[日本語] English
万見
- PDB-7x7e: SARS-CoV-2 RBD and Nb22 -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 7x7e
タイトルSARS-CoV-2 RBD and Nb22
要素
  • Nb22
  • Spike protein S1
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 RBD / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
類似検索 - ドメイン・相同性
Spike glycoprotein
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (ウイルス)
Lama (哺乳類)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.67 Å
データ登録者Wang, Y. / Ye, S.
資金援助 中国, 1件
組織認可番号国
National Natural Science Foundation of China (NSFC)81801998,31971127 中国
引用ジャーナル: Front Immunol / 年: 2022
タイトル: Short-Term Instantaneous Prophylaxis and Efficient Treatment Against SARS-CoV-2 in hACE2 Mice Conferred by an Intranasal Nanobody (Nb22).
著者: Wu, X. / Wang, Y. / Cheng, L. / Ni, F. / Zhu, L. / Ma, S. / Huang, B. / Ji, M. / Hu, H. / Li, Y. / Xu, S. / Shi, H. / Zhang, D. / Liu, L. / Nawaz, W. / Hu, Q. / Ye, S. / Liu, Y. / Wu, Z.
履歴
登録2022年3月9日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年4月20日Provider: repository / タイプ: Initial release
改定 1.12022年11月2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 1.22023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

-
集合体

登録構造単位
C: Spike protein S1
D: Spike protein S1
A: Nb22
E: Nb22
F: Spike protein S1
B: Nb22
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)107,0877
ポリマ－106,8936
非ポリマー1941
水3,081171
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)73.790, 88.684, 172.475
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

-
要素

#1: タンパク質 Spike protein S1


分子量: 21772.391 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
遺伝子: S, 2 / 発現宿主: Insecta environmental sample (昆虫) / 参照: UniProt: P0DTC2
#2: 抗体 Nb22


分子量: 13858.444 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Lama (哺乳類) / 発現宿主: Escherichia coli B (大腸菌)
#3: 化合物 ChemComp-PG4 / TETRAETHYLENE GLYCOL / テトラエチレングリコ-ル


分子量: 194.226 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C8H18O5 / タイプ: SUBJECT OF INVESTIGATION / コメント: 沈殿剤*YM
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 171 / 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

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.64 Å3/Da / 溶媒含有率: 53.4 %
結晶化温度: 290 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 / 詳細: 0.1 M HEPES (pH 480 7.0), 5% MPD, 10% PEG 10000

-
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: SSRF / ビームライン: BL18U1 / 波長: 0.97915 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2021年6月9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: 0.97915 Å / 相対比: 1
反射解像度: 2.67→50 Å / Num. obs: 32672 / % possible obs: 99.8 % / 冗長度: 7.2 % / Biso Wilson estimate: 45.14 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.3
反射 シェル解像度: 2.67→2.75 Å / Num. unique obs: 1579 / CC1/2: 0.763

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
PHENIX1.20-4459モデル構築
HKL-3000データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7cjf

7cjf


解像度: 2.67→37.23 Å / SU ML: 0.3808 / 交差検証法: FREE R-VALUE / σ(F): 1.39 / 位相誤差: 25.2328
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2495 1724 5.3 %
Rwork0.2045 30781 -
obs0.2069 32505 98.52 %
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: 58.83 Å2
精密化ステップサイクル: LAST / 解像度: 2.67→37.23 Å
タンパク質核酸リガンド溶媒全体
原子数7524 0 13 171 7708
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00297746
X-RAY DIFFRACTIONf_angle_d0.544210532
X-RAY DIFFRACTIONf_chiral_restr0.04491119
X-RAY DIFFRACTIONf_plane_restr0.00321392
X-RAY DIFFRACTIONf_dihedral_angle_d13.99452758
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.750.39711400.30752249X-RAY DIFFRACTION87.51
2.75-2.840.31241450.27122544X-RAY DIFFRACTION99.52
2.84-2.940.28951440.25712556X-RAY DIFFRACTION99.89
2.94-3.050.2931310.24622571X-RAY DIFFRACTION99.96
3.05-3.190.31911540.24442564X-RAY DIFFRACTION99.74
3.19-3.360.29251320.22222572X-RAY DIFFRACTION100
3.36-3.570.26971300.21662593X-RAY DIFFRACTION99.96
3.57-3.850.26951380.2022620X-RAY DIFFRACTION100
3.85-4.230.23181610.17692576X-RAY DIFFRACTION99.93
4.23-4.840.19141760.15352581X-RAY DIFFRACTION99.93
4.85-6.10.21241450.18192670X-RAY DIFFRACTION99.96
6.1-37.230.20431280.19532685X-RAY DIFFRACTION96.01
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)
14.64080992405-1.96900473711.232862484464.02939565227-0.9983191419764.950364075770.1008757924480.3088727107850.162097123373-0.3744946893250.0198320325491-0.00471176569906-0.126373258243-0.116967030046-0.0751694542120.257168317565-0.05512279034680.03672283574150.3423773635510.0227713183280.25384932919-40.148273689426.57960879226.9574791256
21.671910188480.6480329225651.027697482736.02572472570.8157889758361.13330137738-0.3274355781880.14480930071-0.130737046336-0.1466597887540.2417959755920.530442517615-0.178495916998-0.1875491891510.05669144873350.2957587513470.0361187982475-0.008996018031870.4835988328020.04465952789130.397700823767-53.618003988629.915104629432.2766682597
36.319858878-3.60556173558-1.385418403574.472884242774.567804836576.16215574938-0.08445720273770.152902014088-0.444519958078-0.0316195405517-0.05347199481120.148483767393-0.0296909557542-0.2163537362530.1925861582460.2011222952530.0706808204393-0.01784819468950.2068076179160.02944991055010.132787615055-43.288457042918.030834015734.2788944802
44.58687756696-2.31825312285-0.3390763111673.84659237943-0.1967916236741.77671597475-0.0486475644546-0.05635972963630.1380152359210.1484272120360.0740676760512-0.174993609723-0.0654251828831-0.0458838700419-0.05380884133540.186242685172-0.0507278456738-0.01077879219760.18729378451-0.01181593799770.213432878786-40.296765119214.134587590634.4581982974
55.51256710729-3.799620769270.639690391123.82091770704-0.874816849861.98513364829-0.00103323675256-0.1769423043850.09199528220470.325908392055-0.0789232827447-0.341004152254-0.04627926974950.3252476249180.1262020720990.281582382215-0.105493660508-0.05506703993270.270708759045-0.02315076429580.314139608341-24.89233613699.1768955018740.0191098132
64.12988980901-2.68489124369-1.157414050053.11657420984-1.166712196452.833416306870.2492670880320.321695617504-0.496004879778-0.15751571029-0.3760776993170.6080194413680.189147610638-0.2329457851940.01183238596230.184999546681-0.03684500555280.008385843236350.266457144662-0.02083821414440.248175363328-44.784862727112.899376580228.9012907557
72.11715655106-2.904449497662.856144806914.37619930599-4.809328544785.921777360930.620980935189-0.1055653671240.43884343068-0.557503748127-1.197626128750.3778809465360.90653527309-0.1400829951320.4395835220730.362255323411-0.06724187941380.002571210690010.36148859968-0.07820708719150.323310997635-46.852463970241.481352884238.5396529621
84.899727891352.913589971122.374565169074.885944136845.832537055357.004424284090.0163059325156-0.3173492075280.06253191144190.2501339285610.169981549401-0.4578487480830.1344107366510.830539347613-0.33694559640.3482044873250.002857239113620.04228606083910.5503881705020.1104470380040.301565744522-14.706059924342.808751941825.0526854621
91.73553048817-1.424702684940.4688713539945.440936633263.35300677334.01274954561-0.0637553963742-0.143185039220.388546526126-0.2769646030820.123604511431-0.287223046002-0.8847166850130.862331638227-0.0630340839980.45036146589-0.165645765980.04878345247780.4901206250430.01077883315170.41088364679-19.664455544455.043109195826.1005037653
102.956296791960.4384055716680.9693949770367.027731970661.464216136640.7529900935160.009334436958060.2005307746040.173190244097-0.186271650272-0.009097040390370.280974037568-0.376468947961-0.3672653944940.06662051951940.2738178213720.01759727829780.05117926545060.3872275233590.0822658390720.230156449095-25.768454793243.410357881514.8255131811
110.7407744227280.1411296588220.3315314407465.431245650221.86708798391.401221875170.1492967745740.1998835790710.128240152709-0.039408808763-0.1463943320460.13899888684-0.08183252370030.01800768547950.03345599944640.3091591817090.02632278008990.07193180239470.384068219850.05879598476030.238431381985-26.146389949133.036535360113.5085160947
125.414872522533.24217460863.38853858288.92392570663-1.591486541075.16245516140.6694737938331.717528610760.194442926163-0.8794564500360.179468366257-0.837053227574-1.127659496220.277305272958-0.5701565052260.4759936838970.04599684338050.1568431615950.6849684406560.06214177360850.326316319805-13.475815366739.45996409484.17267865973
131.39761214088-0.863388883542-2.268053011882.483168672962.362715776526.15132467246-0.169947168705-0.141419106991-0.197821924664-0.0482934273652-0.1219453063640.219011007844-0.7526143909170.03034589201590.3269242412150.441932675024-0.01913806307290.06868570941370.3383978020870.02079482788170.317282852918-24.012648069550.714128649329.7168173442
140.911180736872-2.00658916254-0.6658796168394.939204216491.35671219410.7686757361540.245866771390.261231932016-0.0556872277266-0.25670299291-0.26644325829-0.1638067634010.0088920496933-0.214138566970.006326619549090.2970564074340.05812788847330.08060904858930.4277925405230.0224588012210.231945301257-16.465204647610.91050453092.28621012335
153.52271504221-0.8627759424080.3539716134980.971916941539-0.8703493767650.9222488513030.177262584980.858038289694-0.250012978405-0.367447694742-0.156053996419-0.239492406758-0.0160861201011-0.5917977691990.2997557653720.4875490450280.1337589756580.1112492741310.4363954910070.01038682710380.281127164897-13.57942046636.13470571709-1.28365377638
165.813312668360.251289464499-2.176944168843.0727531042-0.5219765564281.20252688423-0.2253729503730.514873721294-0.482797576823-1.55055927179-1.06091192397-0.1238562896680.307872488163-0.25805916341-0.4977265225370.6229150626840.9941390348880.4236273496620.680679060435-0.1218711232650.156254891923-23.134927886427.2542100362-3.1820881875
176.605880859521.1967949865-3.59996841393.54863761279-2.194133633765.683715406981.125485118471.868060572991.49741476941-0.801874184518-0.3831678882780.147288385878-0.0422783541673-0.988412059960.3507623568330.7214714452510.3448178183530.2373947692630.8015069203240.1826096314070.52191062807-12.779882998619.8673131397-4.38292270645
186.319408124121.2043440769-0.6788059438931.96163772606-1.017850464523.740397450180.3045250744840.612502675714-0.736806168849-0.704449040885-0.624236435329-1.237932722430.103488465570.1074907592820.3847679692530.391742227045-0.03126206581460.1266809839990.236177244531-0.006223301723830.377321396532-7.530760778210.2664024930842.78938971005
197.35920364069-0.238137381634-3.267280705198.738510161765.454838023589.097433995920.55328038501-0.494724030489-0.09662065707351.148621006640.171577720994-0.3592048688521.50334691489-0.03537521517-0.5360075092910.3705844764990.028666307338-0.0802548202160.4780634008860.1395728524570.405286275775-4.189429218634.8688201181530.0452037532
206.640947006181.00260675857-0.7122195270646.03550677166-1.189346199110.5118509575180.6338288896440.2624155136970.366153665648-0.682875428371-0.450100028826-0.0568231576144-0.7144186809950.3099938465380.05200273454750.3644903817690.01513982480240.1423141893950.4008436781780.01390604147250.221163021619-0.5233868035792.684447617725.10799487763
213.171976523931.456954067011.435526692093.28452241608-1.416892191233.318788565630.219405290479-0.3458142006160.267688363991-0.0886211568134-0.314809019085-0.50264497174-0.380652926736-0.2482506712750.2272506386590.165133948205-0.0483589822209-0.02437515776170.3998546780050.02808519489860.4030215395021.206339240659.2694941493623.5195920187
226.67744217101-2.93991339996-1.908649212445.175931332575.511412231218.27617924755-0.3200060714710.0944518965589-1.553338523110.6996706061660.921335438438-0.7006894470120.6446713814581.37702387572-0.5856249700390.321247746050.0820470978397-0.05965585647090.7900690434010.05147796635810.90223295353711.48421256972.072706712819.2696025126
232.453261771851.02367826313-1.799413032130.416899584336-0.7236638624051.34207008325-0.409960430783-0.146951447968-0.08941279755320.896189465499-0.291585111180.192376613243-0.182930125954-0.1038407243810.6361186218060.4310565683750.0513078114339-0.08748578961280.330734223133-0.02816800101110.5502448974219.3997035166118.979386104423.1519360468
240.3101382713630.1978023496491.421546246655.819187617672.605428823367.33459523751-0.01314321642110.137402960677-0.164615777051-0.6210140437390.181339358-0.360357321353-0.315565276766-0.0362406999717-0.3476348714720.290512807489-0.03353171810960.01557789133510.2569072127460.02128947606690.4188981229873.3447889877413.443964595916.6671766314
254.04341803017-4.8949075075-0.1274872198476.095566241820.9188356049065.136142506880.3531555375870.3769838391610.248675930051-0.8435994421470.283814825135-2.21910353901-0.2726891860720.581485009663-0.5988651355370.360163569222-0.03391814191510.1253431086720.499072710413-0.0993014697440.7467382372197.699921931923.517182573416.12034277362
264.89060018109-4.06238191747-4.747644950133.485567158593.736738758195.008787504930.0476342822866-0.454638659532-0.134141307562-0.1977882898140.124001179968-1.08536076603-0.333978335291.03337756442-0.777436835790.2893901489640.04833200810890.04095207873360.4505434850620.153061325650.5842386061544.824160682615.9680037249524.8445985977
270.101778118203-0.0506459393841-0.297718449215.627696718931.765034173662.144707987090.2886332780940.4255542339860.709519356356-0.478132522444-0.955907595474-0.273644462479-0.671613434489-1.666434699210.7189275362490.5027301218610.15839080196-0.1612601687610.838924611486-0.03183853256130.70357893467711.162416595318.16680718932.5699002296
286.999761656993.756617729593.388218648996.879627733314.533936833663.193279709730.1547451065760.072268635873-0.2203098598850.01522971778030.653099421128-1.59314435664-0.5059639316830.345333721614-0.8584454864120.303015597335-0.03671696857950.04513769292930.5751679360.09156615860710.6823480078636.91205618214.5178448552529.430434135
296.05107460298-0.2760555088662.81832669625.224674478311.19627643473.39213699299-0.2498526498620.0825366195798-1.09800847812-0.121401205352-0.301681289289-0.3040407520490.1528355041941.020614715990.3270960401630.2120370303910.01941244570360.1702211169610.301450903004-0.04868144997020.5237784206161.69943804141-1.789638098978.66497343577
301.98309825832.374889699940.00827060041488.01314464299-3.165564151622.07606277696-0.436752064779-0.7102762993250.688719306176-0.01716824482640.02319215851441.68291495264-0.2550575776610.07472286946740.4276656909490.657284939301-0.00781588689488-0.07649726625511.09484687189-0.1832262902610.822880077659-20.482191686516.68888670252.795614206
315.21288607498-0.473800033079-1.28159165975.47534167504-0.7611220952012.12971913338-0.35678268751-0.905635458295-1.195279976042.05022055510.631049545230.220894084418-0.351067966498-1.07428981656-0.2332895509781.113595564190.1894265465440.07257416668511.27554816798-0.01853665340511.13827949127-19.84636208322.278179284856.0124461999
320.6702745718440.265275315467-0.5786641414070.183067127103-0.2954194241720.5278605221140.4578492983-0.6921136482290.2927854718791.24876025680.7481038161630.486433950571-0.270862842590.454137761238-1.114737017551.725682253930.4854145362620.177512950251.80183329817-0.3933387341921.20475213989-15.578987497729.171746068463.9698912738
333.080486434240.674681490357-0.5324269407993.95389148828-0.958133004384.69534219454-0.0846724138017-1.396144660860.9750732797521.211835743410.622813955545-0.0147877707522-1.09981982146-0.133499757589-0.1853131702230.9132418592410.29435158821-0.04497614838351.10859303731-0.405148905730.850168078808-8.0207545871926.819232480550.5667595039
343.230167051390.00933626968485-0.9140709743683.89339024932-0.5070185501056.00959353687-0.204392452334-0.7499269824471.056517715670.4546337575710.1174596532230.143562386635-0.633950578989-0.390981271884-0.150905542340.4602859890630.138878991554-0.1982252725020.62540993514-0.2480629699090.689674916048-4.4166530095323.874626627138.171661982
354.35226399595-0.2569083109342.081618150335.885078612835.615166538276.594036287881.133913899980.0280943055576-0.761594300990.07902042568431.22445476208-0.6376799613-0.3449784925050.127979717975-2.161863859911.22676691416-0.04094600944860.2711324860161.092034832020.2378768223371.77185733014-29.743375832734.21015707660.0950203939
367.45398947875-5.26969868538-4.160268732425.398357388112.637132113863.883196076890.8407433840990.2815209966410.378847591655-0.415429055141-0.410372985638-0.575649514172-0.2105802176680.0973454570778-0.1566526709830.322781744743-0.03703145850550.1173457771040.1809184055290.006285556950630.438628429841-14.7605612814-1.7947891342815.9037977136
375.0700314825-1.30540239527-1.801508063141.784055996770.5681912267343.59206529592-0.235688256964-0.0568141777384-0.428973560950.0397966177539-0.0224530560775-0.1872074127150.4679978476570.1716343238750.2209863777040.318146593786-0.02044023584580.06219447032830.2116008478320.02755109391470.349575086306-17.702136839-7.2883103339823.4061980283
386.47253067101-2.246605650417.690377545217.89157730455-5.066239658439.983195483870.7123617737580.482904937172-2.762661759061.305162558071.089721889180.2564001798161.82919228828-1.14902676124-0.8106536384480.918485696627-0.1575131178840.2593638014970.662665429015-0.1484963070210.930081299268-33.497243142-6.181843239833.2069209954
394.47059859762-3.377905659686.030922771914.83361993412-5.746080836398.78520549929-1.08904953711-1.4642457399-0.5704707741280.3849565022720.7684036318521.527400399911.448514665-1.423361306650.04622439960310.814102934925-0.1293573543940.273246570480.723163533988-0.04539368480270.70007168011-28.7899418496-9.4674606464621.4914466952
404.5351585536-5.743532972031.482104372458.159390343850.6973934258938.41866090659-0.144236224403-0.050285666282-0.569470971333-0.3716628369310.018163216681-0.1829849289761.09044162773-0.1111595392450.09004364159770.35340108689-0.02393734135580.1246187191580.199042084858-0.01003648979650.627783175033-9.75020992148-8.0363203864511.7373677598
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 334 through 358 )
2X-RAY DIFFRACTION2chain 'C' and (resid 359 through 393 )
3X-RAY DIFFRACTION3chain 'C' and (resid 394 through 409 )
4X-RAY DIFFRACTION4chain 'C' and (resid 410 through 459 )
5X-RAY DIFFRACTION5chain 'C' and (resid 460 through 494 )
6X-RAY DIFFRACTION6chain 'C' and (resid 495 through 516 )
7X-RAY DIFFRACTION7chain 'C' and (resid 517 through 527 )
8X-RAY DIFFRACTION8chain 'D' and (resid 334 through 353 )
9X-RAY DIFFRACTION9chain 'D' and (resid 354 through 393 )
10X-RAY DIFFRACTION10chain 'D' and (resid 394 through 421 )
11X-RAY DIFFRACTION11chain 'D' and (resid 422 through 494 )
12X-RAY DIFFRACTION12chain 'D' and (resid 495 through 507 )
13X-RAY DIFFRACTION13chain 'D' and (resid 508 through 527 )
14X-RAY DIFFRACTION14chain 'A' and (resid 1 through 84 )
15X-RAY DIFFRACTION15chain 'A' and (resid 85 through 101 )
16X-RAY DIFFRACTION16chain 'A' and (resid 102 through 111 )
17X-RAY DIFFRACTION17chain 'A' and (resid 112 through 121 )
18X-RAY DIFFRACTION18chain 'A' and (resid 122 through 130 )
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 9 )
20X-RAY DIFFRACTION20chain 'E' and (resid 10 through 19 )
21X-RAY DIFFRACTION21chain 'E' and (resid 20 through 41 )
22X-RAY DIFFRACTION22chain 'E' and (resid 42 through 53 )
23X-RAY DIFFRACTION23chain 'E' and (resid 54 through 61 )
24X-RAY DIFFRACTION24chain 'E' and (resid 62 through 84 )
25X-RAY DIFFRACTION25chain 'E' and (resid 85 through 92 )
26X-RAY DIFFRACTION26chain 'E' and (resid 93 through 101 )
27X-RAY DIFFRACTION27chain 'E' and (resid 102 through 113 )
28X-RAY DIFFRACTION28chain 'E' and (resid 114 through 123 )
29X-RAY DIFFRACTION29chain 'E' and (resid 124 through 130 )
30X-RAY DIFFRACTION30chain 'F' and (resid 334 through 349 )
31X-RAY DIFFRACTION31chain 'F' and (resid 350 through 373 )
32X-RAY DIFFRACTION32chain 'F' and (resid 374 through 393 )
33X-RAY DIFFRACTION33chain 'F' and (resid 394 through 442 )
34X-RAY DIFFRACTION34chain 'F' and (resid 443 through 516 )
35X-RAY DIFFRACTION35chain 'F' and (resid 517 through 527 )
36X-RAY DIFFRACTION36chain 'B' and (resid 1 through 19 )
37X-RAY DIFFRACTION37chain 'B' and (resid 20 through 101 )
38X-RAY DIFFRACTION38chain 'B' and (resid 102 through 111 )
39X-RAY DIFFRACTION39chain 'B' and (resid 112 through 121 )
40X-RAY DIFFRACTION40chain 'B' and (resid 122 through 130 )

+
万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

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

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

+
2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る