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- PDB-7rgu: The crystal structure of RocC bound to a transcriptional terminator -

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基本情報

登録情報
データベース: PDB / ID: 7rgu
タイトルThe crystal structure of RocC bound to a transcriptional terminator
要素
  • Modified SL3 of RocR
  • Repressor of competence, RNA Chaperone
キーワードRNA BINDING PROTEIN/RNA / RNA chaperone / RNA binding protein / FinO / ProQ / RNA BINDING PROTEIN-RNA complex
機能・相同性
機能・相同性情報


RNA strand-exchange activity / RNA strand annealing activity / post-transcriptional regulation of gene expression
類似検索 - 分子機能
RNA chaperone ProQ / ProQ/FinO domain superfamily / ProQ/FINO family / ProQ/FinO domain / ProQ/FINO family
類似検索 - ドメイン・相同性
RNA / RNA (> 10) / ProP effector
類似検索 - 構成要素
生物種Legionella pneumophila (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.2 Å
データ登録者Kim, H.J. / Edwards, R.A. / Glover, J.N.M.
資金援助 カナダ, 1件
組織認可番号国
Natural Sciences and Engineering Research Council (NSERC, Canada) カナダ
引用ジャーナル: Nat Commun / 年: 2022
タイトル: Structural basis for recognition of transcriptional terminator structures by ProQ/FinO domain RNA chaperones.
著者: Kim, H.J. / Black, M. / Edwards, R.A. / Peillard-Fiorente, F. / Panigrahi, R. / Klingler, D. / Eidelpes, R. / Zeindl, R. / Peng, S. / Su, J. / Omar, A.R. / MacMillan, A.M. / Kreutz, C. / ...著者: Kim, H.J. / Black, M. / Edwards, R.A. / Peillard-Fiorente, F. / Panigrahi, R. / Klingler, D. / Eidelpes, R. / Zeindl, R. / Peng, S. / Su, J. / Omar, A.R. / MacMillan, A.M. / Kreutz, C. / Tollinger, M. / Charpentier, X. / Attaiech, L. / Glover, J.N.M.
履歴
登録2021年7月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年11月9日Provider: repository / タイプ: Initial release
改定 1.12022年11月30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 1.22024年4月3日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Repressor of competence, RNA Chaperone
B: Modified SL3 of RocR
C: Repressor of competence, RNA Chaperone
D: Modified SL3 of RocR
E: Repressor of competence, RNA Chaperone
F: Modified SL3 of RocR
G: Repressor of competence, RNA Chaperone
H: Modified SL3 of RocR
I: Repressor of competence, RNA Chaperone
K: Repressor of competence, RNA Chaperone
M: Repressor of competence, RNA Chaperone
O: Repressor of competence, RNA Chaperone
Q: Repressor of competence, RNA Chaperone
S: Repressor of competence, RNA Chaperone


分子量 (理論値)分子数
合計 (水以外)168,21614
ポリマ－168,21614
非ポリマー00
水00
1
A: Repressor of competence, RNA Chaperone
B: Modified SL3 of RocR


分子量 (理論値)分子数
合計 (水以外)22,1402
ポリマ－22,1402
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Repressor of competence, RNA Chaperone
D: Modified SL3 of RocR


分子量 (理論値)分子数
合計 (水以外)22,1402
ポリマ－22,1402
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Repressor of competence, RNA Chaperone
F: Modified SL3 of RocR


分子量 (理論値)分子数
合計 (水以外)22,1402
ポリマ－22,1402
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Repressor of competence, RNA Chaperone
H: Modified SL3 of RocR


分子量 (理論値)分子数
合計 (水以外)22,1402
ポリマ－22,1402
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
5
I: Repressor of competence, RNA Chaperone


分子量 (理論値)分子数
合計 (水以外)13,2761
ポリマ－13,2761
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
6
K: Repressor of competence, RNA Chaperone


分子量 (理論値)分子数
合計 (水以外)13,2761
ポリマ－13,2761
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
7
M: Repressor of competence, RNA Chaperone


分子量 (理論値)分子数
合計 (水以外)13,2761
ポリマ－13,2761
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
8
O: Repressor of competence, RNA Chaperone


分子量 (理論値)分子数
合計 (水以外)13,2761
ポリマ－13,2761
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
9
Q: Repressor of competence, RNA Chaperone


分子量 (理論値)分子数
合計 (水以外)13,2761
ポリマ－13,2761
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
10
S: Repressor of competence, RNA Chaperone


分子量 (理論値)分子数
合計 (水以外)13,2761
ポリマ－13,2761
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)87.809, 135.939, 156.756
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
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 26 through 43 or resid 46...
d_2ens_1(chain "C" and (resid 26 through 43 or resid 46...
d_3ens_1(chain "E" and (resid 26 through 43 or resid 46...
d_4ens_1(chain "G" and (resid 26 through 43 or resid 46...
d_5ens_1(chain "I" and (resid 26 through 43 or resid 46...
d_6ens_1(chain "K" and (resid 26 through 43 or resid 46...
d_7ens_1(chain "M" and (resid 26 through 43 or resid 46...
d_8ens_1(chain "O" and (resid 26 through 43 or resid 46...
d_9ens_1(chain "Q" and (resid 26 through 43 or resid 46...
d_10ens_1(chain "S" and (resid 26 through 43 or resid 46...
d_1ens_2chain "B"
d_2ens_2chain "D"
d_3ens_2chain "F"
d_4ens_2chain "H"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERSERA13 - 30
d_12ens_1ILEILEA33 - 40
d_13ens_1SERTHRA44 - 71
d_14ens_1ARGILEA73 - 109
d_21ens_1SERSERC13 - 30
d_22ens_1ILEILEC33 - 40
d_23ens_1SERTHRC44 - 71
d_24ens_1ARGILEC73 - 109
d_31ens_1SERSERE12 - 29
d_32ens_1ILEILEE32 - 39
d_33ens_1SERTHRE43 - 70
d_34ens_1ARGILEE72 - 108
d_41ens_1SERSERG16 - 33
d_42ens_1ILEILEG36 - 43
d_43ens_1SERTHRG47 - 74
d_44ens_1ARGILEG76 - 112
d_51ens_1SERSERI7 - 24
d_52ens_1ILEILEI27 - 34
d_53ens_1SERTHRI38 - 65
d_54ens_1ARGILEI67 - 103
d_61ens_1SERSERJ8 - 25
d_62ens_1ILEILEJ28 - 35
d_63ens_1SERTHRJ39 - 66
d_64ens_1ARGILEJ68 - 104
d_71ens_1SERSERK8 - 25
d_72ens_1ILEILEK28 - 35
d_73ens_1SERTHRK39 - 66
d_74ens_1ARGILEK68 - 104
d_81ens_1SERSERL1 - 18
d_82ens_1ILEILEL21 - 28
d_83ens_1SERTHRL32 - 59
d_84ens_1ARGILEL61 - 97
d_91ens_1SERSERM4 - 21
d_92ens_1ILEILEM24 - 31
d_93ens_1SERTHRM35 - 62
d_94ens_1ARGILEM64 - 100
d_101ens_1SERSERN4 - 21
d_102ens_1ILEILEN24 - 31
d_103ens_1SERTHRN35 - 62
d_104ens_1ARGILEN64 - 100
d_11ens_2UUB
d_21ens_2UUD
d_31ens_2UUF
d_41ens_2UUH

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(-0.997720406228, 0.0354672366822, -0.0574113762034), (0.0428364478126, 0.990231214596, -0.132692050924), (0.0521443164136, -0.134848866372, -0.98949318012)-47.4500048623, 0.863478858019, -73.8447081795
2given(0.996419717978, 0.0235148563025, 0.0812083564558), (0.0364247634406, -0.98622387971, -0.161355804664), (0.0762953618085, 0.163736100551, -0.983549443161)-45.3235592342, 65.0503736196, -83.260473338
3given(-0.992619876766, 0.0204208443594, -0.119535640559), (-0.01224758505, -0.997561175459, -0.0687146118232), (-0.120647324499, -0.0667434665958, 0.990449157079)-2.24963502453, 64.2396940836, 1.97563576173
4given(-0.103134113129, 0.314680639808, -0.943578004003), (-0.948301524285, 0.255148542952, 0.188741728477), (0.300145920759, 0.914262170255, 0.2720976117)-72.9224470656, 0.446134717754, -59.2323320775
5given(0.0435277223292, -0.127699253677, -0.990857324744), (0.974634656658, -0.212506271005, 0.070202356262), (-0.21952818368, -0.968779637169, 0.115210204306)-14.223404503, 75.364831583, -4.57792313622
6given(-0.0121991240161, -0.154673401239, 0.987890338207), (-0.98115582616, 0.192377452339, 0.0180044612087), (-0.192832637707, -0.969054722284, -0.154105545177)23.315105878, -6.34202883902, -11.0504085233
7given(-0.976594569742, -0.115788056666, -0.181262716201), (-0.170995031901, -0.0932600190575, 0.98084823898), (-0.130475075843, 0.988886087868, 0.0712780457421)-15.9500668733, 22.6959003451, -96.5685790328
8given(-0.0307405529855, -0.11535884149, -0.992848103232), (0.992977211518, -0.117057039387, -0.0171437142063), (-0.114242180516, -0.986402548263, 0.118147098868)-59.2070311653, 6.17808409004, -0.685332233632
9given(0.291101774179, -0.908534215313, -0.299708753083), (-0.91971166136, -0.179503403231, -0.349154676594), (0.263420228966, 0.377285181041, -0.88784327172)-40.7129522299, -9.33063441118, -24.3379373207
10given(-0.998122905602, 0.0279896987322, -0.0544723973855), (0.0349828601763, 0.990633954786, -0.131986996023), (0.0502679301934, -0.133644844234, -0.989753601056)-47.2821586775, 0.613101085043, -73.6038994354
11given(0.997653634039, 0.0503856843178, 0.0463520151125), (0.0562289337509, -0.989264417865, -0.134885946473), (0.0390580785292, 0.137175779067, -0.989776374814)-46.5781116695, 66.0891920212, -83.2914381095
12given(-0.990240093052, 0.0459300121847, -0.131586443428), (-0.0390232788431, -0.997745704415, -0.0545957235494), (-0.133797390937, -0.0489279398939, 0.989800138854)-3.25344045911, 64.264276093, 0.948637690875

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要素

#1: タンパク質
Repressor of competence, RNA Chaperone


分子量: 13276.348 Da / 分子数: 10 / 断片: ProQ/FinO-domain, UNP residues 14-126 / 由来タイプ: 組換発現
由来: (組換発現) Legionella pneumophila (バクテリア)
遺伝子: C3926_00530, DIZ73_10055 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A128QHZ1
#2: RNA鎖
Modified SL3 of RocR


分子量: 8863.197 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Legionella pneumophila (バクテリア)
発現宿主: in vitro transcription vector pT7-Fluc(deltai) (その他)

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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: 2.78 Å3/Da / 溶媒含有率: 55.77 %
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: 8.5
詳細: 0.2 M Lithium Sulfate 0.1 M Tris: HCl, pH 8.5 30 % (w/v) PEG 4000

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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: ALS / ビームライン: 8.2.2 / 波長: 0.99992 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2019年8月31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: 0.99992 Å / 相対比: 1
反射解像度: 3.2→50 Å / Num. obs: 29074 / % possible obs: 91.4 % / 冗長度: 4.4 % / Biso Wilson estimate: 40.86 Å2 / CC1/2: 0.958 / Net I/σ(I): 5
反射 シェル解像度: 3.2→3.31 Å / 冗長度: 4.5 % / Num. unique obs: 2884 / CC1/2: 0.63 / % possible all: 92

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解析

ソフトウェア
名称バージョン分類
Web-Iceデータ収集
HKL-2000データ削減
HKL-2000data processing
HKL-2000データスケーリング
PHASER位相決定
PHENIX1.18.2_3874精密化
精密化構造決定の手法: 分子置換
開始モデル: RocC(1-126)

解像度: 3.2→48.77 Å / SU ML: 0.426 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 26.1635
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2711 1462 5.05 %
Rwork0.2193 27488 -
obs0.2219 28950 91.41 %
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
原子変位パラメータBiso mean: 47.72 Å2
精密化ステップサイクル: LAST / 解像度: 3.2→48.77 Å
タンパク質核酸リガンド溶媒全体
原子数8437 2348 0 0 10785
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002711205
X-RAY DIFFRACTIONf_angle_d0.527415595
X-RAY DIFFRACTIONf_chiral_restr0.03451879
X-RAY DIFFRACTIONf_plane_restr0.00261603
X-RAY DIFFRACTIONf_dihedral_angle_d16.93184725
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.327722172876
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.458911301165
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.44472987146
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.429725133342
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.452742443379
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.451446296797
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.599785155477
ens_1d_9AX-RAY DIFFRACTIONTorsion NCS0.583719662556
ens_1d_10AX-RAY DIFFRACTIONTorsion NCS0.488780859052
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.42675663552
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.58236834295
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS0.559522161374
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.310.33321580.24322705X-RAY DIFFRACTION91.12
3.31-3.450.32141510.2482696X-RAY DIFFRACTION92.26
3.45-3.60.33491280.25012760X-RAY DIFFRACTION92.83
3.6-3.790.24991440.23742766X-RAY DIFFRACTION92.41
3.79-4.030.26791360.22742750X-RAY DIFFRACTION91.97
4.03-4.340.291300.21212747X-RAY DIFFRACTION92.03
4.34-4.780.22771450.21242760X-RAY DIFFRACTION92.08
4.78-5.470.28151710.20262751X-RAY DIFFRACTION91.68
5.47-6.890.26581570.21642765X-RAY DIFFRACTION90.89
6.89-48.770.21931420.18382788X-RAY DIFFRACTION87.18
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)
13.8906203816-0.237345060456-2.193971121276.0171243883-0.3240798817142.905628831510.3366365280080.2302381978080.708713488504-0.118372960540.008420045875050.42241642827-0.630421975967-0.472011565592-0.07086622112070.342950516640.164287569537-0.03788656719520.434690163573-0.1872337751150.424110652771-12.287561660637.1770159315-8.65538557587
25.747446463971.73044279636-0.4291502941367.86710466014-0.2420541165766.483074762180.1553287267140.453482641376-0.2615409853720.468266926418-0.258462480363-0.496944635525-0.3726969455650.08342822003470.04875271087180.1808467999940.04427420454820.01401175343420.140135648704-0.01060027225950.18311758367-1.3499825544121.9442445095-13.5324714497
34.44868522224-0.2390762684210.1410036345184.069446960772.544979776271.610472505660.275235530928-0.3074015957590.07519882496980.442654906978-0.02444450784980.1453854238760.0581685806799-0.168640443683-0.002829269358090.1629003240930.1080065844730.08504800642230.3032398149370.05445507787140.239269817727-14.048169529225.329227269-9.32565833645
42.564913100331.17146460955-2.199464045983.64522308697-1.061897667983.403610075290.237543353075-0.2181181045740.1771153532860.078685216982-0.07214591334780.0663076323008-0.4482957757250.141160165052-0.09678910735930.2958517311270.17372537046-0.06786159456090.369443926596-0.1299515625880.154088166274-1.7300412827528.1126948387-22.902905556
50.7970456544870.0509339878751-0.2031383609910.276433884987-0.04813253256080.465014964912-0.125485539648-0.088400592747-0.2929484199910.09960728401280.08045514324960.1114715102970.06842912870220.1769604728230.1252612780810.02885073800390.09399751132980.09035132437280.339152322979-0.06711626543570.204273853722-1.9276399162214.7232324849-20.2944063793
62.597405880360.78655073992-1.050782938745.412914274310.07694482694412.60162615501-0.003442654611490.894577143145-0.0141263739024-1.35611500809-0.01355243440251.13291168955-0.147347583887-0.532575844685-0.06856532175260.3061482710620.103266518787-0.09875878600880.5525288671740.00100207119280.28722277666-5.5481200171425.8924285092-32.6005253144
71.121409860830.769941757461.186117464272.172051297170.8766919510785.761357785260.4317705698571.408046296751.67384088291-0.827016549052-0.2280679213670.52762861744-1.00732696704-0.728503778831-0.1270210871040.5472789197930.2108089752640.1035106328760.8272089863560.2134624815960.897164103665-30.956818400437.1063657053-14.6901368807
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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 'A' and (resid 14 through 35 )AA14 - 351 - 22
22chain 'A' and (resid 36 through 52 )AA36 - 5223 - 39
33chain 'A' and (resid 53 through 83 )AA53 - 8340 - 72
44chain 'A' and (resid 84 through 90 )AA84 - 9073 - 79
55chain 'A' and (resid 91 through 109 )AA91 - 10980 - 98
66chain 'A' and (resid 110 through 124 )AA110 - 12499 - 113
77chain 'B' and (resid 1 through 10 )BB1 - 10
88chain 'B' and (resid 11 through 28 )BB11 - 28
99chain 'C' and (resid 14 through 35 )CC14 - 351 - 22
1010chain 'C' and (resid 36 through 67 )CC36 - 6723 - 56
1111chain 'C' and (resid 68 through 83 )CC68 - 8357 - 72
1212chain 'C' and (resid 84 through 109 )CC84 - 10973 - 98
1313chain 'C' and (resid 110 through 123 )CC110 - 12399 - 112
1414chain 'D' and (resid 1 through 10 )DD1 - 10
1515chain 'D' and (resid 11 through 15 )DD11 - 15
1616chain 'D' and (resid 16 through 28 )DD16 - 28
1717chain 'E' and (resid 15 through 40 )EE15 - 401 - 26
1818chain 'E' and (resid 41 through 83 )EE41 - 8327 - 71
1919chain 'E' and (resid 84 through 123 )EE84 - 12372 - 111
2020chain 'F' and (resid 1 through 5 )FF1 - 5
2121chain 'F' and (resid 6 through 28 )FF6 - 28
2222chain 'G' and (resid 11 through 17 )GG11 - 171 - 7
2323chain 'G' and (resid 18 through 40 )GG18 - 408 - 30
2424chain 'G' and (resid 41 through 52 )GG41 - 5231 - 42
2525chain 'G' and (resid 53 through 82 )GG53 - 8243 - 74
2626chain 'G' and (resid 83 through 103 )GG83 - 10375 - 95
2727chain 'G' and (resid 104 through 125 )GG104 - 12596 - 117
2828chain 'H' and (resid 1 through 15 )HH1 - 15
2929chain 'H' and (resid 16 through 28 )HH16 - 28
3030chain 'I' and (resid 20 through 83 )II20 - 831 - 66
3131chain 'I' and (resid 84 through 124 )II84 - 12467 - 107
3232chain 'K' and (resid 19 through 40 )KJ19 - 401 - 22
3333chain 'K' and (resid 41 through 67 )KJ41 - 6723 - 51
3434chain 'K' and (resid 68 through 83 )KJ68 - 8352 - 67
3535chain 'K' and (resid 84 through 125 )KJ84 - 12568 - 109
3636chain 'M' and (resid 19 through 83 )MK19 - 831 - 67
3737chain 'M' and (resid 84 through 95 )MK84 - 9568 - 79
3838chain 'M' and (resid 96 through 124 )MK96 - 12480 - 108
3939chain 'O' and (resid 26 through 67 )OL26 - 671 - 44
4040chain 'O' and (resid 68 through 90 )OL68 - 9045 - 67
4141chain 'O' and (resid 91 through 120 )OL91 - 12068 - 97
4242chain 'Q' and (resid 23 through 35 )QM23 - 351 - 13
4343chain 'Q' and (resid 36 through 52 )QM36 - 5214 - 30
4444chain 'Q' and (resid 53 through 67 )QM53 - 6731 - 47
4545chain 'Q' and (resid 68 through 83 )QM68 - 8348 - 63
4646chain 'Q' and (resid 84 through 109 )QM84 - 10964 - 89
4747chain 'Q' and (resid 110 through 124 )QM110 - 12490 - 104
4848chain 'S' and (resid 23 through 35 )SN23 - 351 - 13
4949chain 'S' and (resid 36 through 83 )SN36 - 8314 - 63
5050chain 'S' and (resid 84 through 109 )SN84 - 10964 - 89
5151chain 'S' and (resid 110 through 124 )SN110 - 12490 - 104

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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