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- PDB-9e7e: Crystal structure of HIV-1 RRE SLII A31CG39C mutant in complex wi... -

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基本情報

登録情報
データベース: PDB / ID: 9e7e
タイトルCrystal structure of HIV-1 RRE SLII A31CG39C mutant in complex with Fab BL3-6
要素
  • BL3-6 Fab heavy chain
  • BL3-6 Fab light chain
  • Rev Response Element SLII A31C/G39C
キーワードRNA / HIV-1 / Replication / Fab / Chaperone / Rev response element
機能・相同性: / RNA / RNA (> 10)
機能・相同性情報
生物種Homo sapiens (ヒト)
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: 2.75 Å
データ登録者Ojha, M. / Koirala, D.
資金援助 米国, 1件
組織認可番号
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170660-01/SUBK00019302 米国
引用ジャーナル: To Be Published
タイトル: Crystal structure of HIV-1 RRE SLII A31CG39C mutant in complex with Fab BL3-6
著者: Ojha, M. / Koirala, D.
履歴
登録2024年11月1日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年5月28日Provider: repository / タイプ: Initial release

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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
H: BL3-6 Fab heavy chain
L: BL3-6 Fab light chain
R: Rev Response Element SLII A31C/G39C
A: BL3-6 Fab heavy chain
B: BL3-6 Fab light chain
C: Rev Response Element SLII A31C/G39C
F: Rev Response Element SLII A31C/G39C
D: BL3-6 Fab heavy chain
E: BL3-6 Fab light chain
O: Rev Response Element SLII A31C/G39C
G: BL3-6 Fab heavy chain
I: BL3-6 Fab light chain


分子量 (理論値)分子数
合計 (水以外)285,43712
ポリマ-285,43712
非ポリマー00
2,882160
1
H: BL3-6 Fab heavy chain
L: BL3-6 Fab light chain
R: Rev Response Element SLII A31C/G39C


分子量 (理論値)分子数
合計 (水以外)71,3593
ポリマ-71,3593
非ポリマー00
543
タイプ名称対称操作
identity operation1_555x,y,z1
2
A: BL3-6 Fab heavy chain
B: BL3-6 Fab light chain
C: Rev Response Element SLII A31C/G39C


分子量 (理論値)分子数
合計 (水以外)71,3593
ポリマ-71,3593
非ポリマー00
543
タイプ名称対称操作
identity operation1_555x,y,z1
3
F: Rev Response Element SLII A31C/G39C
D: BL3-6 Fab heavy chain
E: BL3-6 Fab light chain


分子量 (理論値)分子数
合計 (水以外)71,3593
ポリマ-71,3593
非ポリマー00
543
タイプ名称対称操作
identity operation1_555x,y,z1
4
O: Rev Response Element SLII A31C/G39C
G: BL3-6 Fab heavy chain
I: BL3-6 Fab light chain


分子量 (理論値)分子数
合計 (水以外)71,3593
ポリマ-71,3593
非ポリマー00
543
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)84.369, 95.645, 111.239
Angle α, β, γ (deg.)77.480, 76.340, 74.250
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 3 through 89 or resid 91 through 139 or resid 141 through 228))
d_2ens_1(chain "D" and (resid 3 through 89 or resid 91 through 139 or resid 141 through 228))
d_3ens_1(chain "H" and (resid 3 through 89 or resid 91 through 139 or resid 141 through 228))
d_1ens_2(chain "B" and (resid 3 through 24 or resid 26...
d_2ens_2(chain "E" and (resid 3 through 24 or resid 26...
d_3ens_2(chain "I" and (resid 3 through 24 or resid 26...
d_4ens_2(chain "L" and (resid 3 through 24 or resid 26...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERLEULEUAD3 - 893 - 89
d_12ens_1ALAALASERSERAD91 - 13991 - 139
d_13ens_1LYSLYSCYSCYSAD141 - 228141 - 228
d_21ens_1SERSERLEULEUDH3 - 893 - 89
d_22ens_1ALAALASERSERDH91 - 13991 - 139
d_23ens_1LYSLYSCYSCYSDH141 - 228141 - 228
d_31ens_1SERSERLEULEUHA3 - 893 - 89
d_32ens_1ALAALASERSERHA91 - 13991 - 139
d_33ens_1LYSLYSCYSCYSHA141 - 228141 - 228
d_11ens_2ILEILECYSCYSBE3 - 243 - 24
d_12ens_2ALAALAGLYGLYBE26 - 10026 - 100
d_13ens_2GLYGLYILEILEBE102 - 107102 - 107
d_14ens_2ARGARGSERSERBE109 - 122109 - 122
d_15ens_2GLUGLUGLUGLUBE124 - 214124 - 214
d_21ens_2ILEILECYSCYSEI3 - 243 - 24
d_22ens_2ALAALAGLYGLYEI26 - 10026 - 100
d_23ens_2GLYGLYILEILEEI102 - 107102 - 107
d_24ens_2ARGARGSERSEREI109 - 122109 - 122
d_25ens_2GLUGLUGLUGLUEI124 - 214124 - 214
d_31ens_2ILEILECYSCYSIL3 - 243 - 24
d_32ens_2ALAALAGLYGLYIL26 - 10026 - 100
d_33ens_2GLYGLYILEILEIL102 - 107102 - 107
d_34ens_2ARGARGSERSERIL109 - 122109 - 122
d_35ens_2GLUGLUGLUGLUIL124 - 214124 - 214
d_41ens_2ILEILECYSCYSLB3 - 243 - 24
d_42ens_2ALAALAGLYGLYLB26 - 10026 - 100
d_43ens_2GLYGLYILEILELB102 - 107102 - 107
d_44ens_2ARGARGSERSERLB109 - 122109 - 122
d_45ens_2GLUGLUGLUGLULB124 - 214124 - 214

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.958059730623, -0.285979431502, -0.0183662003977), (0.284998093635, 0.957550978919, -0.0432690350701), (0.0299606272208, 0.0362199879829, 0.998894625717)-14.995913312, -20.9674739237, 60.9257239063
2given(-0.999960411306, -0.00824318522683, -0.00335048039954), (-0.00641931893502, 0.929054273748, -0.369887751587), (0.00616183138377, -0.369851600412, -0.929070409338)-80.1332335178, -9.03709848223, -46.2968100528
3given(0.963373336837, -0.267302750354, -0.0214721569748), (0.266445863487, 0.963177209586, -0.0360036770976), (0.0303053741498, 0.0289638151378, 0.999120954495)-15.1929430463, -21.4693691853, 61.1095644477
4given(-0.986125406583, -0.112394220108, 0.122164732138), (-0.145300162403, 0.94029624621, -0.307783742536), (-0.080277925344, -0.321263923667, -0.943580916537)-91.9737807874, -48.7149777205, 8.95583682553
5given(-0.999685011872, -0.0222035984338, -0.0116994553206), (-0.0163442706128, 0.929725272288, -0.367890993214), (0.0190457831643, -0.367583892855, -0.929795321486)-79.9634960557, -9.35881734549, -45.9675152712

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要素

#1: 抗体
BL3-6 Fab heavy chain


分子量: 24766.615 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌)
#2: 抗体
BL3-6 Fab light chain


分子量: 23394.891 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌)
#3: RNA鎖
Rev Response Element SLII A31C/G39C


分子量: 23197.859 Da / 分子数: 4 / Mutation: A31C, G39C / 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)
参照: GenBank: 902798
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 160 / 由来タイプ: 天然 / : 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: 2.9 Å3/Da / 溶媒含有率: 57.61 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.1 / 詳細: 0.2 M Ammonium citrate dibasic, 20% PEG 3,350 / PH範囲: 5.0-6.0

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データ収集

回折平均測定温度: 100 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: NSLS-II / ビームライン: 17-ID-2 / 波長: 0.97934 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2024年10月5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: 0.97934 Å / 相対比: 1
反射解像度: 2.75→106.64 Å / Num. obs: 160531 / % possible obs: 99 % / 冗長度: 3.6 % / Biso Wilson estimate: 65.3 Å2 / CC1/2: 0.832 / Rmerge(I) obs: 0.105 / Net I/σ(I): 15.8
反射 シェル解像度: 2.75→2.8 Å / 冗長度: 3.8 % / Rmerge(I) obs: 1.634 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4084 / CC1/2: 0.305 / % possible all: 97.6

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
Aimlessデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.75→49.66 Å / SU ML: 0.5137 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 34.8227
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.293 3904 2.43 %
Rwork0.2503 156627 -
obs0.2513 160531 96.56 %
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: 132.19 Å2
精密化ステップサイクル: LAST / 解像度: 2.75→49.66 Å
タンパク質核酸リガンド溶媒全体
原子数13308 6152 0 170 19630
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.010420492
X-RAY DIFFRACTIONf_angle_d1.356429212
X-RAY DIFFRACTIONf_chiral_restr0.06353516
X-RAY DIFFRACTIONf_plane_restr0.01052652
X-RAY DIFFRACTIONf_dihedral_angle_d18.62678312
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2DAX-RAY DIFFRACTIONTorsion NCS0.619767992694
ens_1d_3DAX-RAY DIFFRACTIONTorsion NCS0.908139370843
ens_2d_2EBX-RAY DIFFRACTIONTorsion NCS0.820555623114
ens_2d_3EBX-RAY DIFFRACTIONTorsion NCS1.79962723375
ens_2d_4EBX-RAY DIFFRACTIONTorsion NCS0.787461836274
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.790.38691380.37825497X-RAY DIFFRACTION93.33
2.79-2.820.38051360.36025483X-RAY DIFFRACTION95.14
2.82-2.860.37861340.35935334X-RAY DIFFRACTION93.98
2.86-2.90.40181370.34235613X-RAY DIFFRACTION95.23
2.9-2.940.36471360.3535461X-RAY DIFFRACTION94.64
2.94-2.980.36421430.34785574X-RAY DIFFRACTION95.92
2.98-3.030.45691390.37555539X-RAY DIFFRACTION95.33
3.03-3.080.3891360.33785492X-RAY DIFFRACTION95.81
3.08-3.130.37481390.32735581X-RAY DIFFRACTION96.13
3.13-3.190.34111400.32125570X-RAY DIFFRACTION96.19
3.19-3.250.34821430.325576X-RAY DIFFRACTION96.54
3.25-3.320.36681360.29925600X-RAY DIFFRACTION96.73
3.32-3.390.33021420.29125649X-RAY DIFFRACTION96.61
3.39-3.470.28731400.2965544X-RAY DIFFRACTION96.96
3.47-3.560.35431400.29695612X-RAY DIFFRACTION96.51
3.56-3.650.38631370.28535613X-RAY DIFFRACTION96.8
3.65-3.760.32681390.26695602X-RAY DIFFRACTION96.85
3.76-3.880.28041390.25315660X-RAY DIFFRACTION97.2
3.88-4.020.33741410.2435641X-RAY DIFFRACTION97.18
4.02-4.180.28361370.2215624X-RAY DIFFRACTION97.48
4.18-4.370.27181430.21695711X-RAY DIFFRACTION98.25
4.37-4.60.25111400.19765656X-RAY DIFFRACTION98.4
4.6-4.890.221440.1965696X-RAY DIFFRACTION98.52
4.89-5.270.27161390.20395754X-RAY DIFFRACTION98.41
5.27-5.790.28671420.22565617X-RAY DIFFRACTION97.91
5.79-6.630.2691400.23925650X-RAY DIFFRACTION97.74
6.63-8.350.27811420.23955740X-RAY DIFFRACTION98.39
8.35-49.660.21731420.20435538X-RAY DIFFRACTION95.56
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)
18.820079172415.48765298063-3.092071632066.06152593671-0.3129670217883.056922433540.0608544545426-0.303721111097-1.06118312317-0.554269764887-0.0838768813972-0.7594014982910.1746032263090.198296045740.003693550568220.4576337154710.147584149232-0.1139318180960.5410187528780.1356069892330.626298470613-27.7821021342-1.44921431582-10.5564955857
25.373153169322.05034317044-0.03525465847761.317860922730.0481281558071.3995027420.654487075315-0.7532946293780.06525648531310.321847458817-0.452827806837-0.0524706304763-0.332129303454-0.0279099364208-0.1910559361020.605409597743-0.0507387609784-0.03661629811980.504021976549-0.001596702490530.499100024134-32.91667399391.14901904076-4.0418803146
33.604595156421.56569424685-2.324274617332.212323178860.5292227335243.03591997303-0.779292031033-1.339139855960.1256350527020.2911420659850.9469082588791.1069219545-1.23465384266-0.700348426728-0.1338374625270.7391950797850.362387047597-0.113149495190.841991117570.02283627853190.75770402309-72.13553824180.778322486472-14.1166995178
43.428885276690.92730131302-1.278561175423.85778542591.633820160591.607189726470.0860422481145-0.05085695971210.300585454271-0.836439991161-0.415017282226-0.2987378236210.08673651627330.01416776718520.3212513449140.4253635409370.21904601946-0.00325081944860.5730521083720.03049454365540.511192699848-58.7789027684-2.32018053808-14.8044045683
54.079891864580.2843348464490.7861907845785.31221850316-0.4404563160743.410882494070.1414825740690.7248004872790.354431072983-0.757143969409-0.005622425329340.834767753884-0.130475712695-0.929885633804-0.1286034256670.694096768030.3114177173-0.1189511258690.8239084005360.04909608220010.648390565067-67.701061859-4.92073921713-19.6182371491
63.639685894240.81912169199-0.4937254421861.701803020910.6090061221930.6152011328090.481790950127-1.193433970141.097412723630.337945129138-0.2324805417090.432523784365-0.75937295339-0.271943669319-0.003146400842931.03226377718-0.07730596649620.1917608359940.623100259815-0.3303754930130.935208373028-39.464638653621.6172237713-1.1521462071
73.48745995054-0.680253739707-0.7728427148660.1515569736770.02494277094561.416098714210.273165452683-0.078540478081.038743517650.156754173004-0.2052456133530.351439186953-1.118248059970.0682881473052-0.0007625983063261.041400479590.05065839192270.1794155799910.381362681499-0.1041410452191.04639145607-39.112354823320.6326250862-7.84221923697
83.40563307190.1205638645090.1976266450674.95283254403-0.900743911941.746642690080.154121854304-0.8637693961350.427102206799-0.0789932899637-0.1984510920910.231227371978-0.650654956864-0.511512907171-0.05888054873020.6942983577490.403762120712-0.09512517765460.907358334619-0.1703014281950.703666814165-67.17002015425.29981285734-5.84093360965
91.46228681810.229467063928-0.4821737619345.55413931761-1.725317791433.01817403693-0.0103153860576-0.6909090448010.8012475781610.5856987624380.4250104238230.894841107197-0.473552933528-1.38690470905-0.3531929118010.567725394870.49907193304-0.03901054466361.07503987751-0.1138540967140.88869454361-74.01917537794.0862818473-2.07224349725
104.57293367749-1.10185476389-0.9218722034775.418066794162.525330813663.34744620689-0.7521237923530.9755205254820.162442034822.0453195017-0.610103497984-1.5374424081.91284228361.609432417430.7741785128772.250223271790.00687799123911-0.1745063897872.520816977940.5125390746021.56484916603-6.6030966076122.975373580730.4797838918
113.69893398544-1.80518329413-0.632703382032.63406444148-2.780754152075.52620851583-1.358629909170.43218814679-1.5579102875-3.575630443390.4194332825413.271873459251.45080465325-0.2945092936140.3762681032554.136296897240.446004956783-1.818807803794.21735307794-1.026904438234.95092126411-4.152280427643.9724200437330.7606741636
127.419790799021.521054318286.095860520555.386496139135.363083690298.36829844751-1.49953201365-0.900029968906-0.02054772689031.519673310180.136993561853-1.60342745235-0.4560118725212.766264511971.564202253121.49666253798-0.402514513459-0.3424695115422.747591826860.2729335553031.713517718252.8903741710119.900935931817.4218796413
135.105009916070.877857623105-0.9327208195084.38728893847-2.138027366672.655235594570.271784410505-1.132883106870.1203510249480.5344279333220.069836203543-1.10439932138-1.004637065030.43252484129-0.4693180959110.88758400823-0.3589668103870.01416548358760.981145753486-0.1462628856170.957942571022-8.6238875464115.94150443251.91745049461
146.85757774076.13811018147-2.106619122347.24661651298-4.511796507494.628934858120.6566460118480.286788111554-1.039699399240.7737768767490.349422633697-1.07796712479-1.7401302351-0.533623833045-0.08045423648991.844555994170.0770122168712-0.02225192387851.74166818046-0.2332067974991.08130623611-13.423519328527.64187243528.1424195537
158.7221114876-1.94686748761-0.9710556351941.95693336875-0.4715912298975.710880242110.0470647911863-0.773700205714-0.418634012306-0.01715556478940.37612678209-0.430269122718-1.05093033028-0.086312233130.02100531707210.9361298389080.0795993500561-0.2569104131020.2924692808370.07115022087330.586367777994-46.5519978415-8.8556038725-35.3944657127
163.435714517970.331826348641.964013500043.295343667990.5052461638795.348234901510.02297760985490.13842419322-0.244855488267-0.514062357850.125657347815-0.300638629877-0.952547867554-0.299713648273-0.1491130821880.995700604220.0901439137864-0.009754902734130.31530058026-0.03975917116510.520278690648-51.4295474046-7.35658508869-43.6156980278
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503.32440893412-2.13471879868-0.9038712583938.708310624350.7508181405771.84700649930.1382467421392.55603728541-0.14479799739-1.20889760139-1.006203741650.7152887949010.409782618914-0.3573168797620.6412914579750.7529037132570.138903202847-0.08186086187621.70876421898-0.09552095024611.01652148082-27.4985110874-14.003240384591.0186468972
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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 'H' and (resid 3 through 36 )HA3 - 361 - 34
22chain 'H' and (resid 37 through 136 )HA37 - 13635 - 134
33chain 'H' and (resid 137 through 157 )HA137 - 157135 - 155
44chain 'H' and (resid 158 through 187 )HA158 - 187156 - 185
55chain 'H' and (resid 188 through 228 )HA188 - 228186 - 226
66chain 'L' and (resid 1 through 39 )LB1 - 391 - 39
77chain 'L' and (resid 40 through 114 )LB40 - 11440 - 114
88chain 'L' and (resid 115 through 173 )LB115 - 173115 - 173
99chain 'L' and (resid 174 through 215 )LB174 - 215174 - 215
1010chain 'R' and (resid 1 through 15 )RC1 - 15
1111chain 'R' and (resid 16 through 35 )RC16 - 35
1212chain 'R' and (resid 36 through 45 )RC36 - 45
1313chain 'R' and (resid 46 through 60 )RC46 - 60
1414chain 'R' and (resid 61 through 72 )RC61 - 72
1515chain 'A' and (resid 3 through 20 )AD3 - 201 - 18
1616chain 'A' and (resid 21 through 102 )AD21 - 10219 - 100
1717chain 'A' and (resid 103 through 189 )AD103 - 189101 - 187
1818chain 'A' and (resid 190 through 228 )AD190 - 228188 - 226
1919chain 'B' and (resid 1 through 26 )BE1 - 261 - 26
2020chain 'B' and (resid 27 through 39 )BE27 - 3927 - 39
2121chain 'B' and (resid 40 through 62 )BE40 - 6240 - 62
2222chain 'B' and (resid 63 through 103 )BE63 - 10363 - 103
2323chain 'B' and (resid 104 through 114 )BE104 - 114104 - 114
2424chain 'B' and (resid 115 through 129 )BE115 - 129115 - 129
2525chain 'B' and (resid 130 through 151 )BE130 - 151130 - 151
2626chain 'B' and (resid 152 through 164 )BE152 - 164152 - 164
2727chain 'B' and (resid 165 through 175 )BE165 - 175165 - 175
2828chain 'B' and (resid 176 through 198 )BE176 - 198176 - 198
2929chain 'B' and (resid 199 through 215 )BE199 - 215199 - 215
3030chain 'C' and (resid 1 through 10 )CF1 - 10
3131chain 'C' and (resid 11 through 35 )CF11 - 35
3232chain 'C' and (resid 36 through 55 )CF36 - 55
3333chain 'C' and (resid 56 through 72 )CF56 - 72
3434chain 'F' and (resid 1 through 10 )FG1 - 10
3535chain 'F' and (resid 11 through 20 )FG11 - 20
3636chain 'F' and (resid 21 through 25 )FG21 - 25
3737chain 'F' and (resid 26 through 30 )FG26 - 30
3838chain 'F' and (resid 31 through 40 )FG31 - 40
3939chain 'F' and (resid 41 through 45 )FG41 - 45
4040chain 'F' and (resid 46 through 60 )FG46 - 60
4141chain 'F' and (resid 61 through 65 )FG61 - 65
4242chain 'F' and (resid 66 through 72 )FG66 - 72
4343chain 'D' and (resid 3 through 36 )DH3 - 361 - 34
4444chain 'D' and (resid 37 through 102 )DH37 - 10235 - 100
4545chain 'D' and (resid 103 through 157 )DH103 - 157101 - 155
4646chain 'D' and (resid 158 through 228 )DH158 - 228156 - 226
4747chain 'E' and (resid 1 through 76 )EI1 - 761 - 76
4848chain 'E' and (resid 77 through 114 )EI77 - 11477 - 114
4949chain 'E' and (resid 115 through 215 )EI115 - 215115 - 215
5050chain 'O' and (resid 1 through 10 )OJ1 - 10
5151chain 'O' and (resid 11 through 40 )OJ11 - 40
5252chain 'O' and (resid 41 through 60 )OJ41 - 60
5353chain 'O' and (resid 61 through 72 )OJ61 - 72
5454chain 'G' and (resid 3 through 115 )GK3 - 1151 - 113
5555chain 'G' and (resid 116 through 228 )GK116 - 228114 - 226
5656chain 'I' and (resid 1 through 49 )IL1 - 491 - 49
5757chain 'I' and (resid 50 through 114 )IL50 - 11450 - 114
5858chain 'I' and (resid 115 through 175 )IL115 - 175115 - 175
5959chain 'I' and (resid 176 through 215 )IL176 - 215176 - 215

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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