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- PDB-8odp: Structure of human RTCB with GMPCPP in complex with Archease -

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基本情報

登録情報
データベース: PDB / ID: 8odp
タイトルStructure of human RTCB with GMPCPP in complex with Archease
要素
  • Protein archease
  • RNA-splicing ligase RtcB homolog
キーワードLIGASE / archease / RTCB / human / tRNA / GMPCPP
機能・相同性
機能・相同性情報


tRNA-splicing ligase complex / 3'-phosphate/5'-hydroxy nucleic acid ligase / RNA ligase (GTP) activity / tRNA splicing, via endonucleolytic cleavage and ligation / vinculin binding / tRNA processing in the nucleus / tRNA processing / placenta development / nuclear envelope / in utero embryonic development ...tRNA-splicing ligase complex / 3'-phosphate/5'-hydroxy nucleic acid ligase / RNA ligase (GTP) activity / tRNA splicing, via endonucleolytic cleavage and ligation / vinculin binding / tRNA processing in the nucleus / tRNA processing / placenta development / nuclear envelope / in utero embryonic development / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / GTP binding / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
RNA-splicing ligase RtcB homologue, eukaryotic / Archease / Archease domain / Archease domain superfamily / Archease protein family (MTH1598/TM1083) / Uncharacterized protein family UPF0027 signature. / RNA-splicing ligase, RtcB / tRNA-splicing ligase RtcB-like superfamily / tRNA-splicing ligase RtcB
類似検索 - ドメイン・相同性
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / Protein archease / RNA-splicing ligase RtcB homolog
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: 2.3 Å
データ登録者Kopp, J. / Gerber, J.L. / Peschek, J.
資金援助 ドイツ, 1件
組織認可番号国
German Research Foundation (DFG)442512666 ドイツ
引用ジャーナル: Nat Commun / 年: 2024
タイトル: Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease.
著者: Gerber, J.L. / Morales Guzman, S.I. / Worf, L. / Hubbe, P. / Kopp, J. / Peschek, J.
履歴
登録2023年3月9日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年3月27日Provider: repository / タイプ: Initial release
改定 1.12024年4月17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

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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: RNA-splicing ligase RtcB homolog
B: Protein archease
C: RNA-splicing ligase RtcB homolog
D: Protein archease
E: RNA-splicing ligase RtcB homolog
F: Protein archease
G: RNA-splicing ligase RtcB homolog
H: Protein archease
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)308,82824
ポリマ－306,0848
非ポリマー2,74416
水5,350297
1
A: RNA-splicing ligase RtcB homolog
B: Protein archease
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,2076
ポリマ－76,5212
非ポリマー6864
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: RNA-splicing ligase RtcB homolog
D: Protein archease
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,2076
ポリマ－76,5212
非ポリマー6864
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: RNA-splicing ligase RtcB homolog
F: Protein archease
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,2076
ポリマ－76,5212
非ポリマー6864
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: RNA-splicing ligase RtcB homolog
H: Protein archease
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,2076
ポリマ－76,5212
非ポリマー6864
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)98.433, 122.597, 124.759
Angle α, β, γ (deg.)90.000, 107.880, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-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 4 through 9 or resid 11...
d_2ens_1(chain "C" and (resid 4 through 9 or resid 11...
d_3ens_1(chain "E" and (resid 4 through 9 or resid 11...
d_4ens_1(chain "G" and (resid 4 through 9 or resid 11...
d_1ens_2(chain "B" and (resid 42 through 85 or resid 87...
d_2ens_2(chain "D" and (resid 42 through 85 or resid 87...
d_3ens_2(chain "F" and (resid 42 through 85 or resid 87...
d_4ens_2(chain "H" and (resid 42 through 85 or resid 87...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERLEUA4 - 9
d_12ens_1PHEASNA11 - 16
d_13ens_1ASNLEUA18 - 50
d_14ens_1ASNALAA52 - 53
d_15ens_1GLYALAA56 - 165
d_16ens_1ASPLEUA167 - 200
d_17ens_1ALAASNA202 - 239
d_18ens_1ALAALAA242 - 243
d_19ens_1LYSMETA245 - 281
d_110ens_1ASPASPA284
d_111ens_1ILEGLUA286 - 367
d_112ens_1THRSERA369 - 439
d_113ens_1ASNASPA442 - 450
d_114ens_1LEUALAA452 - 458
d_115ens_1ARGGLYA460 - 505
d_21ens_1SERLEUI3 - 8
d_22ens_1PHEASNI10 - 15
d_23ens_1ASNLEUI17 - 49
d_24ens_1ASNALAI51 - 52
d_25ens_1GLYALAI55 - 164
d_26ens_1ASPLEUI166 - 199
d_27ens_1ALAASNI201 - 238
d_28ens_1ALAALAI241 - 242
d_29ens_1LYSMETI244 - 280
d_210ens_1ASPASPI283
d_211ens_1ILEGLUI285 - 366
d_212ens_1THRSERI368 - 438
d_213ens_1ASNASPI441 - 449
d_214ens_1LEUALAI451 - 457
d_215ens_1ARGGLYI459 - 504
d_31ens_1SERLEUQ2 - 7
d_32ens_1PHEASNQ9 - 14
d_33ens_1ASNLEUQ16 - 48
d_34ens_1ASNALAQ50 - 51
d_35ens_1GLYALAQ54 - 163
d_36ens_1ASPLEUQ165 - 198
d_37ens_1ALAASNQ200 - 237
d_38ens_1ALAALAQ240 - 241
d_39ens_1LYSMETQ243 - 279
d_310ens_1ASPASPQ282
d_311ens_1ILEGLUQ284 - 365
d_312ens_1THRSERQ367 - 437
d_313ens_1ASNASPQ440 - 448
d_314ens_1LEUALAQ450 - 456
d_315ens_1ARGGLYQ458 - 503
d_41ens_1SERLEUY3 - 8
d_42ens_1PHEASNY10 - 15
d_43ens_1ASNLEUY17 - 49
d_44ens_1ASNALAY51 - 52
d_45ens_1GLYALAY55 - 164
d_46ens_1ASPLEUY166 - 199
d_47ens_1ALAASNY201 - 238
d_48ens_1ALAALAY241 - 242
d_49ens_1LYSMETY244 - 280
d_410ens_1ASPASPY283
d_411ens_1ILEGLUY285 - 366
d_412ens_1THRSERY368 - 438
d_413ens_1ASNASPY441 - 449
d_414ens_1LEUALAY451 - 457
d_415ens_1ARGGLYY459 - 504
d_11ens_2LYSLEUF33 - 76
d_12ens_2THRTHRF78 - 83
d_13ens_2GLYGLNF85 - 121
d_14ens_2ASNTYRF123 - 157
d_15ens_2GLUILEF160 - 170
d_21ens_2LYSLEUN30 - 73
d_22ens_2THRTHRN75 - 80
d_23ens_2GLYGLNN82 - 118
d_24ens_2ASNTYRN120 - 154
d_25ens_2GLUILEN157 - 167
d_31ens_2LYSLEUV30 - 73
d_32ens_2THRTHRV75 - 80
d_33ens_2GLYGLNV82 - 118
d_34ens_2ASNTYRV120 - 154
d_35ens_2GLUILEV157 - 167
d_41ens_2LYSLEUH32 - 75
d_42ens_2THRTHRH77 - 82
d_43ens_2GLYGLNH84 - 120
d_44ens_2ASNTYRH122 - 156
d_45ens_2GLUILEH159 - 169

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(-0.657067112034, 0.529224794582, 0.536827651191), (-0.161764707611, -0.794530401868, 0.585280804298), (0.736271002862, 0.297728999776, 0.607669690734)-66.9998719218, 67.1994660875, -13.0764078441
2given(0.664738228597, -0.519881366603, -0.536513235719), (-0.56874925183, -0.817813250337, 0.0877825501746), (-0.484404145301, 0.246789084507, -0.839313869648)47.1770868582, 90.8968037572, 53.846143992
3given(-0.999923520308, 0.0122797000615, -0.00147054483017), (0.0107738112649, 0.806511419595, -0.591120338894), (-0.00607276926331, -0.591090973565, -0.80658203702)-19.8098506218, 26.9990879934, 84.4347754797
4given(-0.674710602049, 0.511321335213, 0.532274455182), (-0.130967942052, -0.792655043296, 0.595437133954), (0.726369741687, 0.33203685713, 0.601779464479)-65.1521961279, 65.9372717999, -14.651514008
5given(0.671884183082, -0.519072296529, -0.528332845374), (-0.55647529894, -0.824529358327, 0.102403998585), (-0.488781020698, 0.225200551136, -0.842839145729)46.3851664095, 90.3807306683, 55.417775032
6given(-0.99995906982, 0.00878263132301, -0.00217349293425), (0.00841373408778, 0.814340839408, -0.58032594837), (-0.00332682479118, -0.580320482716, -0.814381403015)-19.4749266987, 25.844089692, 84.134402531

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要素

#1: タンパク質
RNA-splicing ligase RtcB homolog / 3'-phosphate/5'-hydroxy nucleic acid ligase


分子量: 55412.320 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RTCB, C22orf28, HSPC117
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: Q9Y3I0, 3'-phosphate/5'-hydroxy nucleic acid ligase
#2: タンパク質
Protein archease


分子量: 21108.562 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ZBTB8OS / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: A8K0B5
#3: 化合物
ChemComp-MN / MANGANESE (II) ION


分子量: 54.938 Da / 分子数: 12 / 由来タイプ: 合成 / 式: Mn
#4: 化合物
ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMPCPP


分子量: 521.208 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C11H18N5O13P3 / タイプ: SUBJECT OF INVESTIGATION
コメント: GMP-CPP, エネルギー貯蔵分子類似体*YM
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 297 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY

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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: 2.34 Å3/Da / 溶媒含有率: 47.45 %
結晶化温度: 291.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.2 M potassium nitrate, 20% w/v PEG 3350

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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: ESRF / ビームライン: ID23-1 / 波長: 0.97625 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2022年5月10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: 0.97625 Å / 相対比: 1
反射解像度: 2.3→122.6 Å / Num. obs: 124773 / % possible obs: 99.8 % / 冗長度: 7 % / Biso Wilson estimate: 50.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.039 / Net I/σ(I): 11.4
反射 シェル解像度: 2.3→2.34 Å / Rmerge(I) obs: 1.161 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6124 / CC1/2: 0.786 / Rpim(I) all: 0.465

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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
XDS20210205データ削減
Aimless1.12.10データスケーリング
PHASER2.8.3位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.3→51.29 Å / SU ML: 0.2766 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.1046
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2158 6255 5.02 %
Rwork0.1807 118423 -
obs0.1825 124678 99.71 %
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
原子変位パラメータBiso mean: 63.07 Å2
精密化ステップサイクル: LAST / 解像度: 2.3→51.29 Å
タンパク質核酸リガンド溶媒全体
原子数20977 0 140 297 21414
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003321534
X-RAY DIFFRACTIONf_angle_d0.673829139
X-RAY DIFFRACTIONf_chiral_restr0.0473167
X-RAY DIFFRACTIONf_plane_restr0.00483817
X-RAY DIFFRACTIONf_dihedral_angle_d12.58957960
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.560827643408
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.578433185178
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.523181640755
ens_2d_2FX-RAY DIFFRACTIONTorsion NCS0.437614074454
ens_2d_3FX-RAY DIFFRACTIONTorsion NCS0.513478187607
ens_2d_4FX-RAY DIFFRACTIONTorsion NCS0.414101163398
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.36861910.29563904X-RAY DIFFRACTION99.39
2.33-2.350.31572020.2793970X-RAY DIFFRACTION99.33
2.35-2.380.29512090.27153905X-RAY DIFFRACTION99.28
2.38-2.410.29781890.25943926X-RAY DIFFRACTION99.35
2.41-2.440.33352260.26423912X-RAY DIFFRACTION99.59
2.44-2.480.29681990.25253904X-RAY DIFFRACTION99.81
2.48-2.510.29372000.2523957X-RAY DIFFRACTION99.24
2.51-2.550.32052260.28013907X-RAY DIFFRACTION99.71
2.55-2.590.32962110.26273940X-RAY DIFFRACTION99.64
2.59-2.630.2782240.2463851X-RAY DIFFRACTION99.46
2.63-2.680.29282250.23863935X-RAY DIFFRACTION99.69
2.68-2.730.28962170.2383937X-RAY DIFFRACTION99.74
2.73-2.780.25432380.21083927X-RAY DIFFRACTION99.78
2.78-2.840.28032010.20973972X-RAY DIFFRACTION99.88
2.84-2.90.2522120.21433930X-RAY DIFFRACTION99.86
2.9-2.970.28411780.22043997X-RAY DIFFRACTION99.81
2.97-3.040.25982140.22393877X-RAY DIFFRACTION99.9
3.04-3.120.26081880.23064000X-RAY DIFFRACTION99.76
3.12-3.210.27271950.22793942X-RAY DIFFRACTION99.83
3.21-3.320.24932010.21263975X-RAY DIFFRACTION99.93
3.32-3.440.24042030.18793944X-RAY DIFFRACTION99.9
3.44-3.570.20972130.18033981X-RAY DIFFRACTION100
3.57-3.740.20662090.17363926X-RAY DIFFRACTION100
3.74-3.930.1962210.16793998X-RAY DIFFRACTION99.95
3.93-4.180.19251930.15313954X-RAY DIFFRACTION99.95
4.18-4.50.16372310.13333957X-RAY DIFFRACTION99.98
4.5-4.950.1562060.12993967X-RAY DIFFRACTION99.88
4.95-5.670.15982300.14333978X-RAY DIFFRACTION99.74
5.67-7.140.18892010.15243989X-RAY DIFFRACTION99.71
7.14-51.290.15952020.13554061X-RAY DIFFRACTION99.37
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)
10.412090564073-0.119767331815-0.4393755143890.629079457378-0.1706863951510.7756332861320.0474439455083-0.258384811588-0.03266136704290.240855601249-0.122859857646-0.01140708309710.1297867918-0.277299123824-0.0001823323281440.56576324445-0.08205931445740.04443325208190.515757333871-0.04371698829360.50680468909417.64359.97480.341
20.6625768444570.435047729899-0.1058757412370.9188747992730.142874070830.66074231798-0.0290895333142-0.100212379356-0.03494000366190.1160052773360.001500562291630.04296885428560.0356772338494-0.06136008368940.000103745381840.3481775375660.0171142449923-4.58081015042E-60.301730360155-0.02101894018080.38976995597329.15566.32865.487
30.2223534746060.005621571839830.3191502089271.00257876324-0.1233746900391.049179342770.007663542380950.0700188051638-0.0358402472979-0.0494417795412-0.0110747890339-0.1371065934450.04954993276620.24394850385-7.28413541375E-50.343633687910.01701637119250.02442831927320.380783544418-0.07966281363340.4678300054645.68863.91450.86
40.706953244492-0.360278264621-0.4180440673920.60239406161-0.4148085936230.8755116842960.06324413976060.07544447996390.1357903789440.219385935289-0.0531367844212-0.0874986617583-0.1132897195650.239517335860.0008211948953210.400957799882-0.007243566662340.0219489919240.269988965472-0.03534211881980.46979138153343.06783.57964.366
50.2380831995240.4037453280630.001885063682630.3541436508410.1942038954370.09640125098590.0144452318501-0.0765371085097-0.3644401432850.0784737809637-0.048858987145-0.05597879698050.314245475413-0.007122453820324.849852571330.4327364690930.0218349128323-0.01443192869530.2637208915020.02352001739020.48497882410131.7846.1762.059
60.2970798909440.4042034096050.1666112355851.01572648590.3906109656160.349686569116-0.054639178344-0.00188304317773-0.1039133574530.01630845136060.172935058409-0.2932387410910.1178465939140.03854019419540.0001453046763180.3170765529590.02305104579310.04526953739310.356071428637-0.04795474294170.4391644604245.32468.19456.899
71.012939403840.7414239385890.4541691309990.9681397042810.5098340015060.2493643546850.0216876082368-0.249790894503-0.03845932909920.3600026723130.0295231717511-0.169993355363-0.0101958771389-0.00476115705849-0.000362431870.4531971688340.02768603126620.0139151639260.396418010559-0.01061782615130.49734126406342.75367.88472.172
81.078970871160.540308557216-0.04852884692721.504014004830.4363424068340.6065546256070.0604312219485-0.09630276193490.155012506604-0.021960325770.0440615566890.2751698693880.00895518565544-0.0932531625471-0.0001832225830.4354003298980.02695883630130.01962388691870.282037827067-0.02810326695970.53363903110827.62677.15761.576
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331.067172632020.2613514765870.3073945586690.3236344353160.01402589116521.29896653062-0.08594839026170.2745354090190.0203754145249-0.113539522052-0.00913071159919-0.119540373515-0.04144508000180.448025608666-0.006055811768130.645591006121-0.0932743891057-0.1345318454060.696413872108-0.01574405583090.517400392451-51.82344.47-3.731
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:32 )A1 - 32
2X-RAY DIFFRACTION2( CHAIN A AND RESID 33:150 )A33 - 150
3X-RAY DIFFRACTION3( CHAIN A AND RESID 151:234 )A151 - 234
4X-RAY DIFFRACTION4( CHAIN A AND RESID 235:262 )A235 - 262
5X-RAY DIFFRACTION5( CHAIN A AND RESID 263:300 )A263 - 300
6X-RAY DIFFRACTION6( CHAIN A AND RESID 301:363 )A301 - 363
7X-RAY DIFFRACTION7( CHAIN A AND RESID 364:407 )A364 - 407
8X-RAY DIFFRACTION8( CHAIN A AND RESID 408:505 )A408 - 505
9X-RAY DIFFRACTION9( CHAIN B AND RESID 10:19 )B10 - 19
10X-RAY DIFFRACTION10( CHAIN B AND RESID 20:34 )B20 - 34
11X-RAY DIFFRACTION11( CHAIN B AND RESID 35:51 )B35 - 51
12X-RAY DIFFRACTION12( CHAIN B AND RESID 52:85 )B52 - 85
13X-RAY DIFFRACTION13( CHAIN B AND RESID 86:125 )B86 - 125
14X-RAY DIFFRACTION14( CHAIN B AND RESID 126:179 )B126 - 179
15X-RAY DIFFRACTION15( CHAIN C AND RESID 2:112 )C2 - 112
16X-RAY DIFFRACTION16( CHAIN C AND RESID 113:262 )C113 - 262
17X-RAY DIFFRACTION17( CHAIN C AND RESID 263:300 )C263 - 300
18X-RAY DIFFRACTION18( CHAIN C AND RESID 301:505 )C301 - 505
19X-RAY DIFFRACTION19( CHAIN D AND RESID 13:35 )D13 - 35
20X-RAY DIFFRACTION20( CHAIN D AND RESID 36:60 )D36 - 60
21X-RAY DIFFRACTION21( CHAIN D AND RESID 61:153 )D61 - 153
22X-RAY DIFFRACTION22( CHAIN D AND RESID 154:179 )D154 - 179
23X-RAY DIFFRACTION23( CHAIN E AND RESID 3:113 )E3 - 113
24X-RAY DIFFRACTION24( CHAIN E AND RESID 114:262 )E114 - 262
25X-RAY DIFFRACTION25( CHAIN E AND RESID 263:300 )E263 - 300
26X-RAY DIFFRACTION26( CHAIN E AND RESID 301:505 )E301 - 505
27X-RAY DIFFRACTION27( CHAIN F AND RESID 13:26 )F13 - 26
28X-RAY DIFFRACTION28( CHAIN F AND RESID 27:51 )F27 - 51
29X-RAY DIFFRACTION29( CHAIN F AND RESID 52:125 )F52 - 125
30X-RAY DIFFRACTION30( CHAIN F AND RESID 126:153 )F126 - 153
31X-RAY DIFFRACTION31( CHAIN F AND RESID 154:179 )F154 - 179
32X-RAY DIFFRACTION32( CHAIN G AND RESID 2:52 )G2 - 52
33X-RAY DIFFRACTION33( CHAIN G AND RESID 53:164 )G53 - 164
34X-RAY DIFFRACTION34( CHAIN G AND RESID 165:262 )G165 - 262
35X-RAY DIFFRACTION35( CHAIN G AND RESID 263:300 )G263 - 300
36X-RAY DIFFRACTION36( CHAIN G AND RESID 301:435 )G301 - 435
37X-RAY DIFFRACTION37( CHAIN G AND RESID 436:505 )G436 - 505
38X-RAY DIFFRACTION38( CHAIN H AND RESID 11:20 )H11 - 20
39X-RAY DIFFRACTION39( CHAIN H AND RESID 21:32 )H21 - 32
40X-RAY DIFFRACTION40( CHAIN H AND RESID 33:42 )H33 - 42
41X-RAY DIFFRACTION41( CHAIN H AND RESID 43:60 )H43 - 60
42X-RAY DIFFRACTION42( CHAIN H AND RESID 61:85 )H61 - 85
43X-RAY DIFFRACTION43( CHAIN H AND RESID 86:96 )H86 - 96
44X-RAY DIFFRACTION44( CHAIN H AND RESID 97:125 )H97 - 125
45X-RAY DIFFRACTION45( CHAIN H AND RESID 126:143 )H126 - 143
46X-RAY DIFFRACTION46( CHAIN H AND RESID 144:153 )H144 - 153
47X-RAY DIFFRACTION47( CHAIN H AND RESID 154:179 )H154 - 179

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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る