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- PDB-7x7d: SARS-CoV-2 Delta RBD and Nb22 -

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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: 7x7d
タイトルSARS-CoV-2 Delta RBD and Nb22
要素
  • Nb22
  • Spike protein S1
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 Delta RBD and Nb22 / 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 / symbiont-mediated suppression of host innate immune response / structural constituent of virion ...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 / symbiont-mediated suppression of host innate immune response / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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)
Vicugna pacos (アルパカ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.92 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13日Provider: repository / タイプ: Initial release
改定 1.12023年4月26日Group: Database references / Refinement description
カテゴリ: citation / citation_author / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id
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

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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
D: Spike protein S1
C: Nb22
A: Spike protein S1
B: Nb22
E: Spike protein S1
F: Nb22


分子量 (理論値)分子数
合計 (水以外)107,1096
ポリマ－107,1096
非ポリマー00
水00
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)151.824, 108.557, 115.310
Angle α, β, γ (deg.)90.000, 126.235, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1chain "A"
d_2ens_1chain "D"
d_3ens_1chain "E"
d_1ens_2chain "B"
d_2ens_2chain "C"
d_3ens_2chain "F"

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1ASNASNPROPROAC334 - 5271 - 194
d_2ens_1ASNASNPROPRODA334 - 5271 - 194
d_3ens_1ASNASNPROPROEE334 - 5271 - 194
d_1ens_2GLYGLYSERSERBD1 - 1301 - 130
d_2ens_2GLYGLYSERSERCB1 - 1301 - 130
d_3ens_2GLYGLYSERSERFF1 - 1301 - 130

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.988647682371, 0.0710344978056, -0.132400378641), (-0.0801839123387, -0.495783993895, -0.864736243949), (-0.127068093339, 0.865535863797, -0.484459872576)-1.05083947977, -108.503118906, 1.02576403112
2given(0.989115420376, -0.0750370801578, -0.126570619721), (0.0717986421169, -0.504705654006, 0.8603006206), (-0.128435354032, -0.860024208622, -0.493824584665)-8.51338308782, -55.4258206825, -93.5744775964
3given(0.988616240278, 0.0916213871623, -0.11934592944), (-0.0581700379342, -0.498783393532, -0.864772440023), (-0.138759418225, 0.861870435594, -0.48777574366)0.999570297166, -108.503800923, 0.528197928428
4given(0.988754126338, -0.0634232552419, -0.135435476679), (0.0854644360096, -0.503533578151, 0.859738196111), (-0.122723705234, -0.861644605606, -0.492450470407)-7.87425796153, -55.2133023957, -93.5977183388

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要素

#1: タンパク質 Spike protein S1 / S glycoprotein / E2 / Peplomer protein


分子量: 21844.504 Da / 分子数: 3 / 断片: Delta RBD / 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) Vicugna pacos (アルパカ) / 発現宿主: Escherichia coli B (大腸菌)

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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: 3.58 Å3/Da / 溶媒含有率: 65.62 %
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 Tris (pH 7.0), 37.5% Jeffamine

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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: SSRF / ビームライン: BL02U1 / 波長: 0.97918 Å
検出器タイプ: DECTRIS EIGER2 X 9M / 検出器: PIXEL / 日付: 2021年11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: 0.97918 Å / 相対比: 1
反射解像度: 2.9→93 Å / Num. obs: 30832 / % possible obs: 93.8 % / 冗長度: 3.2 % / Biso Wilson estimate: 67.95 Å2 / CC1/2: 0.985 / Net I/σ(I): 6.9
反射 シェル解像度: 2.9→3 Å / Num. unique obs: 3106 / CC1/2: 0.836

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20-4459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: 2.92→61.23 Å / SU ML: 0.3776 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 27.7216
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2557 1495 4.85 %
Rwork0.2054 29303 -
obs0.2079 30798 93.8 %
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: 85.72 Å2
精密化ステップサイクル: LAST / 解像度: 2.92→61.23 Å
タンパク質核酸リガンド溶媒全体
原子数7539 0 0 0 7539
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00917728
X-RAY DIFFRACTIONf_angle_d1.099910500
X-RAY DIFFRACTIONf_chiral_restr0.06041110
X-RAY DIFFRACTIONf_plane_restr0.00871389
X-RAY DIFFRACTIONf_dihedral_angle_d13.15762760
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS0.929676456702
ens_1d_3CX-RAY DIFFRACTIONTorsion NCS0.896361594179
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.50997268951
ens_2d_3DX-RAY DIFFRACTIONTorsion NCS0.625687196475
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-3.020.32911280.27392693X-RAY DIFFRACTION95.63
3.02-3.120.26421250.24592709X-RAY DIFFRACTION95.36
3.12-3.250.29841550.24082656X-RAY DIFFRACTION95.48
3.25-3.40.2951450.22512733X-RAY DIFFRACTION96.19
3.4-3.580.26971140.21942725X-RAY DIFFRACTION95.36
3.58-3.80.29921330.20882687X-RAY DIFFRACTION95.11
3.8-4.090.30841200.21372683X-RAY DIFFRACTION94.16
4.09-4.50.21051210.17322669X-RAY DIFFRACTION93
4.5-5.160.21581460.17122610X-RAY DIFFRACTION92.11
5.16-6.490.24311540.20632588X-RAY DIFFRACTION91.74
6.5-61.230.24261540.20392550X-RAY DIFFRACTION88.05
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)
13.412924611252.311930548641.267004942391.81066955211.943491006397.27924080893-0.1313170710370.0418353319979-0.74395156771-0.700164692850.319583746636-0.574872158278-0.03400552727360.265691040563-0.274291999441.061933368640.1346166597470.1705858017870.5102229414740.1978220935551.052280462219.24230222568-56.1989019091-50.8806060611
22.1537191329-9.19987001551-7.512764522246.446464873544.345495548234.95205048687-0.669980344260.0233214986515-1.64946076615-0.999256618533-0.293147854921-0.8347810790180.8977731948920.1430528533920.5686512721610.99730680424-0.06601493803730.4169435478561.11182812682-0.05785097157581.6954964278719.3620659489-58.9135751911-49.7419062719
32.36356306996-7.084549643341.960503087224.55486176578-1.217917801826.881486008320.7358642962881.73727641658-0.543972208346-0.633842997897-0.0175156985996-0.591966171578-0.383304739260.908652515765-0.6486445279310.8469893879130.003538054600170.2661688198211.02828951324-0.02007224501931.2103020091721.8046275576-50.7725164262-60.2671293747
44.312740641481.09948507586-0.6478851823393.94550484630.3304414310075.2857686616-0.0531810845391-0.0386777775884-0.369050546292-0.0483650888131-0.181260885865-0.6758089567180.1456859270180.41954695270.2003000249950.4228415545930.1162437388710.1113854581260.3700582646750.1156951002260.5818386141326.31186230842-41.6474589072-46.4620524739
53.72265846668-0.25454641972-2.271785671850.8803883336180.3723645428933.40844291429-0.111752262099-0.218674564549-0.0865175551511-0.0769186670305-0.0724601263203-0.31980206625-0.206193091090.09560866044210.2123020070780.5932219691630.0207409156136-0.0008045982240510.3605468847370.07020820209810.589579499591-0.52707561923-41.1171932342-47.3107844639
64.565294348741.961582788394.311783963172.238767287860.04709260380246.16841739583-0.7504095108451.089591909030.224653326126-0.0584622840965-0.6279721458890.9087520766890.07636322959920.06089332517750.9910132219610.5306218208650.07910635074020.06579834009671.19999660114-0.104923679011.8789827130630.2372236047-57.3659544739-47.7257475223
78.71135138295-2.40540470124-3.274204214027.99422953917-0.6924680987538.02655710707-0.905002749630.858348085361-2.08694105367-1.470977899370.1280127636620.4658540934772.60723915252-0.340188161040.5948297713870.757547757659-0.0178027158039-0.01046937109420.459497446-0.0772121791520.805086366919-17.902421775-51.4516631931-44.1136086347
84.098541525833.21401074925-3.641374612412.49754633144-1.20543103494.26437016856-0.127942171018-0.314646456356-0.377758492890.0246022291915-0.1649319978840.372258167476-0.287216417085-0.1661264756790.32531755110.2835359725310.114398344811-0.01971857355110.5288631107190.01196883568970.663967824794-24.4695127156-44.443569508-35.3092722301
95.357852640284.05944749317-2.251797313563.32696076775-0.8390618559094.158217142990.2127369778120.6355361823580.375386277928-0.6307073466550.008541706148781.487216929090.0357759492054-1.1438895875-0.135214711430.5394846958690.0367502386815-0.2058386399290.629444052366-0.06058266925390.999430371582-32.4059940097-39.2196077871-41.5882268539
104.691377046432.86852952238-1.029214621038.97006926312-1.417772490186.21748325329-0.003356754746450.6000235827291.198882784540.9433519267110.3155780986710.917389754063-0.929331155092-0.388134705151-0.243083119340.6536782838450.02417480020530.03999907481330.564452918896-0.04956720164220.66701998337-23.492407409-31.2389608559-36.0028981752
116.283860450494.90050828817-2.158165019245.2013204104-1.127284507715.43543685337-0.543818367742-0.1805894424681.060250191580.4076454708870.4996883815560.275183252344-0.21848446324-0.350394751195-0.2924199963860.5349360440910.0413870800834-0.06417302594760.37562996002-0.06790064567410.607934284811-24.3875950687-40.8714955359-31.5524320288
121.907222806843.478279420881.449156113453.08771437189-2.936056687919.275894189650.2999651131250.8235356302461.37764529255-1.186502103110.2902151981480.7310575678040.340343247264-1.32774086778-0.2212655082190.661196668046-0.0349816811748-0.2210913851970.3017630350360.0101985833650.747423312444-23.9470563908-42.8593505551-42.7225023986
139.139027547676.532526153095.877112278376.182509087843.731765419275.19623001063-1.01061300965-1.61588831149-0.232781522385-0.08469907831580.610424345274-0.461240225816-1.02552340569-1.106395062620.4897448426230.6858362151720.241419995193-0.000940208054170.6014719211670.1252113591310.719384193484-12.2034024383-31.1963409309-47.6048671197
145.40895878916-6.65691172018-5.418517636892.017103763858.534989022216.51940451569-0.4297639929751.130467147062.21554008235-3.24397084131-0.03674811804610.208745224464-2.4380850597-0.6721065450380.0696903947291.129427363580.0148942476469-0.2192536110680.6622855520170.183996995791.00598066427-23.1516785991-39.1534578667-48.2610242363
150.903096658290.2867158774421.361748243193.25173583699-0.2465951991922.00930089397-1.346033618040.588905937036-0.283361353260.736562636467-0.1462449162970.6549275122260.196324987558-0.466192578540.8099680233010.2781660230460.0710265603367-0.09666250832061.027487646740.05840226669991.02731530697-34.1905519254-49.1401055624-32.6302994537
164.431777837374.37257226924-1.635742654417.281579168841.508641060896.936688104390.266694271552-1.293896182820.6043412439571.74987887547-0.24091870034-1.15564491735-0.4378637422191.36541046419-0.06437306120550.9757515307470.0182800838674-0.3663569903360.822468377785-0.201638202921.1538075349413.2703026954-68.9857571347-22.208110066
179.89291612473-3.04737314328-0.1250224311256.17779253622-2.447333583486.724979610080.617834952568-2.109668602130.6237641701870.00572066247087-0.00187039169536-1.28188683170.9141398455641.45866100603-0.6296923230260.996847384370.156286267214-0.1109074156131.20275414668-0.1443700104071.5220928940822.617983635-78.4182383112-20.709128966
184.8900754735-2.775629115246.175868905914.18602336363-3.15727755747.641345015190.9267434712750.37549933852-0.03074665192180.0619840046051-1.823164927810.980570366077-0.3951632370191.314984997020.8536935513010.7923780224420.0101918711714-0.01998740415931.608791255160.1493606445771.2707506842832.3200202626-76.5837888632-24.6520682369
194.105633293952.21046612474-1.011417928378.17033204140.03829888634212.62171334770.03686111266140.312587991268-0.7532953919460.411870025630.285699561702-2.05358503657-0.1966788042150.501030383075-0.4354328668220.436358720077-0.0636350377964-0.1732311172240.6310654065330.02974350830581.0190634182912.3755466945-76.3518519531-31.376462527
205.81578504492-1.774740002990.1785277756963.37987733812-0.6672604999534.76466554725-0.140941222923-0.05415811206530.7177528067790.00348622683390.26209611957-0.67195692247-0.3129523296150.393599166132-0.1015430242540.444492862405-0.00883622790881-0.06449592330440.328991145686-0.09337901786660.7148493404517.03699853757-73.0750195803-36.7820314694
216.1734869331-2.255218244051.523806684783.55742273451-2.154501594584.5885961504-0.150711465759-0.1481279607330.416667511795-0.1815924433630.193786906861-0.32861613725-0.03178593317030.0746883645825-0.02555243744940.5761467726030.0316325674525-0.006456723801510.300829007339-0.09626072887750.6044076381971.30523766418-75.1749154088-34.9632019312
222.896601046611.116880894571.611169954870.5418252483910.4503037988731.456704489543.25827359998-2.216775143121.31049304641.15950398481-0.638722090212.477443255860.02840375923170.0592609988852-2.633584051262.35008940607-0.5676111731240.5128403186111.77064717516-0.5706518017612.7825960642631.8588162163-65.0727369042-25.0215938211
238.85241099799-6.69698487193-2.25345503095.821172720880.515550253562.516210428980.0324494588822-0.810349059623-0.190961180970.002095247947330.4046637575410.3464847668310.285905270742-0.152734372659-0.1619129788740.507168695091-0.1976920722820.07628079326170.52296183628-0.07204274086910.591542903503-24.7124228548-62.4868444468-30.8870204305
249.63589305852-7.77419707332-0.2410761881335.526391755231.109383378582.68685518105-0.477770313953-0.508858555421-0.1876942593030.451410870010.3625220372990.3950712834830.244099183996-0.3636440474150.01871162403430.464166735188-0.0438075257128-0.005657922862660.3365851320530.03927660370380.581858859207-20.0824322131-68.6000233269-34.1858430189
256.511251003480.688103113351-4.820920971457.7161753096-1.45059983857.92153507302-0.293370622658-0.221204448985-1.615040013410.516094421229-0.06614311092311.812852844181.52896858492-1.068286984510.9016441767870.554442158137-0.145664688080.03318406560780.760697599667-0.02227942125441.17008270118-31.2382711092-74.047025764-35.4179118728
262.03329666115-2.94238035572-4.385324244878.13133839193-0.2720954341818.38119785228-0.518117927973-0.0446585272135-1.1762098993-1.71513703074-0.502235211543-0.07275144131530.928508724459-0.09492136129740.8478903709260.761027352333-0.04732330881920.02549659522140.3632880404430.0943104795780.628559249684-17.3825682941-73.8681726202-45.6903197207
273.77311029931-4.42811642106-2.651117215257.94704579707-0.8715764354967.375366181250.03699660549911.1224621908-0.534545319186-0.843954371403-0.04770300952610.457815629575-0.0733466413523-0.1418294679880.04336056603830.532343645764-0.0496334501002-0.03037868670810.359483853047-0.02840100319160.480831523807-22.1811790648-65.5884980846-41.512075535
286.67662572187-5.814972411660.5545712038556.34848320659-0.9571242585393.469086546840.5054222164550.548250120818-1.74160269474-0.30380475882-0.1811508539721.594591020260.0409208865886-0.536248156507-0.1959010200860.451960646276-0.06385508673840.07626402820540.512542900978-0.07742309498570.805351868348-29.5169681206-67.9046567546-36.3963248117
291.68051556047-3.732506788142.165559892849.81915046843-2.569425087542.09515393839-0.2671920508220.639140781016-0.582871254054-1.509959458660.6126819414641.44698325441-0.993631552880.145622964235-0.5341562413210.70688789893-0.1987475905750.004084075812550.531989714528-0.1625162973121.02731944893-10.9504693497-81.3293465933-41.7006982665
305.86565176118-2.469734324587.285496062018.90162801474-4.848651148362.066885794410.07078408421630.528795824947-1.787804661790.1173601543130.752738866957-0.5891773196861.484511769640.0108276702679-0.4944047694950.928081854421-0.05163303588060.1695867325460.558763437813-0.1738661684270.817670371411-21.2183941402-78.9030161041-33.214310918
312.24640875208-7.793415130116.285797169676.54783581153-4.694491079892.40648353550.123908904423-0.930043653433-0.8036783246640.3629310724370.2059597597941.26519665074-0.26801912478-0.976518802133-0.2563814334410.4450551991570.01897742588980.05745279197330.6897464186270.03318576637660.906550051441-33.8353439136-61.4064763121-30.969013145
323.58394805936-2.663318972021.060841341282.959810741341.134932364813.97919398125-0.425294115841.188216036970.650278408609-1.330998496170.0707619451776-0.479644213219-1.704737610910.6643235093490.2085582429811.66466411463-0.7040889277410.0456030034081.375668371010.0007571687505730.658509066311.6074618214-37.3384891154-24.3176038553
335.211481857470.665348835745-0.8076647984765.36477827912-0.3273424994572.75059631410.1520017749860.9110682071021.53339598154-0.1961977076870.146377848403-1.50350559094-1.275768120251.28822051917-0.01237009001871.63819933433-0.415421730989-0.01673287713972.169850016720.1302393319261.3985770631321.5275209783-37.8280438931-28.7382665405
345.8650148873-2.892107600151.109000460755.070508521770.948874369934.176104451550.2317284792830.1718177729322.87317208779-0.297936755458-0.515859540727-1.29046980595-1.954955301831.075122809320.1001950347641.42117673223-0.4554669770110.07236437797671.65213292945-0.06118755406011.5054848858920.966468178-31.086848795-13.4566834559
358.35711359341-4.55242091507-2.400167459361.96040770328-3.053509164365.796628874730.13937657480.9277943959170.6568809987381.812524067710.12770991537-2.06398682998-0.737603532287-1.6690966543-0.02811948735191.663481281-0.157836246364-0.05553291933271.475855743840.2370372817521.5015224848231.7087274004-36.9490105634-20.6774016703
366.413123261591.210666678421.868521279645.288061813640.1212229217214.46239793788-0.296784955470.7875887082420.108603075423-0.4058592358590.244188672939-0.518059379389-0.5785178549951.205821567440.05732053647710.618979604127-0.2546755246780.05789137705230.8226914500360.01621754507490.3951218923299.13085817025-48.5579509365-13.2731188909
375.142414467521.320958077831.37812263245.073634809880.3231312766063.90732118643-0.2848262838010.4181021517110.134490899832-0.04809818901990.1220985194140.0465269309473-0.7134478606410.4240304118120.1461711730.507171847732-0.1244783280360.04471494209120.5390437466070.03096792235070.3342676918751.09549399736-47.6963570222-11.0533769726
389.354543447750.884021687890.4833285826985.4675886169-8.424949298562.026508852240.0479751266321.97712622145-0.472167238097-2.28015513456-2.79806883222-1.097968509441.511690304362.237022132232.757505743581.860946749230.04489944561870.2695675628273.33785779365-0.4157211257541.5473453780630.3454334387-42.074052784-27.8765972664
392.03788833492-7.85892390907-4.552093896445.907403879264.067299904529.72481226798-0.7536141427541.22134517572.335374671910.2266564867180.007934976173840.0438402948202-2.01990480777-0.4005706383020.6205081891251.143381816770.0206269643477-0.1133725485530.6085125005080.224857404260.642764844779-15.6471561188-43.7482688971-19.8295248001
405.098659013522.101958484983.276179400251.746022101240.1975214784362.129346748540.1975861755160.8052601259410.4876173290330.5129073692050.1750578132690.5728299104550.119477183923-0.00264933490211-0.3904315094760.582890218688-0.02517922776750.2150680291860.708941221857-0.05330041032440.590374033383-24.2902407888-56.9823046201-21.3697786731
419.574626660374.485245533284.176914212133.135174558311.117561073594.61253272314-0.671146973001-1.200159614261.406702226120.001894763943290.3293613517450.695478130305-0.44350289393-0.7092110249990.3907769792480.4929745249510.1451082703280.006394989546670.466067185985-0.001709505030310.46546004109-19.4780906424-50.8851629165-11.5592470626
429.69966421291-5.883291445325.922744316955.26462689044-4.979574127145.33247204525-0.093046775198-1.646469802252.208591340610.806110151178-0.556781912478-0.0817181778695-0.703059921562-1.246681211210.4447069244950.5923944607550.03471860185840.1135394845570.967400654512-0.158371462380.958796842202-29.6353993708-50.9780683282-8.82972982012
434.541755433170.8715696719316.892826044185.900585394231.736199180172.072687393330.383937929555-0.5749289935680.2429363336180.1191405408160.288431217502-0.6283750991220.823361512276-0.463609531121-0.3934161549550.5088953828790.063839283899-0.01739481382550.54644826504-0.04919773933050.599403144532-14.2178915831-58.8104706059-5.28263513782
445.604569852370.370989216677.240934944975.795966804391.466501510259.495128064360.93952690689-1.91290964591-0.4462846038520.331545211069-0.4848691252710.3012366541351.07978637276-0.779738584455-0.4090068107270.706934514509-0.0273591510540.1405794092080.5802184957030.09136642603930.579251128522-23.1386520096-61.3853847822-10.1369817321
458.400322295861.236527043147.127204732185.24636520021.238223880966.942048983240.439876422863-0.746595181758-0.838892580659-0.166607157162-0.2878921697040.351563612550.105319680602-0.653210829915-0.2935145140660.5036713431970.04381920810290.1039540337020.4264671334450.07203636532010.594467726551-24.565789931-59.2741336343-16.9171839996
462.051296468994.798408668837.285607315053.633515118652.904433294955.76006797399-0.140980885441-1.069885293070.1932168525870.0880104305015-0.3717047162630.566812412391-0.618226591079-0.6895410541460.7385736789230.5817286346460.2104942018650.07460968611910.66683517553-0.0132727506360.492562701528-21.0130319339-48.7893260494-12.4309154398
476.877437897983.190130677044.601733953899.70713529185-3.6513200787.57469314881-0.0279862438836-0.916332795873-0.2295605388610.536287632824-0.7936600542730.632440797195-0.275908116304-0.2699044879470.7145441737130.5041144192740.03823819470250.1154505575170.713993903149-0.09519120500530.476709013875-7.85063332916-51.1523480088-1.69348244708
489.718493709887.32701662971-6.135546502018.02807287096-0.2830596673111.99268689465-0.720859083185-3.20243265686-0.3128862251962.01123626922-0.37243765819-0.32380880424-1.497962217780.7111232767050.9912260012790.9783280430660.2246485663790.1075583685321.1054151211-0.01116781807510.547589619118-19.3485382929-45.8758278208-6.81157197565
496.613627435784.974434471414.27708783948.97801840749.160461121092.14693336258-1.402809741720.2924620762370.263850991783-1.26943077270.8087016387911.36242971101-0.102963777471-0.515041574080.5205760419560.411261929859-0.0544279908070.0623470784680.687879954680.02485639688230.731219422153-33.1330164205-53.8525946326-21.2623358369
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 'D' and (resid 334 through 353 )DA334 - 3531 - 20
22chain 'D' and (resid 354 through 365 )DA354 - 36521 - 32
33chain 'D' and (resid 366 through 393 )DA366 - 39333 - 60
44chain 'D' and (resid 394 through 479 )DA394 - 47961 - 146
55chain 'D' and (resid 480 through 516 )DA480 - 516147 - 183
66chain 'D' and (resid 517 through 527 )DA517 - 527184 - 194
77chain 'C' and (resid 1 through 9 )CB1 - 91 - 9
88chain 'C' and (resid 10 through 42 )CB10 - 4210 - 42
99chain 'C' and (resid 43 through 53 )CB43 - 5343 - 53
1010chain 'C' and (resid 54 through 68 )CB54 - 6854 - 68
1111chain 'C' and (resid 69 through 92 )CB69 - 9269 - 92
1212chain 'C' and (resid 93 through 101 )CB93 - 10193 - 101
1313chain 'C' and (resid 102 through 111 )CB102 - 111102 - 111
1414chain 'C' and (resid 112 through 121 )CB112 - 121112 - 121
1515chain 'C' and (resid 122 through 130 )CB122 - 130122 - 130
1616chain 'A' and (resid 334 through 357 )AC334 - 3571 - 24
1717chain 'A' and (resid 358 through 380 )AC358 - 38025 - 47
1818chain 'A' and (resid 381 through 393 )AC381 - 39348 - 60
1919chain 'A' and (resid 394 through 409 )AC394 - 40961 - 76
2020chain 'A' and (resid 410 through 479 )AC410 - 47977 - 146
2121chain 'A' and (resid 480 through 516 )AC480 - 516147 - 183
2222chain 'A' and (resid 517 through 527 )AC517 - 527184 - 194
2323chain 'B' and (resid 1 through 19 )BD1 - 191 - 19
2424chain 'B' and (resid 20 through 42 )BD20 - 4220 - 42
2525chain 'B' and (resid 43 through 53 )BD43 - 5343 - 53
2626chain 'B' and (resid 54 through 61 )BD54 - 6154 - 61
2727chain 'B' and (resid 62 through 84 )BD62 - 8462 - 84
2828chain 'B' and (resid 85 through 101 )BD85 - 10185 - 101
2929chain 'B' and (resid 102 through 111 )BD102 - 111102 - 111
3030chain 'B' and (resid 112 through 121 )BD112 - 121112 - 121
3131chain 'B' and (resid 122 through 130 )BD122 - 130122 - 130
3232chain 'E' and (resid 334 through 353 )EE334 - 3531 - 20
3333chain 'E' and (resid 354 through 365 )EE354 - 36521 - 32
3434chain 'E' and (resid 366 through 380 )EE366 - 38033 - 47
3535chain 'E' and (resid 381 through 395 )EE381 - 39548 - 62
3636chain 'E' and (resid 396 through 479 )EE396 - 47963 - 146
3737chain 'E' and (resid 480 through 514 )EE480 - 514147 - 181
3838chain 'E' and (resid 515 through 527 )EE515 - 527182 - 194
3939chain 'F' and (resid 1 through 9 )FF1 - 91 - 9
4040chain 'F' and (resid 10 through 30 )FF10 - 3010 - 30
4141chain 'F' and (resid 31 through 41 )FF31 - 4131 - 41
4242chain 'F' and (resid 42 through 53 )FF42 - 5342 - 53
4343chain 'F' and (resid 54 through 61 )FF54 - 6154 - 61
4444chain 'F' and (resid 62 through 74 )FF62 - 7462 - 74
4545chain 'F' and (resid 75 through 92 )FF75 - 9275 - 92
4646chain 'F' and (resid 93 through 101 )FF93 - 10193 - 101
4747chain 'F' and (resid 102 through 111 )FF102 - 111102 - 111
4848chain 'F' and (resid 112 through 121 )FF112 - 121112 - 121
4949chain 'F' and (resid 122 through 130 )FF122 - 130122 - 130

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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://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

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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