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- PDB-8fym: Crystal structure of Fab235 in complex with MPER peptide -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 8fym
タイトルCrystal structure of Fab235 in complex with MPER peptide
要素
  • ALA-SER-LEU-TRP-ASN-TRP-PHE-ASN-ILE-THR-ASN-TRP-LEU-TRP-TYR-ILE-LYS-LYS-LYS
  • Fab235, H chain
  • Fab235, L chain
キーワードIMMUNE SYSTEM / MPER / membrane proximal external region / Vaccucine / Fab
機能・相同性prop-2-enamide
機能・相同性情報
生物種Mus musculus (ハツカネズミ)
Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
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Tan, K. / Kim, M. / Reinherz, E.L.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145509 米国
引用ジャーナル: Nat Commun / 年: 2023
タイトル: Inadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility.
著者: Tan, K. / Chen, J. / Kaku, Y. / Wang, Y. / Donius, L. / Khan, R.A. / Li, X. / Richter, H. / Seaman, M.S. / Walz, T. / Hwang, W. / Reinherz, E.L. / Kim, M.
履歴
登録2023年1月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年10月11日Provider: repository / タイプ: Initial release
改定 1.12024年2月28日Group: Source and taxonomy / カテゴリ: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific
改定 1.22024年3月6日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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
改定 1.32024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
L: Fab235, L chain
H: Fab235, H chain
P: ALA-SER-LEU-TRP-ASN-TRP-PHE-ASN-ILE-THR-ASN-TRP-LEU-TRP-TYR-ILE-LYS-LYS-LYS
A: Fab235, L chain
B: Fab235, H chain
C: ALA-SER-LEU-TRP-ASN-TRP-PHE-ASN-ILE-THR-ASN-TRP-LEU-TRP-TYR-ILE-LYS-LYS-LYS
D: Fab235, L chain
E: Fab235, H chain
F: ALA-SER-LEU-TRP-ASN-TRP-PHE-ASN-ILE-THR-ASN-TRP-LEU-TRP-TYR-ILE-LYS-LYS-LYS
G: Fab235, L chain
I: Fab235, H chain
J: ALA-SER-LEU-TRP-ASN-TRP-PHE-ASN-ILE-THR-ASN-TRP-LEU-TRP-TYR-ILE-LYS-LYS-LYS
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)205,27624
ポリマ－204,46112
非ポリマー81612
水7,800433
1
L: Fab235, L chain
H: Fab235, H chain
P: ALA-SER-LEU-TRP-ASN-TRP-PHE-ASN-ILE-THR-ASN-TRP-LEU-TRP-TYR-ILE-LYS-LYS-LYS
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,2074
ポリマ－51,1153
非ポリマー921
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Fab235, L chain
B: Fab235, H chain
C: ALA-SER-LEU-TRP-ASN-TRP-PHE-ASN-ILE-THR-ASN-TRP-LEU-TRP-TYR-ILE-LYS-LYS-LYS
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,3706
ポリマ－51,1153
非ポリマー2553
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
3
D: Fab235, L chain
E: Fab235, H chain
F: ALA-SER-LEU-TRP-ASN-TRP-PHE-ASN-ILE-THR-ASN-TRP-LEU-TRP-TYR-ILE-LYS-LYS-LYS
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,2786
ポリマ－51,1153
非ポリマー1633
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Fab235, L chain
I: Fab235, H chain
J: ALA-SER-LEU-TRP-ASN-TRP-PHE-ASN-ILE-THR-ASN-TRP-LEU-TRP-TYR-ILE-LYS-LYS-LYS
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)51,4208
ポリマ－51,1153
非ポリマー3055
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)43.481, 108.300, 121.209
Angle α, β, γ (deg.)85.630, 82.950, 85.590
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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要素

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タンパク質・ペプチド , 1種, 4分子 PCFJ

#3: タンパク質・ペプチド
ALA-SER-LEU-TRP-ASN-TRP-PHE-ASN-ILE-THR-ASN-TRP-LEU-TRP-TYR-ILE-LYS-LYS-LYS


分子量: 2644.120 Da / 分子数: 4 / 由来タイプ: 合成
由来: (合成) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)

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抗体 , 2種, 8分子 LADGHBEI

#1: 抗体
Fab235, L chain


分子量: 24203.967 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / Cell (発現宿主): 293-F cells / 発現宿主: Homo sapiens (ヒト)
#2: 抗体
Fab235, H chain


分子量: 24267.115 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / Cell (発現宿主): 293-F cells / 発現宿主: Homo sapiens (ヒト)

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非ポリマー , 4種, 445分子

#4: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C3H8O3
#5: 化合物 ChemComp-1HC / prop-2-enamide / アクリルアミド


分子量: 71.078 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C3H5NO
#6: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Cl
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 433 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN
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: 2.76 Å3/Da / 溶媒含有率: 55.37 %
結晶化温度: 289 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 1% (w/v) Tryptone, 0.05M HEPES:NaOH, 2% (v/v) PEG 400

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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: APS / ビームライン: 19-ID / 波長: 0.97918 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2022年4月26日
放射モノクロメーター: Si 111 / 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: 0.97918 Å / 相対比: 1
反射解像度: 2.45→48 Å / Num. obs: 78049 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / 冗長度: 2.9 % / Biso Wilson estimate: 32.41 Å2 / CC1/2: 0.974 / CC star: 0.993 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.097 / Rrim(I) all: 0.174 / Χ2: 0.91 / Net I/σ(I): 6.96
反射 シェル解像度: 2.45→2.49 Å / 冗長度: 2.7 % / Rmerge(I) obs: 0.811 / Mean I/σ(I) obs: 1 / Num. unique obs: 3908 / CC1/2: 0.386 / CC star: 0.746 / Rpim(I) all: 0.579 / Rrim(I) all: 1 / Χ2: 0.626 / % possible all: 96.9

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解析

ソフトウェア
名称バージョン分類
SBC-Collectデータ収集
PHENIX1.20.1_4487精密化
HKL-3000データ削減
HKL-3000データスケーリング
HKL-3000位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.45→47.95 Å / SU ML: 0.3527 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 25.9064
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2435 3808 4.96 %
Rwork0.1998 73026 -
obs0.202 76834 95.72 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 40.82 Å2
精密化ステップサイクル: LAST / 解像度: 2.45→47.95 Å
タンパク質核酸リガンド溶媒全体
原子数12654 0 49 433 13136
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00213031
X-RAY DIFFRACTIONf_angle_d0.483717726
X-RAY DIFFRACTIONf_chiral_restr0.04141960
X-RAY DIFFRACTIONf_plane_restr0.00412222
X-RAY DIFFRACTIONf_dihedral_angle_d5.01771775
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.480.35341220.28152671X-RAY DIFFRACTION93.66
2.48-2.510.34651210.2732714X-RAY DIFFRACTION94.56
2.51-2.550.30841510.26682733X-RAY DIFFRACTION95.62
2.55-2.580.35621470.27162716X-RAY DIFFRACTION96.99
2.58-2.620.37741290.26132708X-RAY DIFFRACTION96.6
2.62-2.660.31171550.25952723X-RAY DIFFRACTION97.2
2.66-2.710.33561400.25682813X-RAY DIFFRACTION97.11
2.71-2.750.27941330.24972675X-RAY DIFFRACTION96.83
2.75-2.80.2921410.23582700X-RAY DIFFRACTION95.88
2.8-2.860.30331480.23882723X-RAY DIFFRACTION96.6
2.86-2.920.30211320.24372806X-RAY DIFFRACTION97.32
2.92-2.980.29281250.24332747X-RAY DIFFRACTION97.39
2.98-3.050.29791400.22872761X-RAY DIFFRACTION97.74
3.05-3.130.27011740.22242722X-RAY DIFFRACTION97.12
3.13-3.210.26681380.21432718X-RAY DIFFRACTION97.01
3.21-3.30.2721650.20942727X-RAY DIFFRACTION96.85
3.3-3.410.20341330.20162748X-RAY DIFFRACTION96.68
3.41-3.530.24851480.19442686X-RAY DIFFRACTION95.68
3.53-3.670.23421350.18132691X-RAY DIFFRACTION94.48
3.67-3.840.21281260.17072701X-RAY DIFFRACTION96.12
3.84-4.040.20051480.17092735X-RAY DIFFRACTION96.13
4.04-4.30.2091560.15742719X-RAY DIFFRACTION96.15
4.3-4.630.18451570.14482630X-RAY DIFFRACTION94.93
4.63-5.090.18481470.14572653X-RAY DIFFRACTION94.31
5.09-5.830.19691380.16662621X-RAY DIFFRACTION92.65
5.83-7.340.21671330.20012642X-RAY DIFFRACTION92.84
7.34-47.950.19771260.18712543X-RAY DIFFRACTION90.08
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)
12.601384816530.5770455369080.6386407183394.747294390194.398197462174.17031367636-0.1727498503370.101083545593-0.177402732439-0.0117248746129-0.007415252989520.0186410019708-0.175693314462-0.04663371454110.3055618061820.416590800580.0552477667484-0.006281010900190.2425684398040.003991195019850.3391616786427.62556869139.10222340721.71890196451
23.07871722040.0506328956231-1.084846274610.1938416643940.705401464342.90759994595-0.1231225907320.041948877179-0.43525820730.3921770145740.009386700133480.05053068706470.3906693122080.0346334498670.08131021220530.3577478417220.113061107809-0.001489492860280.2114178502940.006573015278670.30972531157916.055171277632.0690418166-3.32497134234
33.33717572628-1.38025611904-2.332650605418.782446511890.9700032921961.63056540435-0.08630113207-0.002783166326210.08094626975120.5509202705120.117919368812-0.1660618720070.1128764437640.819233207198-0.01900351728250.3685400501220.0946426172247-0.1190171827220.2924451161190.0202415184650.32021598954924.665270891436.01386199111.99545403612
41.61969184066-0.2659537665230.1645150774724.218041876043.777960331784.42475175398-0.197308263983-0.0637938325-0.1479823571460.3891072769710.179889459878-0.1140640481730.00494299546580.1393259844590.01072015401490.3649053217050.06696459640780.008799357700750.2550522966090.03446280919470.23404115404115.047389052738.0368377272.54541189911
52.12867173577-3.17920493066-1.521479477214.134958513682.472412366542.05552898995-0.2455899243730.0605793119833-0.2010931489320.5402424050450.08213523997880.1852910032610.510957279065-0.1250555830150.1860429890030.277364377131-0.0249215804290.05079169004450.184138241704-0.001651248852580.2874614739088.4729038646940.9643583214-2.91181988124
66.11875896814-1.32981303742.025514890772.491739288822.359604609677.12510392791-0.2149372745270.6815568911780.574384267593-0.546260328614-0.7931160727560.179357711542-0.889357675574-0.06354011962390.9532439290190.2855660084830.0852185115584-0.07133012433340.274085493542-0.02203033358960.534608934268-10.668629357371.1731790718-15.2843401669
72.51194820975-0.8551201838392.88196548591.54174303641-0.2891208144184.073560348670.2862428014840.121821673677-0.528562699840.276318363501-0.4472068811010.8150720638730.173887574995-0.0874714856082-0.0701926634840.1683874754980.108929727856-0.03407380357740.2332085438-0.08238269058910.602493742416-8.7230004046559.5839126215-5.38225292448
86.971776585880.2077246220272.36589386220.233102893023-0.2243235305161.215413643170.19370311330.340253729708-0.275622899938-0.224509317548-0.2196799222990.8107324281540.0683045677863-0.2878759163390.06366539336030.293684509092-0.0158455280023-0.1092164460470.329343251415-0.1393591068440.695419658483-14.472457146156.945112963-12.2507045217
95.57286748492-1.247382491994.490740825733.87569107263-1.050254026858.214885450460.2516049695970.377228355936-0.4862853781180.108350737833-0.0452023441442-0.929181741380.009853396900690.756449108655-0.06330686053050.2125751155930.0383734201493-0.0289608709970.2624595456130.02212358683360.3998772975235.6434544543259.38520290350.766638668714
106.44352383183-0.9257436747552.921590401552.74337472786-0.9972069006265.68484282091-0.1356988627531.11789156122-0.488217998293-0.3949680155910.2520321905610.3086055995520.0119578243197-0.0824153926528-0.1343717736430.2701197387310.100557064442-0.09702791831760.392361220241-0.08662496615860.541166471628-15.500396450863.9984441037-18.2295829451
115.17312527564-1.345417342983.193411162172.5127887126-1.565751010955.884471826710.0407073797774-0.305794700883-0.292280767474-0.00263332345921-0.09451113335680.8743294213560.0984539967196-0.855885630354-0.1503262652930.1174665646960.04516556963910.02107071904420.2900784607220.02757636147540.710313520746-17.36492884264.7205847522-4.46806538554
124.69122417876-1.20794533471.008128832454.52954761351-0.571977231983.160833033-0.09334427051990.02741340300640.4460104440230.06715711584460.00754306624065-0.257570200033-0.2898867740830.05797863262230.07874380720210.2455694544480.0376153862681-0.01841433478830.158596289155-0.007184532096710.20649803745520.72166745642.6265884431-21.776180318
131.06384141303-1.18698732401-0.7023763035712.527622606540.921307031670.5753506467890.05122441938410.08141670557010.064580000076-0.118620178926-0.1102450857420.03995651187790.00515203942545-0.07343251677130.06179233326460.2105486385690.0338374660056-0.06089330785410.2503809692280.02042743531990.2009834112212.513597697547.4489027198-19.6176367229
140.707203180097-0.4897597292880.01825522759334.530020755631.874622633124.846486113610.1530530432510.1583191987480.167795756823-0.30158875363-0.1308441558150.265457753669-0.2475809705360.0143006429144-0.05491025505080.1125280571290.0522256946868-0.02733809865850.2815023188290.04016631006760.3571911466721.8546456973571.6826550794-13.6724710757
155.043229082031.814663140931.94306784311.88746142521.362541180264.30785281116-0.226870259395-0.8119933681520.449074847416-0.0500838940158-0.1292208715-0.002895648571620.0403154793458-0.1377775836820.3224151990670.3169031101260.127480461202-0.03559231268170.24274738492-0.05714623520820.31442635377628.297357801119.435651563-21.2375625491
161.94066983750.143861176095-0.6079094476680.887860641156-0.8937726790444.28946109638-0.0640545621242-0.1508514083820.4111699482210.117853965991-0.00276865434129-0.279470720796-0.101771123839-0.1068186107380.1944448195220.544060695145-0.0569110529386-0.05729902355740.3078350971130.03930142601090.4801054595029.060327210487.3926650252511.1760304573
174.698370201190.993867275450.03264012648224.98238017984-1.286044666474.32326620055-0.0712364050655-0.1750313162630.1242278168060.5115156105860.06913441360280.100316955435-0.606198231654-0.239383038539-0.01719627738670.3815474191450.0896803118659-0.06040405091650.211004574313-0.03015853473930.227422212733-1.660757766249.655857725436.11458104769
180.965273435882-0.9852555814291.046225928322.60601888629-2.086815917512.34595396629-0.0808687324022-0.0661714205925-0.1141211808730.2539172611030.0935595396126-0.000421508068725-0.3304706024880.0516137746965-0.02381400142130.196985477841-0.01832440915770.008137361830990.3067127084740.03021099194820.2586229573556.92549761154-8.7299852406113.5344641099
193.41943610522-2.83316530195-1.013398246853.974239802141.335424601262.250980874990.00554399516794-0.1605607828410.116101561730.109937396709-0.155204443638-0.5026702849-0.1695984033770.3089931274030.1017031299850.205648972436-0.0253136424442-0.03920514247680.3989840453190.1380026395760.43720680680419.8143223798-22.906153890821.8463652944
202.90217717799-2.69041981523-0.1825304191917.379123778360.6630761645631.887180112570.192567851342-0.27006736991-0.3147370926670.0561171926346-0.15962465029-0.1914215474360.1296406900570.0405918372308-0.0145118635120.18276611598-0.0106960851402-0.02336699667790.4235880422480.1104308930130.40337938730417.4096374079-26.22175766724.5349983074
211.19830106486-1.327400704350.2943154516514.86151289006-0.5982726237112.69177311101-0.0666346412308-0.00344341515753-0.1657075016810.1037032234190.03753257620180.103800852759-0.0234297708749-0.02435133314410.01750249239760.1449887796620.0072965505567-0.01087413847060.187481220362-0.00630718268390.235853518204-2.95660772432-6.29184933121-8.40503675348
222.1895048713-0.33835750537-1.156110580571.474159630750.2281535385773.106753884810.0889268024703-0.320853941188-0.2779459228310.0990930867820.0540076199082-0.1394592031710.17054796286-0.00454946829453-0.122411767570.1386468129890.00628604607051-0.04285746450640.3327956949040.09380673866250.4616290057053.7896892599-28.691299954414.6932712081
232.02662189023-2.138863001441.103862136132.280187684-0.7823506659735.32441654669-0.74639463147-1.592834685270.5874841763992.25369813273-0.970967859951-2.20170910976-1.650727636212.230524819191.587807671430.6521452453880.0367495403073-0.2759829359280.875383283350.137785850420.782619626552-1.4860845232615.4639547085-20.0192363596
243.810752728781.201125674633.205103006647.5654400817-1.514611260776.332931744330.398755578086-0.361054071647-0.3794899344690.380785438810.004294636967130.2549722360250.13335114197-0.365359466115-0.3184984773740.2511766657090.1011199744490.02404419086510.217841814250.02541029206890.334852731225-13.88663595368.3563649369-17.7774547452
252.967931019550.644507097-1.327236655023.18445830153-1.110954261254.3563372282-0.1054210530010.1955823965980.205286656514-0.2952785200170.149299058584-0.0373868765197-0.6307283725980.223977670962-0.03344762849840.354591205523-0.0711968735848-0.06746933183040.2743686002310.02805552154530.2160313416235.3231769337336.2206717042-45.426654539
260.07904145072130.239843648549-0.3454635310191.15189801287-1.675029721953.478433732-0.1254878217030.2597521620970.487244224691-0.1481999131650.2257477715360.12175806087-0.5247823545170.1184783002670.0035014923150.438999415697-0.161770114674-0.07330891438150.3449555562430.03362518049840.3207805973665.9035725078536.1475095225-54.139932011
273.022633055631.723721944313.020090698082.038667303260.4919996129528.715518661640.191486950343-0.372930589406-0.07059157247370.18787893296-0.235015038547-0.1005836247020.105884387327-0.1286528376890.03684247129330.577401062533-0.0282245560991-0.01257384701580.3945576326830.02868382971920.2542202965165.2553032476338.1363763964-86.5991627585
282.078859690.7911671285860.07749344199942.74376189846-0.08465886876353.80175968771-0.33709437750.480103464185-0.0385901944478-0.6760961880640.3113371056630.15712454737-0.0301375442887-0.07808041767350.02917759186140.309834968597-0.0896221336285-0.06312903156280.3654095836890.01011417450580.225356132566-5.1777306332417.1556693657-51.1272036947
295.358802095352.4976791132-0.1788070323283.056317200460.04303393305743.564259548140.280712087988-0.291106644279-0.66976428233-0.190693894425-0.245045267902-0.5059773643291.196778619250.1600635918850.03524228202760.8923671491930.0144234251884-0.1313748324170.4388258500730.09989290946480.4389177490838.3471326934422.5211490422-82.9557892104
304.657749709352.99244213377-0.2152407110275.291707858795.013618032457.87514779443-0.1653051770060.8529931573751.50705964719-0.7470459059260.05998527099930.671808852433-0.2027616096170.145083607040.1142902152120.474735872712-0.0555001671791-0.04468418487480.3076128671590.1218157619810.284933278761-14.958165221124.9084133749-32.5362201703
313.96702299847-0.568587769357-3.85209232018.789322869380.9190304884078.26856337259-0.1896960204050.150755296029-0.3611990353170.429273162528-0.177143313442-0.5133091500160.04775759498910.0597014639330.3769106693730.145752800380.0386071500744-0.03259376365890.228956043761-0.008424601036410.218524116922-6.8237347228413.3911768009-30.8965068832
322.837390790620.746453590611-0.9182102194640.5959196435321.205112230485.798531379310.248018904289-0.540105527773-0.04519064208460.168041049274-0.448874511870.4051686935431.264465917180.0276467797720.2701542660570.5461801989780.22966990430.1666415694140.279340114362-0.01753467182730.61410773251823.3487149405-20.4351655196-29.9186359131
333.342209947732.12458995371.283114480992.858291605641.500623064852.52472262548-0.1781743400150.116607696143-1.007019161030.497968445579-0.267219912059-0.238976673611.17967152271-0.5880918323840.1034940179861.02614138992-0.2415198451890.3250065780870.388572613794-0.1883787067640.7411780339639.23951092151-28.4081242989-31.6300082683
342.706115784431.40292294608-0.6917313637044.53542761742.545889156574.53603855721-0.260850214847-0.682427691830.2212327156180.297658633438-0.0107829908407-0.03807331045150.3279366655580.7831242789370.2791009495170.3580242197230.1191055466310.03369029925950.2508890724310.04052347443020.30185981296819.2085955046-9.62566436988-19.7780719205
352.44247079848-0.742268845638-3.00670324491.56952094861.778093017365.60863668611-0.3534928370710.819474822082-0.609491392367-0.9267851454980.992248312520.08996043032610.307288003029-0.871324300548-0.1075319251040.704113969111-0.2138661806420.1429868462220.361632515983-0.1847328794320.4880948130810.5586340539-15.5797385226-38.4785575884
361.7267682649-2.69402688011-0.1815080079164.662268294910.2501259098516.310644302810.100358621652-0.412201999339-0.2087344331480.06208831666260.1411616243571.267807946740.770857634253-1.31437532443-0.002069140224650.299991244596-0.1327038008430.08077855794970.4315671996370.001511239820140.5451601113484.33077115031-12.1192055509-29.7210237287
371.413781249211.33901679954-1.243658748613.247312558681.712130448195.26044673341-0.5112171342450.129338518762-1.006843613310.130308869482-0.5963535089740.09893535344551.36238408263-0.4107635401030.5994424334260.670173299785-0.08856515783870.3022243130860.184194648346-0.02517401787910.58895624336710.2832445961-20.0699521161-25.169332928
383.25357383798-2.36504954167-0.02703006518331.89586825976-0.6852972136792.882023469750.356670135725-0.101727248991-0.272665014744-1.04863141005-0.2935644812681.51110329971-0.1605858503-1.186784423040.4541087512621.03963937201-0.3801727294480.1383740072560.69803516177-0.4113273483410.8877742051.01170525124-24.290477486-38.2082952148
392.83362292938-0.715356072458-1.226211124175.125270937760.01301101939263.21584707578-0.32383634922-0.234588814454-0.545023038287-0.441000572282-0.123660796789-0.2485787585930.811902987670.08980285234270.2345699437770.3738207252580.01130463194970.1559507178620.2362241497440.001866923196180.44460781910219.8510945488-14.434799353-32.3287465548
401.837417599460.7252115920590.9329761002261.72900903040.5678956849160.5508709403030.8866231750631.03960622837-1.212882420020.7907526228350.282870457934-0.4525779965420.6245065353750.169887264915-0.9519149192820.857037894768-0.1734542846380.07851865088210.513175582289-0.2946405345490.8474353909356.66548721894-32.1100173886-40.4771255244
411.32153763452-0.378530402915-0.8802742465264.031865892360.5449741882993.019845413360.2488634164510.4201275348320.0454895499748-0.97976963062-0.214673902047-0.396668174673-0.0269370485782-0.05731591182590.1509594141210.665735435887-0.09160190635750.09395570255860.572403283555-0.02460827167140.28876552450420.420922877-5.01104130347-53.506253939
424.006923356770.1364165027272.145065272372.02281511021-0.9479241966173.40998037687-0.3608031315530.0535194309669-0.531035219101-0.3412038538450.128950866406-0.2444186883940.487311675244-0.0207927153070.2490725584050.289496042695-0.002013573160340.1642274061250.291505665816-0.01714776488340.37414153131321.0754529337-4.52363633509-41.128874613
435.34239961369-4.55793060013-3.410739945467.76343657496.10507295075.11765107508-0.06675133678580.242593217864-0.315257127390.1734703501770.112423613964-0.8686003521451.127757508780.4194374704240.06704688885530.4446999145480.1072453529730.1427353162730.377915252162-0.06863734869160.58489385301132.7104019157-6.87632287525-39.8369263958
443.587935214410.1129453862560.7617974943772.644257324310.6836793228594.84906306701-0.4576782683940.807728484090.379351189655-0.8719075494070.0732930058704-0.559501005318-0.2470005403110.2198323264820.2337735833320.390934209351-0.08412172080940.1305918742670.4246843833160.03284871911180.33336107600224.31114542292.305488233-48.2532154897
452.819694262550.03669192487180.5250474542170.0733321689140.3544799741053.75480804861-0.214761022380.698944762478-0.579223258081-0.9070577015710.415007730277-0.6656952834140.7014120115720.1074676105780.05511617549610.674778582964-0.1030048836410.3248162650960.349837280536-0.1434427524990.58705436815825.3601617177-11.1566126106-48.2997741871
464.783897726661.582252916292.888835057563.77570075625-0.765716278445.95042398475-0.0797207820082-0.294271886546-0.472960200445-0.16104016728-0.0612174717088-0.0547113801990.248237029522-1.162914578750.09782981034620.1997610341130.06649186776340.09122933525120.220245637321-0.0435908438740.29121466318115.5610704492-2.59101742155-33.6592133114
471.283255101350.9893585068911.200058580142.055274769710.3929514145441.343321335510.02299015413180.08615626322430.393582229644-1.192582208150.476716054955-0.167465048660.9955627505760.532941433952-0.3075990387981.17948167454-0.1972479079740.3859513129570.740742659589-0.25828630120.66621343996225.8940903347-15.4907277442-60.7570049871
482.680767206080.439009226895-4.147922813395.27016358871-3.910882721278.464954514210.136080638461-0.327767594382-1.327430923010.587685116028-0.127373483359-0.532795583211.55390894710.4738467047650.07497197690240.4954813023230.0397724292468-0.11599760770.222480497020.008548959179510.66805919217131.8097167836-1.04672183433-24.583366412
493.652299676781.652712748411.411486963534.02908304234-0.4934690629662.42503148108-0.30124571110.0785713814727-0.02812507386430.1628966871980.1184153534530.123412442546-0.243146884528-0.3938988464080.1708562234580.2124363740720.1168183015920.02180182364880.276297254144-0.008183690924390.29333306485423.76345634219.40104376484-29.6506337204
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'L' and (resid 1 through 18 )LA1 - 181 - 18
22chain 'L' and (resid 19 through 54 )LA19 - 5419 - 54
33chain 'L' and (resid 55 through 67 )LA55 - 6755 - 67
44chain 'L' and (resid 68 through 96 )LA68 - 9668 - 96
55chain 'L' and (resid 97 through 119 )LA97 - 11997 - 119
66chain 'L' and (resid 120 through 134 )LA120 - 134120 - 134
77chain 'L' and (resid 135 through 156 )LA135 - 156135 - 156
88chain 'L' and (resid 157 through 169 )LA157 - 169157 - 169
99chain 'L' and (resid 170 through 180 )LA170 - 180170 - 180
1010chain 'L' and (resid 181 through 194 )LA181 - 194181 - 194
1111chain 'L' and (resid 195 through 220 )LA195 - 220195 - 220
1212chain 'H' and (resid 1 through 44 )HB1 - 441 - 44
1313chain 'H' and (resid 45 through 167 )HB45 - 16745 - 167
1414chain 'H' and (resid 168 through 225 )HB168 - 225168 - 225
1515chain 'P' and (resid 668 through 685 )PC668 - 6851 - 18
1616chain 'A' and (resid 1 through 25 )AD1 - 251 - 25
1717chain 'A' and (resid 26 through 81 )AD26 - 8126 - 81
1818chain 'A' and (resid 82 through 134 )AD82 - 13482 - 134
1919chain 'A' and (resid 135 through 169 )AD135 - 169135 - 169
2020chain 'A' and (resid 170 through 220 )AD170 - 220170 - 220
2121chain 'B' and (resid 1 through 121 )BE1 - 1211 - 121
2222chain 'B' and (resid 122 through 225 )BE122 - 225122 - 221
2323chain 'C' and (resid 667 through 671 )CF667 - 6711 - 5
2424chain 'C' and (resid 672 through 685 )CF672 - 6856 - 19
2525chain 'D' and (resid 1 through 81 )DG1 - 811 - 81
2626chain 'D' and (resid 82 through 119 )DG82 - 11982 - 119
2727chain 'D' and (resid 120 through 219 )DG120 - 219120 - 219
2828chain 'E' and (resid 1 through 121 )EH1 - 1211 - 121
2929chain 'E' and (resid 122 through 225 )EH122 - 225122 - 220
3030chain 'F' and (resid 667 through 671 )FI667 - 6711 - 5
3131chain 'F' and (resid 672 through 685 )FI672 - 6856 - 19
3232chain 'G' and (resid 1 through 7 )GJ1 - 71 - 7
3333chain 'G' and (resid 8 through 25 )GJ8 - 258 - 25
3434chain 'G' and (resid 26 through 38 )GJ26 - 3826 - 38
3535chain 'G' and (resid 39 through 54 )GJ39 - 5439 - 54
3636chain 'G' and (resid 55 through 67 )GJ55 - 6755 - 67
3737chain 'G' and (resid 68 through 81 )GJ68 - 8168 - 81
3838chain 'G' and (resid 82 through 90 )GJ82 - 9082 - 90
3939chain 'G' and (resid 91 through 108 )GJ91 - 10891 - 108
4040chain 'G' and (resid 109 through 114 )GJ109 - 114109 - 114
4141chain 'I' and (resid 1 through 25 )IK1 - 251 - 25
4242chain 'I' and (resid 26 through 57 )IK26 - 5726 - 57
4343chain 'I' and (resid 58 through 67 )IK58 - 6758 - 67
4444chain 'I' and (resid 68 through 83 )IK68 - 8368 - 83
4545chain 'I' and (resid 84 through 99 )IK84 - 9984 - 99
4646chain 'I' and (resid 100 through 116 )IK100 - 116100 - 116
4747chain 'I' and (resid 117 through 126 )IK117 - 126117 - 126
4848chain 'J' and (resid 667 through 671 )JL667 - 6711 - 5
4949chain 'J' and (resid 672 through 685 )JL672 - 6856 - 19

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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