 333 through 474 or resid 500))B3 - 331
221(chain B and (resid 3 through 331 or resid 333 through 474 or resid 500))B333 - 474
231(chain B and (resid 3 through 331 or resid 333 through 474 or resid 500))B500
311(chain C and (resid 3 through 331 or resid 333 through 474 or resid 500))C3 - 331
321(chain C and (resid 3 through 331 or resid 333 through 474 or resid 500))C333 - 474
331(chain C and (resid 3 through 331 or resid 333 through 474 or resid 500))C500
411(chain D and (resid 3 through 331 or resid 333 through 474 or resid 500))D3 - 331
421(chain D and (resid 3 through 331 or resid 333 through 474 or resid 500))D333 - 474
431(chain D and (resid 3 through 331 or resid 333 through 474 or resid 500))D500
511(chain E and (resid 3 through 331 or resid 333 through 474 or resid 500))E3 - 331
521(chain E and (resid 3 through 331 or resid 333 through 474 or resid 500))E333 - 474
531(chain E and (resid 3 through 331 or resid 333 through 474 or resid 500))E500
611(chain F and (resid 3 through 331 or resid 333 through 474 or resid 500))F3 - 331
621(chain F and (resid 3 through 331 or resid 333 through 474 or resid 500))F333 - 474
631(chain F and (resid 3 through 331 or resid 333 through 474 or resid 500))F500
711(chain G and (resid 3 through 331 or resid 333 through 474 or resid 500))G3 - 331
721(chain G and (resid 3 through 331 or resid 333 through 474 or resid 500))G333 - 474
731(chain G and (resid 3 through 331 or resid 333 through 474 or resid 500))G500
811(chain H and (resid 3 through 331 or resid 333 through 474 or resid 500))H3 - 331
821(chain H and (resid 3 through 331 or resid 333 through 474 or resid 500))H333 - 474
831(chain H and (resid 3 through 331 or resid 333 through 474 or resid 500))H500

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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: 52653.215 Da / 分子数: 8 / 変異: P453L / 由来タイプ: 組換発現
詳細: Sequence of the Strep-tag with the linker amino acids: MASWSHPQFEKGALEVLFQGPG
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: 合成 / 式: C27H33N9O15P2 / コメント: FAD*YM
#3: 化合物...
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 27 / 由来タイプ: 合成 / 式: SO4
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 452 / 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: 2.61 Å3/Da / 溶媒含有率: 52.81 %
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: 7.3
詳細: 2 M ammonium sulfate, 1.5 (v/v)% PEG 400, 0.1 M Hepes (pH7.3)

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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: 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: 2017年8月26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: 0.9184 Å / 相対比: 1
反射解像度: 2.34→46.567 Å / Num. obs: 164477 / % possible obs: 96.6 % / 冗長度: 4.972 % / Biso Wilson estimate: 47.64 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.161 / Χ2: 0.97 / Net I/σ(I): 7.45
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
2.34-2.43.6010.9721.22107870.6021.13485.6
2.4-2.473.7370.8271.47115720.6690.96194.6
2.47-2.543.7310.6911.73113570.7520.80494.8
2.54-2.625.3530.6572.29115350.8380.72999.5
2.62-2.75.2770.5352.79111060.8740.59499.2
2.7-2.84.910.4213.34106950.9070.47198
2.8-2.95.5870.3554.25104770.9480.39199.6
2.9-3.025.5820.2795.35100260.9650.30899.5
3.02-3.165.5410.2276.5596170.9740.25199.6
3.16-3.315.4970.1758.392390.9830.19499.5
3.31-3.495.3520.1459.8787320.9850.16199.1
3.49-3.74.4560.13810.4173970.9760.15888.5
3.7-3.965.3630.12612.2571300.9880.1491.2
3.96-4.285.4930.09415.772170.9910.10499.3
4.28-4.685.3550.08517.4266370.9920.09499.3
4.68-5.245.0360.08616.3959430.990.09698.9
5.24-6.055.270.0915.9352530.9930.198
6.05-7.415.5340.08617.0444780.9930.09599.5
7.41-10.474.9440.06719.8434230.9950.07597.5
10.47-46.5675.1260.05821.3318560.9960.06497.6

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位相決定

位相決定手法: 分子置換
Phasing MRR rigid body: 0.586
最高解像度最低解像度
Rotation46.57 Å2.76 Å

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解析

ソフトウェア
名称バージョン分類
MxCuBEデータ収集
XDSデータ削減
XSCALEデータスケーリング
MOLREP位相決定
PHENIX精密化
PDB_EXTRACT3.24データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 1ZMD

1zmd


解像度: 2.342→46.567 Å / SU ML: 0.35 / 交差検証法: THROUGHOUT / σ(F): 1.93 / 位相誤差: 28.01
詳細: TLS groups, NCS torsion-angle restraints and occupancy refinement were included, hydrogen atoms were added to the final model during refinement
Rfactor反射数%反射
Rfree0.249 2465 1.5 %
Rwork0.2272 --
obs0.2276 164323 96.56 %
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: 173.35 Å2 / Biso mean: 64.3838 Å2 / Biso min: 15.98 Å2
精密化ステップサイクル: final / 解像度: 2.342→46.567 Å
タンパク質核酸リガンド溶媒全体
原子数28064 0 807 452 29323
Biso mean--55.03 45.04 -
残基数----3776
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A17708X-RAY DIFFRACTION14.242TORSIONAL
12B17708X-RAY DIFFRACTION14.242TORSIONAL
13C17708X-RAY DIFFRACTION14.242TORSIONAL
14D17708X-RAY DIFFRACTION14.242TORSIONAL
15E17708X-RAY DIFFRACTION14.242TORSIONAL
16F17708X-RAY DIFFRACTION14.242TORSIONAL
17G17708X-RAY DIFFRACTION14.242TORSIONAL
18H17708X-RAY DIFFRACTION14.242TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.342-2.3870.31841170.30957633775082
2.387-2.43580.31981340.2998827896195
2.4358-2.48870.30941350.28568854898995
2.4887-2.54660.30151350.28328848898395
2.5466-2.61030.28311410.269492579398100
2.6103-2.68090.32181410.26649258939999
2.6809-2.75970.26871400.25519182932298
2.7597-2.84880.27081390.24829134927399
2.8488-2.95060.30091410.253193289469100
2.9506-3.06870.29111420.254292939435100
3.0687-3.20840.27981400.245892299369100
3.2084-3.37750.27441420.23679298944099
3.3775-3.5890.25471390.22129121926099
3.589-3.8660.32211190.28427890800984
3.866-4.25480.20641400.19629193933398
4.2548-4.86990.1861400.16689191933199
4.8699-6.13340.22941400.19449211935198
6.1334-46.57640.18011400.19379111925198
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)
10.3792-0.5745-0.12171.20810.38890.3584-0.09560.30180.05790.19680.0487-0.17650.12410.0102-0.20830.05570.00710.00520.46370.03690.388118.1685-7.0516-7.7046
21.5987-0.44420.05522.52690.35141.8193-0.23120.14020.29250.761-0.0893-0.1086-0.23040.02390.0790.29420.0557-0.0740.29710.06590.4278-0.735423.951.9589
31.1483-0.69980.10481.23370.03220.8078-0.0480.14160.0704-0.029-0.0206-0.06720.0120.02990.06010.1668-0.02590.02530.41360.04950.34477.1691.8803-12.0489
41.62660.09050.57850.5806-0.04010.361-0.20140.09640.0610.02920.23880.1362-0.2047-0.35290.07280.04070.03190.00940.4787-0.00160.367-16.52467.2477-5.5398
50.6813-0.6029-0.09710.68650.02750.6364-0.05150.0744-0.12020.09380.05130.10550.05290.04160.02260.1289-0.03470.01370.33410.00280.35731.7791-10.8645-5.2792
61.1382-0.1340.62231.7765-0.49651.3987-0.2168-0.13510.01880.55330.1160.1466-0.088-0.21940.03640.33710.07220.06810.4008-0.01120.3375-6.02331.636219.9745
70.31520.20480.07071.95090.00161.8832-0.1474-0.46590.11540.76430.15720.5082-0.0944-0.12590.25891.28960.39550.09160.752-0.12310.4202-8.363816.251842.2442
81.4811-0.1940.11861.50490.59792.1505-0.17840.02940.34620.2716-0.0859-0.4048-0.28720.37390.23930.44550.0752-0.16160.26850.01220.47815.331428.59079.4101
93.32241.5903-1.09791.4866-1.62012.2973-0.6126-0.22890.39270.48820.5650.2516-0.4199-0.41950.04980.87320.3332-0.07190.5262-0.06990.4418-8.066625.496226.6879
101.0217-0.03030.16590.4131-0.38770.6505-0.5182-0.48670.99141.3360.39780.1862-0.7293-0.22880.03711.78250.5508-0.20010.7445-0.32490.4026-0.728926.329943.4854
110.44950.28530.07920.57640.40580.3593-0.46840.18990.28490.73440.0324-0.2776-0.65410.1733-0.06451.0009-0.0298-0.47560.4747-0.04830.765217.918527.136425.1176
120.36090.6048-0.10161.1058-0.02990.0623-0.3933-0.04340.60410.5884-0.3298-0.8314-0.67770.0262-1.12631.0949-0.0803-0.65660.4884-0.10591.043924.255232.03526.7618
130.4910.21830.20830.543-0.39080.5554-0.3403-0.71760.24480.6570.062-0.0155-0.3245-0.2319-0.19861.84320.3299-0.4930.6209-0.26250.40568.547317.565849.7986
140.65880.0864-0.66840.0166-0.20961.9103-0.3218-0.3512-0.05881.14520.1163-0.1108-0.15850.11120.07571.06280.294-0.07710.5188-0.01950.46944.02927.546141.0278
151.3411-0.1470.11032.1252-0.84971.3259-0.11820.01470.10240.39030.0174-0.335-0.17110.10350.21030.27680.0222-0.09970.3802-0.05230.424716.51072.961917.2021
160.66040.8772-0.18741.6804-0.08340.5875-0.1269-0.0452-0.0435-0.18530.05-0.0703-0.05210.1373-0.02690.07030.03010.02340.40250.01020.3454-11.5082-14.4782-45.6052
170.63880.74950.07981.18840.16781.1715-0.1845-0.2437-0.4003-0.2210.0201-0.36870.3135-0.00130.10370.28790.02330.12230.35060.03090.4777-16.286-33.0201-48.7743
180.76770.62230.00311.11260.06270.80150.1262-0.21090.00250.196-0.1106-0.0096-0.02880.03390.09330.13020.00070.00720.42250.01720.3516-17.5429-11.0623-35.6093
192.01550.5236-1.07421.1856-0.38541.281-0.11470.0774-0.1463-0.13060.01250.19580.2963-0.40530.00050.1711-0.0540.02030.4852-0.04680.4063-38.9224-22.0419-45.7734
200.2369-0.11010.05140.3071-0.21920.23250.2827-0.2011-0.0769-0.2097-0.28640.2910.30520.12410.02430.0489-0.01560.06150.570.00930.3627-34.3168-14.0869-36.4571
210.6370.6426-0.03521.61240.2511.219-0.0381-0.1638-0.0293-0.1281-0.0150.0884-0.3575-0.12410.06460.09370.0093-0.02580.33850.0140.353-17.93541.2648-49.2881
221.2430.7352-0.60721.9812-0.4821.5187-0.31350.0830.0233-0.64380.17950.2440.131-0.31570.07150.4122-0.0984-0.06340.3933-0.00440.3304-30.0802-15.6253-70.9668
230.2835-0.397-0.28821.4176-0.10060.7992-0.28560.6113-0.1299-0.61070.16510.51930.1829-0.3202-0.08511.6413-0.8653-0.26470.6856-0.26370.3527-32.1379-30.4498-93.2677
241.29840.46850.27711.5911-0.43531.7169-0.43850.0946-0.2778-0.63020.1795-0.35460.3346-0.120.19040.7167-0.17040.23250.4283-0.0720.5249-24.116-41.381-67.2996
250.90870.5111-0.41370.62890.18911.0049-0.85640.4092-0.8575-1.39110.338-0.1970.75740.1589-1.42651.6899-0.54750.35650.5345-0.37730.5438-20.8675-41.2236-89.903
260.54510.3274-0.22690.5185-0.30050.2062-0.2943-0.1223-0.4445-0.4948-0.0373-0.53590.35920.3417-0.85430.6590.0450.56220.4352-0.10690.8462-1.3494-36.0928-73.0366
270.93170.6135-0.2121.0870.4090.4731-0.51810.3566-0.426-1.15350.2721-0.49640.4450.0548-0.08981.4107-0.24980.52460.6507-0.10960.7278-10.9625-36.32-91.1738
282.4896-0.12660.99461.0594-0.50421.3864-0.45590.0505-0.1755-1.1830.4229-0.2652-0.0811-0.1090.18610.9653-0.21210.15880.4363-0.1050.4651-13.2905-22.2534-80.0434
291.0461-0.25020.07071.59250.0380.9626-0.1507-0.0185-0.1509-0.56830.047-0.33470.00410.14690.14950.263-0.01650.13410.3866-0.03780.4242-7.3181-15.6699-67.4988
300.4113-0.0654-0.22451.37610.11670.6209-0.01470.31560.1033-0.8801-0.084-0.1612-0.5434-0.13520.06691.2365-0.06860.03930.52860.01820.4362-15.620826.681-85.5513
310.543-0.28920.48040.6638-0.86021.2145-0.2051-0.13770.2031-0.94440.02560.1178-0.0578-0.8092-0.12661.0640.1797-0.28290.6607-0.050.5917-38.270834.4289-78.882
321.0073-0.0023-0.05721.5091-0.29490.3544-0.05850.1691-0.1273-0.64180.1180.2663-0.3445-0.20560.05650.7932-0.0079-0.05210.5157-0.00320.3519-23.870613.1724-81.1455
331.5473-0.09610.09921.9934-0.10651.146-0.0085-0.17330.0671-0.16140.03580.2893-0.4943-0.24280.04640.55040.0376-0.00720.4665-0.02810.3725-25.171826.1072-55.2272
341.43610.71380.18141.6203-0.13251.17490.1515-0.52530.38810.3961-0.14860.2493-0.5186-0.1983-0.05230.8709-0.00210.12230.6473-0.12780.5338-21.241640.3988-32.9703
350.80780.31160.24550.73850.14222.2254-0.03560.12750.4949-0.40570.1174-0.0048-0.2724-0.07810.01111.0445-0.054-0.0060.46210.08840.6201-11.152950.9729-67.5039
361.62510.6068-0.06081.4879-0.37561.11940.0293-0.3440.48850.29430.0070.0767-0.6838-0.043-0.01241.0153-0.01430.03320.5899-0.12090.5775-13.184249.4213-38.252
371.47120.3398-0.06181.8112-0.05821.0942-0.0725-0.03610.1265-0.07330.005-0.3945-0.45450.33460.0410.9577-0.21960.11510.6265-0.00540.64836.927148.1531-54.6407
381.44330.7007-0.01182.043-0.6831.41770.162-0.52820.1610.051-0.3491-0.0977-0.65970.13130.02520.7847-0.16090.00730.6496-0.08530.58811.679444.0258-35.1029
391.46510.6827-0.62811.418-0.33381.3854-0.138-0.7335-0.06990.1697-0.1535-0.2229-0.4961-0.0924-0.00850.5982-0.0968-0.00590.60570.00640.3758-11.451331.3931-33.1371
402.78290.0987-0.72980.93440.77341.0051-0.07-0.2554-0.0370.1928-0.0418-0.2632-0.5590.17030.06620.7075-0.08980.06490.4176-0.04980.3819-6.183229.5903-48.7854
411.62260.30140.30771.81480.02891.2859-0.06070.0421-0.0858-0.43330.0503-0.3178-0.46210.21340.01670.6007-0.12630.10450.4604-0.00610.459-3.510422.4426-62.2428
421.70990.02390.08070.5444-0.46291.6245-0.1422-0.12570.13260.6466-0.1006-0.40610.60160.20440.11580.88810.1099-0.17520.42790.03640.403116.265-27.935835.454
430.2887-0.1941-0.26110.6672-0.28330.46150.1582-0.1209-0.37210.43210.0535-0.36270.57560.0420.11281.2942-0.0346-0.09460.55240.14050.6079.5194-55.114227.3367
440.239-0.1612-0.0640.9629-0.16291.05770.1203-0.3142-0.08931.0385-0.21280.06940.6677-0.4733-0.08711.1967-0.1630.0640.63190.00070.4294-0.7717-39.58134.02
450.6203-0.3416-0.36410.3725-0.13971.1163-0.3233-0.3019-0.30720.977-0.0846-0.0142-0.17570.0177-0.39411.4488-0.36380.4690.76470.11140.5572-17.6086-49.994836.7111
461.07160.9103-0.12372.4124-0.75730.24910.1407-0.14180.14020.9788-0.12930.4230.6546-0.3435-0.00350.9808-0.18460.21960.5-0.01460.3854-6.6952-30.801636.0648
471.20230.3922-0.15112.63011.01241.4230.0679-0.09070.12080.7109-0.1128-0.04080.3177-0.24440.02520.62750.0131-0.04290.38590.02720.37684.7661-27.332522.791
482.0825-0.4759-0.82221.92990.28112.1128-0.0462-0.10960.0128-0.00990.11680.21330.2942-0.40560.07380.414-0.1380.06250.5138-0.01310.3762-5.7767-39.78564.3475
491.70740.0494-0.26262.06640.00281.9550.03340.1008-0.1894-0.1684-0.03520.06320.8243-0.43190.07670.5346-0.05560.00550.4258-0.02550.38812.6222-39.68721.6388
501.0398-0.21090.09251.3743-0.30291.2793-0.09010.1772-0.31050.2374-0.0436-0.02680.5614-0.0108-0.1070.8464-0.10010.00090.4351-0.00310.51177.3862-59.1103-2.3026
511.3068-0.210.23561.351-0.22621.3037-0.07810.1043-0.1908-0.0230.1004-0.23340.63490.0565-0.05280.72460.01390.01670.4162-0.09340.503619.4804-59.4771-9.4001
522.4599-0.07681.04021.00650.92751.8124-0.26430.2078-0.12380.11180.0551-0.38470.18210.2021-0.00120.44920.0786-0.04450.3585-0.07770.457117.8079-43.5557-2.1331
531.73310.061-0.1122.0979-0.01361.61450.0104-0.0369-0.01010.60460.0289-0.36710.34030.2005-0.01550.46520.0822-0.10060.3507-0.01590.385320.5014-36.440211.2593
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 49 )A3 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 84 )A50 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 199 )A85 - 199
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 260 )A200 - 260
5X-RAY DIFFRACTION5chain 'A' and (resid 261 through 358 )A261 - 358
6X-RAY DIFFRACTION6chain 'A' and (resid 359 through 474 )A359 - 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 109 )B85 - 109
10X-RAY DIFFRACTION10chain 'B' and (resid 110 through 179 )B110 - 179
11X-RAY DIFFRACTION11chain 'B' and (resid 180 through 219 )B180 - 219
12X-RAY DIFFRACTION12chain 'B' and (resid 220 through 276 )B220 - 276
13X-RAY DIFFRACTION13chain 'B' and (resid 277 through 307 )B277 - 307
14X-RAY DIFFRACTION14chain 'B' and (resid 308 through 358 )B308 - 358
15X-RAY DIFFRACTION15chain 'B' and (resid 359 through 474 )B359 - 474
16X-RAY DIFFRACTION16chain 'C' and (resid 3 through 67 )C3 - 67
17X-RAY DIFFRACTION17chain 'C' and (resid 68 through 109 )C68 - 109
18X-RAY DIFFRACTION18chain 'C' and (resid 110 through 187 )C110 - 187
19X-RAY DIFFRACTION19chain 'C' and (resid 188 through 260 )C188 - 260
20X-RAY DIFFRACTION20chain 'C' and (resid 261 through 288 )C261 - 288
21X-RAY DIFFRACTION21chain 'C' and (resid 289 through 358 )C289 - 358
22X-RAY DIFFRACTION22chain 'C' and (resid 359 through 474 )C359 - 474
23X-RAY DIFFRACTION23chain 'D' and (resid 3 through 49 )D3 - 49
24X-RAY DIFFRACTION24chain 'D' and (resid 50 through 109 )D50 - 109
25X-RAY DIFFRACTION25chain 'D' and (resid 110 through 199 )D110 - 199
26X-RAY DIFFRACTION26chain 'D' and (resid 200 through 233 )D200 - 233
27X-RAY DIFFRACTION27chain 'D' and (resid 234 through 342 )D234 - 342
28X-RAY DIFFRACTION28chain 'D' and (resid 343 through 370 )D343 - 370
29X-RAY DIFFRACTION29chain 'D' and (resid 371 through 474 )D371 - 474
30X-RAY DIFFRACTION30chain 'E' and (resid 3 through 199 )E3 - 199
31X-RAY DIFFRACTION31chain 'E' and (resid 200 through 260 )E200 - 260
32X-RAY DIFFRACTION32chain 'E' and (resid 261 through 358 )E261 - 358
33X-RAY DIFFRACTION33chain 'E' and (resid 359 through 474 )E359 - 474
34X-RAY DIFFRACTION34chain 'F' and (resid 3 through 49 )F3 - 49
35X-RAY DIFFRACTION35chain 'F' and (resid 50 through 84 )F50 - 84
36X-RAY DIFFRACTION36chain 'F' and (resid 85 through 187 )F85 - 187
37X-RAY DIFFRACTION37chain 'F' and (resid 188 through 260 )F188 - 260
38X-RAY DIFFRACTION38chain 'F' and (resid 261 through 307 )F261 - 307
39X-RAY DIFFRACTION39chain 'F' and (resid 308 through 342 )F308 - 342
40X-RAY DIFFRACTION40chain 'F' and (resid 343 through 370 )F343 - 370
41X-RAY DIFFRACTION41chain 'F' and (resid 371 through 474 )F371 - 474
42X-RAY DIFFRACTION42chain 'G' and (resid 3 through 49 )G3 - 49
43X-RAY DIFFRACTION43chain 'G' and (resid 50 through 109 )G50 - 109
44X-RAY DIFFRACTION44chain 'G' and (resid 110 through 233 )G110 - 233
45X-RAY DIFFRACTION45chain 'G' and (resid 234 through 260 )G234 - 260
46X-RAY DIFFRACTION46chain 'G' and (resid 261 through 307 )G261 - 307
47X-RAY DIFFRACTION47chain 'G' and (resid 308 through 370 )G308 - 370
48X-RAY DIFFRACTION48chain 'G' and (resid 371 through 414 )G371 - 414
49X-RAY DIFFRACTION49chain 'G' and (resid 415 through 474 )G415 - 474
50X-RAY DIFFRACTION50chain 'H' and (resid 3 through 84 )H3 - 84
51X-RAY DIFFRACTION51chain 'H' and (resid 85 through 342 )H85 - 342
52X-RAY DIFFRACTION52chain 'H' and (resid 343 through 370 )H343 - 370
53X-RAY DIFFRACTION53chain 'H' and (resid 371 through 474 )H371 - 474

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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