[日本語] English
- PDB-8ugo: Structure of the complex between Human LIAS and H-protein in the ... -

+
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: 8ugo
タイトルStructure of the complex between Human LIAS and H-protein in the presence of 5'-deoxyadenosine
要素
  • Glycine cleavage system H protein, mitochondrial
  • Lipoyl synthase, mitochondrial
キーワードBIOSYNTHETIC PROTEIN / Lipoyl synthase / LIAS
機能・相同性
機能・相同性情報


lipoyl synthase / lipoate synthase activity / lipoate biosynthetic process / Glycine degradation / glycine decarboxylation via glycine cleavage system / glycine cleavage complex / Protein lipoylation / neural tube closure / 4 iron, 4 sulfur cluster binding / response to oxidative stress ...lipoyl synthase / lipoate synthase activity / lipoate biosynthetic process / Glycine degradation / glycine decarboxylation via glycine cleavage system / glycine cleavage complex / Protein lipoylation / neural tube closure / 4 iron, 4 sulfur cluster binding / response to oxidative stress / response to lipopolysaccharide / mitochondrial matrix / inflammatory response / mitochondrion / metal ion binding
類似検索 - 分子機能
Lipoyl synthase, N-terminal / N-terminal domain of lipoyl synthase of Radical_SAM family / Lipoyl synthase / Glycine cleavage system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily ...Lipoyl synthase, N-terminal / N-terminal domain of lipoyl synthase of Radical_SAM family / Lipoyl synthase / Glycine cleavage system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / Radical SAM core domain profile. / Radical SAM / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Aldolase-type TIM barrel
類似検索 - ドメイン・相同性
5'-DEOXYADENOSINE / FE3-S4 CLUSTER / METHIONINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / IRON/SULFUR CLUSTER / : / Lipoyl synthase, mitochondrial / Glycine cleavage system H protein, 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: 2.45 Å
データ登録者Esakova, O.A. / Warui, D.M. / Neti, S.S. / Alumasa, J.N. / Booker, S.J.
資金援助 米国, 3件
組織認可番号
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-122595 米国
National Science Foundation (NSF, United States)MCB1716686 米国
Howard Hughes Medical Institute (HHMI)SJB 米国
引用ジャーナル: To Be Published
タイトル: Structural basis for the mechanism of the human lipoyl synthase (LIAS) and its complex with the H-protein
著者: Esakova, O.A. / Warui, D.M. / Neti, S.S. / Alumasa, J.N. / Booker, S.J.
履歴
登録2023年10月5日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年7月9日Provider: repository / タイプ: Initial release

-
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: Lipoyl synthase, mitochondrial
E: Glycine cleavage system H protein, mitochondrial
B: Lipoyl synthase, mitochondrial
C: Glycine cleavage system H protein, mitochondrial
D: Lipoyl synthase, mitochondrial
F: Glycine cleavage system H protein, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)185,71226
ポリマ-181,0806
非ポリマー4,63220
3,531196
1
A: Lipoyl synthase, mitochondrial
E: Glycine cleavage system H protein, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,8849
ポリマ-60,3602
非ポリマー1,5257
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-47 kcal/mol
Surface area18620 Å2
手法PISA
2
B: Lipoyl synthase, mitochondrial
C: Glycine cleavage system H protein, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)62,24410
ポリマ-60,3602
非ポリマー1,8848
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-48 kcal/mol
Surface area19160 Å2
手法PISA
3
D: Lipoyl synthase, mitochondrial
F: Glycine cleavage system H protein, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,5847
ポリマ-60,3602
非ポリマー1,2245
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-49 kcal/mol
Surface area18660 Å2
手法PISA
単位格子
Length a, b, c (Å)48.681, 169.209, 183.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
要素

-
タンパク質 , 2種, 6分子 ABDECF

#1: タンパク質 Lipoyl synthase, mitochondrial / Lipoate synthase / LS / Lip-syn / Lipoic acid synthase


分子量: 41457.461 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: LIAS, LAS, HUSSY-01 / 発現宿主: Escherichia (バクテリア) / 参照: UniProt: O43766, lipoyl synthase
#2: タンパク質 Glycine cleavage system H protein, mitochondrial / Lipoic acid-containing protein


分子量: 18902.498 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: GCSH / 発現宿主: Escherichia (バクテリア) / 参照: UniProt: P23434

-
非ポリマー , 11種, 216分子

#3: 化合物 ChemComp-5AD / 5'-DEOXYADENOSINE / 5′-デオキシアデノシン


分子量: 251.242 Da / 分子数: 3 / 由来タイプ: 合成 / : C10H13N5O3 / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物 ChemComp-SF4 / IRON/SULFUR CLUSTER


分子量: 351.640 Da / 分子数: 3 / 由来タイプ: 合成 / : Fe4S4 / タイプ: SUBJECT OF INVESTIGATION
#5: 化合物 ChemComp-F3S / FE3-S4 CLUSTER


分子量: 295.795 Da / 分子数: 3 / 由来タイプ: 合成 / : Fe3S4
#6: 化合物 ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 1 / 由来タイプ: 合成 / : C4H10O3
#7: 化合物 ChemComp-PG4 / TETRAETHYLENE GLYCOL / テトラエチレングリコ-ル


分子量: 194.226 Da / 分子数: 1 / 由来タイプ: 合成 / : C8H18O5 / コメント: 沈殿剤*YM
#8: 化合物 ChemComp-MET / METHIONINE / メチオニン


タイプ: L-peptide linking / 分子量: 149.211 Da / 分子数: 3 / 由来タイプ: 合成 / : C5H11NO2S
#9: 化合物 ChemComp-YVI / 6-THIOOCTANOIC ACID / 6-sulfanyloctanoic acid


分子量: 176.276 Da / 分子数: 3 / 由来タイプ: 組換発現 / : C8H16O2S / タイプ: SUBJECT OF INVESTIGATION
#10: 化合物 ChemComp-2PE / NONAETHYLENE GLYCOL / 3,6,9,12,15,18,21,24-オクタオキサヘキサコサン-1,26-ジオ-ル


分子量: 414.488 Da / 分子数: 1 / 由来タイプ: 合成 / : C18H38O10 / コメント: 沈殿剤*YM
#11: 化合物 ChemComp-PGE / TRIETHYLENE GLYCOL / トリエチレングリコ-ル


分子量: 150.173 Da / 分子数: 1 / 由来タイプ: 合成 / : C6H14O4
#12: 化合物 ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 1 / 由来タイプ: 合成 / : PO4
#13: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 196 / 由来タイプ: 天然 / : H2O

-
詳細

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

-
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: 2.64 Å3/Da / 溶媒含有率: 53.32 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.1M Potassium phosphate pH8.0, 0.2 M potassium chloride, 20% PEG 3350

-
データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 21-ID-G / 波長: 0.97856 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2021年9月17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: 0.97856 Å / 相対比: 1
反射解像度: 2.45→50 Å / Num. obs: 320427 / % possible obs: 94.5 % / 冗長度: 3.3 % / CC1/2: 0.976 / Net I/σ(I): 7.78
反射 シェル解像度: 2.45→2.53 Å / Num. unique obs: 4299 / CC1/2: 0.348

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.45→38.06 Å / SU ML: 0.3 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 22.68 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2229 3038 3.95 %
Rwork0.1846 --
obs0.1862 76992 71.41 %
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: 2.45→38.06 Å
タンパク質核酸リガンド溶媒全体
原子数9948 0 159 196 10303
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00310326
X-RAY DIFFRACTIONf_angle_d0.58413972
X-RAY DIFFRACTIONf_dihedral_angle_d13.9953879
X-RAY DIFFRACTIONf_chiral_restr0.0411559
X-RAY DIFFRACTIONf_plane_restr0.0041770
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.480.2506360.2687936X-RAY DIFFRACTION20
2.48-2.530.3367570.28051191X-RAY DIFFRACTION25
2.53-2.570.299590.25671528X-RAY DIFFRACTION32
2.57-2.620.3287600.26061628X-RAY DIFFRACTION35
2.62-2.670.3314870.24642031X-RAY DIFFRACTION43
2.67-2.720.2533940.24742331X-RAY DIFFRACTION49
2.72-2.780.2736900.24972461X-RAY DIFFRACTION53
2.78-2.840.25321130.22782870X-RAY DIFFRACTION60
2.84-2.920.28641370.22992961X-RAY DIFFRACTION64
2.92-2.990.27541300.21783220X-RAY DIFFRACTION69
2.99-3.080.25561340.2153569X-RAY DIFFRACTION75
3.08-3.180.27111630.22113702X-RAY DIFFRACTION79
3.18-3.30.24271750.20014034X-RAY DIFFRACTION85
3.3-3.430.23371740.19114296X-RAY DIFFRACTION91
3.43-3.580.24251680.18454464X-RAY DIFFRACTION95
3.58-3.770.20762010.16724633X-RAY DIFFRACTION98
3.77-4.010.19641920.16274649X-RAY DIFFRACTION99
4.01-4.320.20171930.15774698X-RAY DIFFRACTION100
4.32-4.750.19941980.14984674X-RAY DIFFRACTION100
4.75-5.440.20591980.15854748X-RAY DIFFRACTION100
5.44-6.840.21461880.18764678X-RAY DIFFRACTION100
6.84-38.060.18241910.17844652X-RAY DIFFRACTION99
精密化 TLS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.6707-2.71581.74894.8667-3.23084.41580.72411.49892.0631-1.3974-0.4091-0.846-0.64510.6948-0.15671.05850.11310.31010.81620.14040.783318.5952-26.6343-55.5002
29.6176-3.49750.67864.0307-3.36082.0385-0.20260.3613-0.7121-1.34910.1242-0.04371.25590.1774-0.02630.5476-0.05880.17780.4107-0.09680.353613.6916-39.5379-46.9327
35.471-3.9112-4.58446.90213.65713.8739-0.54780.12220.2176-0.40610.372-0.48970.50440.17560.27730.3843-0.03580.13090.4260.00160.3629-6.277-46.2462-38.4679
45.39072.2308-1.83253.7046-0.72273.6463-0.05730.34760.2115-0.31890.25380.40730.3956-0.5802-0.20360.3037-0.0343-0.08410.29840.00370.2779-6.7243-37.2616-39.3668
54.4328-1.76392.00276.8322-4.85783.5768-0.4474-0.0861-1.2451-0.08010.3904-1.36830.82560.3843-0.00650.68390.15860.07770.8832-0.0370.8571-2.1047-47.7769-30.1349
63.7365-0.90260.50533.1515-0.83043.1216-0.0790.81310.3873-0.47110.51970.74010.0789-1.0018-0.33970.2549-0.0206-0.04470.47340.15160.3574-5.8239-24.1725-44.5441
74.9596-0.82272.20815.3963-5.51866.2980.1056-0.1739-0.4336-0.9812-0.1747-0.23971.2237-0.0941-0.02330.35970.0116-0.00220.21990.01170.412-17.0263-31.6366-32.5992
82.9936-0.59910.91153.7479-1.24063.6949-0.12810.0670.1249-0.07460.12990.0918-0.0464-0.0081-0.1360.2025-0.001-0.00610.27690.04740.3111-8.9655-23.5686-34.0004
94.30471.9578-0.17552.0583-4.13489.9161-0.0432-0.9052-0.21390.70240.38881.4756-0.1638-0.7379-0.22830.29690.06240.03620.45840.05950.4003-15.0981-26.3475-24.8197
104.12870.1138-1.28925.3287-1.73453.41090.0017-0.33580.3980.38770.19360.3391-0.1999-0.3229-0.16010.25610.0362-0.01610.27030.01980.2272-4.9602-19.2107-28.1623
115.4873-0.77141.5732.7194-0.61266.50110.0490.40750.32270.00130.1305-0.2161-0.7107-0.1813-0.16330.285-0.0246-0.00050.26920.14240.35996.2331-14.3078-40.1637
126.4576-2.53822.95565.6330.14954.5196-0.5434-0.67970.26281.16420.53090.2092-0.2233-0.8793-0.03140.45690.03420.05420.37070.030.32691.7681-17.3875-23.9113
134.4794-0.117-2.15964.0514-0.78194.555-0.0371-0.3969-0.0080.08120.0347-0.7547-0.17550.66810.06370.2545-0.036-0.05970.24430.08830.311817.0694-19.6026-35.6405
142.1045-0.64550.51324.34125.19422.3368-0.0453-0.05030.141-0.15470.1962-0.1907-0.37580.0776-0.11020.3622-0.02120.03030.29950.13170.26539.6737-24.8526-34.5343
158.05311.10797.15957.091.86068.8763-0.12091.80960.7518-0.7651-0.05780.10790.72910.89850.18440.5564-0.05890.06960.43840.05730.23629.2549-28.0425-52.5231
165.2841.6610.32333.70141.60684.15390.0005-0.4538-0.63150.2611-0.0166-0.40410.11540.16290.01350.22680.0152-0.01420.26430.08460.298315.0223-30.038-31.0654
175.9128-3.16383.61727.009-5.53652.12510.1741-0.5882-0.17720.3176-0.0398-0.11670.0987-0.16310.0890.26460.01390.00580.31130.00620.32835.0026-32.0292-22.0893
184.8259-0.00170.41152.1685-3.76038.22470.05110.0028-0.56030.60470.27530.72630.3671-0.8432-0.22170.3583-0.05960.07890.3042-0.08280.4598-9.8757-73.4254-17.4609
195.78442.4291-1.4733.3001-4.27052.0252-0.00561.1377-0.486-1.29560.19460.38690.2885-0.9215-0.18590.4156-0.0777-0.00630.4246-0.13790.41526.2165-66.2089-31.1415
202.0284-1.09615.22242.0287.03286.82630.20271.44020.2186-0.83480.2799-0.4494-0.0980.3924-0.40330.3116-0.06880.06390.4449-0.05180.280916.7163-60.5126-30.1002
214.40171.4759-0.80943.1195-0.24063.22670.10180.042-0.1983-0.1433-0.1315-0.15870.03750.14020.00630.1895-0.01140.02480.2476-0.07060.215413.6855-62.3759-21.2553
224.0803-5.88486.67728.4475-9.58011.9991.00421.7861-0.2489-3.2053-0.6980.88280.2401-0.6526-0.34960.88810.1755-0.16640.75650.03540.48427.2919-49.9518-33.1329
234.20151.4544-0.47342.5274-0.65211.5673-0.1142-0.0549-0.8608-0.0716-0.0957-0.37060.33080.20560.20130.22080.04070.02620.1787-0.00710.291612.556-65.1667-9.7199
243.6958-0.94922.20187.6266-3.23355.0174-0.08070.1684-0.54440.01510.2993-0.31550.2294-0.2132-0.17580.2312-0.029-0.04540.2853-0.05740.347224.3624-58.5983-11.845
257.09425.19271.44222.01532.82838.84890.04550.8377-0.4967-1.19350.39870.4826-0.3859-0.1187-0.46930.250.0014-0.0030.45730.03080.248417.3655-49.7522-24.9342
260.65310.4795-0.92973.6989-0.842.9363-0.0326-0.2153-0.23780.3736-0.0363-0.1539-0.08410.06720.13740.2616-0.0076-0.08310.2046-0.00770.332116.5653-57.5587-5.6109
278.0492-4.08143.06427.9256-4.40646.1201-0.19750.83520.75220.2786-0.3173-1.3726-0.60660.92490.44620.2527-0.0504-0.01950.2625-0.03010.387920.3206-46.2829-12.6896
286.65470.07521.56694.96041.8124.6971-0.1407-1.09190.59040.5456-0.23410.0140.0652-0.33510.31410.2677-0.0009-0.04940.2717-0.02650.182313.2164-52.38010.1916
294.06341.4116-0.19843.5189-0.40771.9414-0.0679-0.6444-0.10420.5157-0.01430.0517-0.0161-0.02220.08490.30190.04720.03250.24150.00310.11753.5765-57.1578-0.6872
305.89314.19652.81837.42362.42314.75370.0345-0.34840.66390.7198-0.29590.58240.10550.09110.28610.19470.02970.04320.1924-0.0380.23485.048-46.6394-3.6711
312.6869-0.40940.59553.50970.48451.8764-0.2437-0.4068-0.06720.38640.20920.4349-0.2186-0.34130.03920.23590.03410.03610.29710.00590.1708-6.3195-57.5529-6.5861
322.0788-4.53395.60533.8279-3.40472.30990.4027-0.3331-1.3895-0.5557-0.38560.44450.27340.07470.12510.3717-0.02250.09370.35520.01370.45-1.8998-74.8001-10.8687
334.37240.0427-0.20774.83181.87611.75540.00820.54130.248-0.2362-0.00110.1781-0.1392-0.0945-0.02280.1759-0.00760.00830.20210.04050.1464-7.6862-53.7565-14.9555
345.7223-3.16092.63242.0867-2.26246.2231-0.0523-0.45960.2521-0.6854-0.114-0.185-0.6084-0.14610.21310.2137-0.0306-0.02240.36280.06860.27031.5405-41.7421-14.8066
351.13522.3486-0.76245.7577-2.13630.840.06060.0247-0.3801-1.12790.2765-0.36441.11890.2801-0.27920.6280.02160.01820.6703-0.42481.083515.8888-88.686-41.0634
362.0313-1.9922.42468.7384-3.14478.94670.2430.73320.4923-0.44450.02770.0172-0.29920.2508-0.14180.3823-0.04740.03010.3621-0.16950.48769.0398-75.326-39.5991
372.97072.42611.29418.2499.5992.1983-0.0715-0.0248-0.4775-0.690.7518-0.0596-0.93840.6345-0.59590.3435-0.05610.05170.4707-0.17150.44488.8659-88.3453-40.8319
381.7075-0.8041-3.47563.42961.70847.1057-0.3985-0.7034-0.2477-0.16370.5061-0.0916-0.25151.4808-0.12830.2265-0.03970.0540.3753-0.16270.55959.1366-76.8034-28.7997
396.30235.5837.04082.10341.97662.11670.4305-1.00070.11330.3659-0.50220.86331.3517-1.29690.1160.3866-0.09150.02020.4564-0.11460.5241-3.1348-83.5047-27.299
402.01361.52911.8722.0196-5.47058.84360.23031.0603-0.564-0.7443-0.4580.70140.02820.33310.38660.27530.05120.02530.448-0.10190.4081-5.9394-86.7755-43.6847
412.29211.54871.41383.8484.23975.4592-0.19060.0748-0.2451-0.3178-0.51920.4454-0.1098-0.52290.57190.26110.02030.01590.258-0.04040.433-0.9075-75.29-30.8664
421.3270.40033.41210.12151.10372.0108-0.4093-0.24130.7858-0.2026-0.48041.2897-1.4044-1.05670.72510.45620.09030.07030.3166-0.10730.5548-0.8348-75.8255-34.9749
432.7330.54861.59752.32480.45878.6473-0.07830.2395-0.626-0.18220.1811-0.25310.86870.1073-0.21380.2932-0.02150.10250.3469-0.19720.5832-0.0139-89.0288-40.142
448.1783-9.77020.04862.0139-1.11262.01770.1341-0.2112-0.9966-0.1790.31630.41550.8533-0.8022-0.46820.4715-0.0274-0.02830.3266-0.040.56590.2243-90.9293-23.616
452.3036-1.752-1.02911.749-0.01211.9171-0.2093-0.3592-0.10560.5613-0.3878-0.02840.06950.26230.0444-0.1913-1.6047-1.5199-2.734-3.3244-2.3237.1672-84.2248-23.0439
465.60577.1741-4.432.0035-8.31172.01190.5103-0.6897-0.2245-0.62580.1924-0.70231.26181.1831-0.52060.44880.0531-0.07550.4955-0.3030.712212.169-86.4109-29.3075
472.21980.93040.54351.06892.99842.0043-0.21180.4844-0.4038-0.54120.0906-0.18210.04150.70250.06870.36540.00310.0380.3927-0.21810.43063.462-88.1301-41.5532
484.7214.16013.9018.76530.59794.8131-0.08511.0699-0.1198-1.1194-0.12-0.0373-0.4840.92970.19670.6130.01430.15330.6075-0.0740.36018.6214-80.3904-50.6086
493.89364.94141.7637.38094.39765.5005-0.10950.0194-0.3671-0.86090.2208-0.9123-0.3740.7597-0.05210.4171-0.030.0870.5815-0.1840.405516.8116-72.3673-39.1386
504.6527-3.57461.13046.9211-1.71237.9975-0.42480.1342-1.0209-0.77081.41310.08672.36950.5982-0.93391.2906-0.0029-0.08070.5915-0.18861.0135-1.406-112.84020.4893
515.6053-5.8426-0.25077.62332.42732.8997-0.10030.8170.7725-0.18130.2212-0.1610.18370.0771-0.17850.6104-0.1018-0.05540.80840.1370.73685.5905-99.4583-9.3877
524.7878-0.2616-0.24665.802-0.96112.9426-0.25270.3403-0.1801-0.83380.0259-0.23310.35090.29780.28380.5665-0.01110.02560.76170.0450.625727.3715-92.9456-10.6765
531.99722.92582.3227.55960.06886.84620.5941-0.5857-0.42660.0376-0.678-0.95830.49870.7260.08260.46740.02390.02530.50180.19320.480622.5216-98.0955-1.2563
542.752-0.61950.65312.2469-0.17253.01110.25780.7411-0.0765-0.2638-0.6373-0.1259-0.28690.76810.48060.50480.05330.00730.50430.13940.521.0167-92.8315-0.9696
552.016-7.28326.77387.0516-2.04648.42130.6699-0.1358-0.5776-0.156-0.1605-0.08340.56590.3654-0.62530.4510.07640.03950.47250.14650.51820.5016-106.70919.7567
562.2962-1.13741.73083.1426-2.42033.9144-0.13920.3586-0.1095-0.37650.0415-0.1725-0.1690.38630.13620.5268-0.14530.0850.73540.26740.716132.4419-88.88231.8673
572.9448-1.96612.19443.953-3.42446.0706-0.28540.10410.40620.1088-0.1379-0.3618-0.37340.34640.42010.4037-0.0537-0.05750.43950.19030.670426.404-93.553612.4774
584.15860.8893-0.66493.0241-0.843.23250.04240.02480.4473-0.0719-0.246-0.3671-0.31390.68960.2190.3635-0.0269-0.08590.40910.08210.580426.5011-84.943312.8574
592.13058.3933-2.8476.565-3.31036.1983-0.34320.48420.07170.16660.3857-0.368-0.0143-0.3250.04790.37490.0530.08460.38520.11170.772912.3371-91.258313.7022
608.54850.39412.39514.8648-0.43625.40150.0859-0.8675-0.030.7324-0.10970.36870.3093-0.60940.03490.3288-0.01030.0630.36480.06790.351611.8419-99.093819.3496
614.74532.04452.43484.12032.87377.3017-0.0541-0.08040.17620.20250.2042-1.2132-0.66760.3163-0.11220.42420.0068-0.04460.36640.00250.694113.8107-84.53516.1413
622.39590.12830.18184.10070.81143.73650.0247-0.08660.15270.29290.06350.4709-0.2772-0.4818-0.1030.36190.09270.06240.48880.18710.51991.8286-91.006413.5144
639.6971-4.68460.33182.0931-2.17482.1340.31170.6962-0.6023-0.4072-0.4930.47811.27520.04560.28060.63930.0504-0.06270.4426-0.02170.48697.9934-108.20072.773
642.0575-3.2108-0.67572.0469-2.07345.24470.21930.6110.3143-0.85230.38060.02990.6274-0.4493-0.63680.45-0.00070.01790.72180.05860.4899-3.6058-93.89020.8438
658.70836.08230.29514.65770.74615.2727-0.34470.84150.5755-0.27420.79250.2435-0.7721-0.4357-0.29790.41380.03920.05130.61090.09620.610.2206-82.96588.7475
666.67942.32191.19942.70390.86893.4518-0.40040.48530.617-0.49880.0296-0.47390.1210.32850.37940.43890.02240.04050.4670.17370.45089.8367-86.82780.2162
672.2164-1.31641.73322.8623-2.23635.6291-0.4252-0.08230.18050.02550.4729-0.4099-0.92-0.22180.11070.659-0.0766-0.0040.47610.25050.851611.4252-78.68295.1041
687.18852.78251.05797.24791.51816.9980.28030.0408-0.99770.5684-0.60041.01310.9874-0.71840.23920.6427-0.10940.12030.4118-0.16720.5548-3.4697-57.4572-53.5255
692.8031-1.3999-1.50051.4416-0.02021.5318-0.16120.3656-0.2282-0.16650.0295-0.3810.9812-0.1660.20150.5389-0.07970.06420.3468-0.02650.3598-1.4083-55.8302-57.4322
709.85879.82486.6312.0287.60367.2229-0.8426-0.19930.5576-1.2753-0.34080.7413-0.3794-0.69970.9270.57-0.0934-0.04980.4952-0.15090.3695-0.1706-60.0847-67.077
718.29855.2342.20963.63580.26384.6014-0.17460.18810.50210.3151-0.01750.8638-0.56220.17070.07080.33160.07650.05560.38310.02040.3356-2.5324-45.6663-52.4791
722.14870.2697-1.3389.6339-0.19715.7102-0.3368-0.58390.3692-0.9060.3402-0.32140.52210.6091-0.00780.4776-0.04710.0270.6117-0.10080.36097.2612-40.562-56.4112
739.2475-1.84082.18659.18966.85596.5198-0.59310.08010.54520.3963-0.4024-0.5506-0.95811.07510.74380.6179-0.13460.09390.471-0.1280.405614.4345-54.2974-63.5679
742.7356-0.03861.54049.19150.77223.13040.30550.2089-0.45110.41040.07310.03390.36440.474-0.38930.35960.0710.05320.4337-0.0580.486810.5597-55.5585-54.8393
752.62570.90580.317.87995.68094.0804-0.14650.0629-0.01510.18120.8395-0.38911.05290.1215-0.66060.4758-0.06450.05940.3581-0.07710.31556.9213-41.5623-48.0055
760.5872-1.7509-1.48515.23294.44923.80660.1675-0.78660.2968-0.2174-0.71450.79760.0313-0.12960.54310.6407-0.0895-0.05130.5577-0.20150.44526.6649-60.5154-55.62
775.7583.08151.51798.9915-5.35325.62510.14830.8908-0.0138-1.03-0.1228-0.52420.1494-0.2469-0.01360.60370.0110.14840.6497-0.14310.57499.5508-57.2023-67.4424
788.75424.31927.5782.015-0.62948.20040.69851.1405-0.3492-2.2316-0.0485-0.87330.1430.348-0.63740.73770.11010.00180.6577-0.21560.47047.1462-42.3261-66.7467
792.02286.17292.01279.0487-0.1978.0735-0.0875-0.18420.6063-0.0709-0.33381.2361-1.3282-0.54370.33970.52740.0592-0.07970.4511-0.13140.4816-2.2359-43.8688-60.2518
802.1273-0.7229-0.74034.29231.26670.57470.10790.0628-0.2667-0.5608-0.22430.67280.07-0.14370.20310.55060.02220.02490.439-0.09920.33151.9124-59.8489-61.9533
810.7921-0.50280.74179.4823-0.89316.3719-0.403-0.119-0.36110.84590.37350.9495-0.114-0.56780.09140.5089-0.03280.03450.45-0.00740.4846-7.312-59.1798-51.2692
823.4765-2.1576-3.88854.1316-0.51547.401-0.58130.73560.3338-0.40530.91390.19160.1024-0.5664-0.29060.5599-0.24280.14420.5002-0.02970.703-9.5412-53.2655-44.9047
833.4052-1.58310.0814.37851.172.03610.9011-0.21540.0859-1.2247-0.45380.05430.40941.3161-0.56331.3070.4401-0.04041.3225-0.19950.569419.2326-107.8907-24.0703
84-0.00280.00090.002-0.00410.0115-0.0083-0.43691.2308-0.5803-0.7048-0.150.01260.0703-0.44120.51282.07940.3647-0.09791.4715-0.23570.758518.3998-120.3113-31.5866
856.1944-1.4332-0.52682.5287-2.99194.4763-0.55110.03630.2576-0.6086-0.9009-0.16090.4018-0.17211.35120.7290.2118-0.02590.8479-0.11590.853518.9374-110.0504-17.1782
861.4643-0.0401-2.37677.3431-6.25569.29570.03280.1116-0.2746-0.2953-0.69420.2882-0.504-0.27540.66571.11260.2794-0.62640.8087-0.51231.509515.8971-108.379-8.2061
870.11-0.2541-0.62982.80942.52974.7761-0.43890.03630.2535-1.64560.6074-0.3720.4963-1.1535-0.09191.64810.0577-0.46091.0395-0.34771.22384.7626-115.4931-15.8459
881.8763-0.60150.09370.1858-0.02440.01140.56210.1554-0.09910.40270.4509-0.6057-0.77820.3771-0.92511.7356-0.05970.12881.0124-0.16640.69363.7203-114.8152-30.995
892.68741.0631.48432.48941.95887.48360.45930.4250.0624-0.6801-1.1040.38030.9375-0.46490.55110.97360.13-0.14090.8338-0.09090.64228.9118-106.1774-15.7782
905.03282.2090.81894.89483.09338.2596-0.05720.30540.15370.11321.2820.0193-0.1465-0.4672-1.22471.2440.2904-0.19720.8461-0.1530.79659.4297-111.6175-27.4506
910.93220.441-0.26891.0413-0.88460.7605-0.8091.0571-0.5366-1.92080.77630.52660.86630.11740.0391.69-0.0619-0.05221.068-0.24390.83299.0849-123.1814-16.5781
920.0111-0.0675-0.07530.48040.54680.6233-0.29840.1673-0.232-1.01640.39290.3022-0.7231-0.0177-0.01521.46440.3356-0.11151.1446-0.30780.719714.7629-117.2251-9.9203
930.45160.5183-0.29981.1184-0.23990.22880.54280.535-1.211-0.3436-0.26950.66760.27510.5794-0.21951.36280.4166-0.14770.7245-0.08051.206520.0892-117.9105-16.021
94-0.023-0.0065-0.0054-0.0128-0.0091-0.00580.45550.455-0.18290.84630.183-0.30950.9693-0.8993-0.45771.49140.5145-0.12561.2624-0.11520.671511.8022-117.7074-28.8249
951.6598-0.9482-0.51481.2076-1.0042.69490.3322-0.41880.13050.56550.1402-0.26390.05210.8269-0.42231.0540.0863-0.10841.3484-0.31940.955318.1958-108.2955-36.2691
960.80630.933-2.1975.73881.29619.2125-0.5557-0.6122-0.6351-0.4308-0.440.08620.031-0.36120.91610.71040.24570.03021.3875-0.20751.048127.042-104.6987-24.16
970.2239-0.58490.48191.4913-1.24431.05270.69090.68530.0799-0.7349-0.2208-0.1315-0.04230.0549-0.23691.04240.18120.06421.3787-0.12660.626427.0031-97.2829-20.8545
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 67:72)
2X-RAY DIFFRACTION2(chain A and resid 73:83)
3X-RAY DIFFRACTION3(chain A and resid 84:94)
4X-RAY DIFFRACTION4(chain A and resid 95:118)
5X-RAY DIFFRACTION5(chain A and resid 119:126)
6X-RAY DIFFRACTION6(chain A and resid 127:152)
7X-RAY DIFFRACTION7(chain A and resid 153:170)
8X-RAY DIFFRACTION8(chain A and resid 171:190)
9X-RAY DIFFRACTION9(chain A and resid 191:205)
10X-RAY DIFFRACTION10(chain A and resid 206:238)
11X-RAY DIFFRACTION11(chain A and resid 239:261)
12X-RAY DIFFRACTION12(chain A and resid 262:278)
13X-RAY DIFFRACTION13(chain A and resid 279:297)
14X-RAY DIFFRACTION14(chain A and resid 298:312)
15X-RAY DIFFRACTION15(chain A and resid 313:321)
16X-RAY DIFFRACTION16(chain A and resid 322:355)
17X-RAY DIFFRACTION17(chain A and resid 356:531)
18X-RAY DIFFRACTION18(chain B and resid 66:81)
19X-RAY DIFFRACTION19(chain B and resid 82:87)
20X-RAY DIFFRACTION20(chain B and resid 88:95)
21X-RAY DIFFRACTION21(chain B and resid 96:119)
22X-RAY DIFFRACTION22(chain B and resid 120:125)
23X-RAY DIFFRACTION23(chain B and resid 126:149)
24X-RAY DIFFRACTION24(chain B and resid 150:168)
25X-RAY DIFFRACTION25(chain B and resid 169:173)
26X-RAY DIFFRACTION26(chain B and resid 174:190)
27X-RAY DIFFRACTION27(chain B and resid 191:210)
28X-RAY DIFFRACTION28(chain B and resid 211:227)
29X-RAY DIFFRACTION29(chain B and resid 228:263)
30X-RAY DIFFRACTION30(chain B and resid 264:279)
31X-RAY DIFFRACTION31(chain B and resid 280:313)
32X-RAY DIFFRACTION32(chain B and resid 314:321)
33X-RAY DIFFRACTION33(chain B and resid 322:355)
34X-RAY DIFFRACTION34(chain B and resid 356:531)
35X-RAY DIFFRACTION35(chain C and resid 47:51)
36X-RAY DIFFRACTION36(chain C and resid 52:57)
37X-RAY DIFFRACTION37(chain C and resid 58:68)
38X-RAY DIFFRACTION38(chain C and resid 69:80)
39X-RAY DIFFRACTION39(chain C and resid 81:89)
40X-RAY DIFFRACTION40(chain C and resid 90:95)
41X-RAY DIFFRACTION41(chain C and resid 96:108)
42X-RAY DIFFRACTION42(chain C and resid 109:114)
43X-RAY DIFFRACTION43(chain C and resid 115:124)
44X-RAY DIFFRACTION44(chain C and resid 125:130)
45X-RAY DIFFRACTION45(chain C and resid 131:136)
46X-RAY DIFFRACTION46(chain C and resid 137:141)
47X-RAY DIFFRACTION47(chain C and resid 142:152)
48X-RAY DIFFRACTION48(chain C and resid 153:157)
49X-RAY DIFFRACTION49(chain C and resid 158:171)
50X-RAY DIFFRACTION50(chain D and resid 67:75)
51X-RAY DIFFRACTION51(chain D and resid 76:84)
52X-RAY DIFFRACTION52(chain D and resid 85:100)
53X-RAY DIFFRACTION53(chain D and resid 101:112)
54X-RAY DIFFRACTION54(chain D and resid 113:139)
55X-RAY DIFFRACTION55(chain D and resid 140:151)
56X-RAY DIFFRACTION56(chain D and resid 152:173)
57X-RAY DIFFRACTION57(chain D and resid 174:191)
58X-RAY DIFFRACTION58(chain D and resid 192:230)
59X-RAY DIFFRACTION59(chain D and resid 231:243)
60X-RAY DIFFRACTION60(chain D and resid 244:261)
61X-RAY DIFFRACTION61(chain D and resid 262:280)
62X-RAY DIFFRACTION62(chain D and resid 281:308)
63X-RAY DIFFRACTION63(chain D and resid 309:321)
64X-RAY DIFFRACTION64(chain D and resid 322:330)
65X-RAY DIFFRACTION65(chain D and resid 331:343)
66X-RAY DIFFRACTION66(chain D and resid 344:359)
67X-RAY DIFFRACTION67(chain D and resid 360:531)
68X-RAY DIFFRACTION68(chain E and resid 50:56)
69X-RAY DIFFRACTION69(chain E and resid 57:62)
70X-RAY DIFFRACTION70(chain E and resid 63:69)
71X-RAY DIFFRACTION71(chain E and resid 70:78)
72X-RAY DIFFRACTION72(chain E and resid 79:85)
73X-RAY DIFFRACTION73(chain E and resid 86:92)
74X-RAY DIFFRACTION74(chain E and resid 93:105)
75X-RAY DIFFRACTION75(chain E and resid 106:112)
76X-RAY DIFFRACTION76(chain E and resid 113:118)
77X-RAY DIFFRACTION77(chain E and resid 119:123)
78X-RAY DIFFRACTION78(chain E and resid 124:131)
79X-RAY DIFFRACTION79(chain E and resid 132:139)
80X-RAY DIFFRACTION80(chain E and resid 140:156)
81X-RAY DIFFRACTION81(chain E and resid 157:164)
82X-RAY DIFFRACTION82(chain E and resid 165:170)
83X-RAY DIFFRACTION83(chain F and resid 50:60)
84X-RAY DIFFRACTION84(chain F and resid 61:67)
85X-RAY DIFFRACTION85(chain F and resid 68:76)
86X-RAY DIFFRACTION86(chain F and resid 77:82)
87X-RAY DIFFRACTION87(chain F and resid 83:89)
88X-RAY DIFFRACTION88(chain F and resid 90:95)
89X-RAY DIFFRACTION89(chain F and resid 96:110)
90X-RAY DIFFRACTION90(chain F and resid 111:121)
91X-RAY DIFFRACTION91(chain F and resid 122:129)
92X-RAY DIFFRACTION92(chain F and resid 130:135)
93X-RAY DIFFRACTION93(chain F and resid 136:143)
94X-RAY DIFFRACTION94(chain F and resid 144:150)
95X-RAY DIFFRACTION95(chain F and resid 151:158)
96X-RAY DIFFRACTION96(chain F and resid 159:165)
97X-RAY DIFFRACTION97(chain F and resid 166:172)

+
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