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- PDB-7zf9: SARS-CoV-2 Omicron BA.2 RBD in complex with COVOX-150 Fab (P21) -

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基本情報

登録情報
データベース: PDB / ID: 7zf9
タイトルSARS-CoV-2 Omicron BA.2 RBD in complex with COVOX-150 Fab (P21)
要素
  • COVOX-150 heavy chain
  • COVOX-150 light chain
  • Spike protein S1
キーワードVIRAL PROTEIN / SARS-CoV-2 / Omicron / BA.1 / BA.2 / RBD / antibody / Fab / COVOX-150 / VIRAL PROTEIN/IMMUNE SYSTEM
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 / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Spike glycoprotein
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Severe acute respiratory syndrome coronavirus 2 (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.25 Å
データ登録者Zhou, D. / Huo, J. / Ren, J. / Stuart, D.I.
資金援助 英国, 2件
組織認可番号国
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 英国
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 英国
引用ジャーナル: Cell / 年: 2022
タイトル: Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
著者: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / ...著者: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / Donal Skelly / Thomas G Ritter / Ali Amini / Sagida Bibi / Sandra Adele / Sile Ann Johnson / Bede Constantinides / Hermione Webster / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / Derrick Crook / Andrew J Pollard / Teresa Lambe / Philip Goulder / / Neil G Paterson / Mark A Williams / David R Hall / Juthathip Mongkolsapaya / Elizabeth E Fry / Wanwisa Dejnirattisai / Jingshan Ren / David I Stuart / Gavin R Screaton /
要旨: Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA. ...Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site; however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focused in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains, and many show broad reactivity with variants of concern.
履歴
登録2022年4月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年6月1日Provider: repository / タイプ: Initial release
改定 1.12022年6月15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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22022年6月22日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.42024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
H: COVOX-150 heavy chain
L: COVOX-150 light chain
E: Spike protein S1
A: COVOX-150 heavy chain
B: COVOX-150 light chain
C: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)140,2458
ポリマ－139,8036
非ポリマー4422
水00
1
H: COVOX-150 heavy chain
L: COVOX-150 light chain
E: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)70,1234
ポリマ－69,9013
非ポリマー2211
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: COVOX-150 heavy chain
B: COVOX-150 light chain
C: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)70,1234
ポリマ－69,9013
非ポリマー2211
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)89.967, 83.885, 110.704
Angle α, β, γ (deg.)90.000, 101.971, 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 1 through 130 or resid 132 or resid 138 through 220))
d_2ens_1(chain "H" and (resid 1 through 130 or resid 132 or resid 138 through 220))
d_1ens_2chain "B"
d_2ens_2chain "L"
d_1ens_3(chain "C" and (resid 333 through 368 or resid 370...
d_2ens_3(chain "E" and (resid 333 through 368 or resid 370...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNPROE1 - 130
d_12ens_1SERSERE132
d_13ens_1GLYCYSE134 - 216
d_21ens_1GLNPROA1 - 130
d_22ens_1SERSERA132
d_23ens_1GLYCYSA138 - 220
d_11ens_2GLUGLUF1 - 215
d_21ens_2GLUGLUB1 - 215
d_11ens_3THRLEUG1 - 36
d_12ens_3ASNPROG38 - 41
d_13ens_3PHELYSG43 - 195
d_14ens_3NAGNAGH
d_21ens_3THRLEUC1 - 36
d_22ens_3ASNPROC38 - 41
d_23ens_3PHELYSC43 - 195
d_24ens_3NAGNAGD

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(0.921645042851, 0.0453972656819, -0.385369307621), (0.045288159019, -0.998930064837, -0.00936526656358), (-0.385382144942, -0.00882121498128, -0.922714900999)-38.037215117, 6.6390322602, 34.5488589072
2given(0.920981318381, 0.0376266667501, -0.387785565929), (0.0374787371472, -0.999265823303, -0.00794724107834), (-0.387799890995, -0.00721445272913, -0.921715355311)-37.9401191568, 7.32521849414, 34.8199130423
3given(0.924509981329, 0.0362322541429, -0.379431836016), (0.032229285533, -0.99933763177, -0.0168988426217), (-0.379792795583, 0.00339433169337, -0.925065354954)-38.1332777492, 7.90139990877, 34.0138410701

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要素

#1: 抗体 COVOX-150 heavy chain


分子量: 23415.322 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#2: 抗体 COVOX-150 light chain


分子量: 23456.035 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#3: タンパク質 Spike protein S1 / SARS-CoV-2 Omicron BA.2 Spike protein


分子量: 23030.000 Da / 分子数: 2 / 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: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2
#4: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
研究の焦点であるリガンドがあるかN
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.92 Å3/Da / 溶媒含有率: 57.92 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.1 M Sodium acetate trihydrate pH 4.5 and 30% (w/v) PEG 1500

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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: Diamond / ビームライン: I03 / 波長: 0.9762 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2022年1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: 0.9762 Å / 相対比: 1
反射解像度: 3.25→67 Å / Num. obs: 25693 / % possible obs: 99.9 % / 冗長度: 14.2 % / Biso Wilson estimate: 87.8 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.629 / Rpim(I) all: 0.173 / Net I/σ(I): 3.2
反射 シェル解像度: 3.25→3.3 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1215 / CC1/2: 0.428

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解析

ソフトウェア
名称バージョン分類
GDA1.19_4092データ収集
PHENIX1.19_4092精密化
xia2データ削減
xia2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: 7BEI

7bei


解像度: 3.25→62.27 Å / SU ML: 0.5915 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.4515
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2648 1205 4.7 %
Rwork0.2215 24438 -
obs0.2235 25643 99.75 %
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: 94.33 Å2
精密化ステップサイクル: LAST / 解像度: 3.25→62.27 Å
タンパク質核酸リガンド溶媒全体
原子数9611 0 28 0 9639
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0029874
X-RAY DIFFRACTIONf_angle_d0.50213438
X-RAY DIFFRACTIONf_chiral_restr0.04311500
X-RAY DIFFRACTIONf_plane_restr0.00541725
X-RAY DIFFRACTIONf_dihedral_angle_d10.93473510
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2HX-RAY DIFFRACTIONTorsion NCS0.308943755799
ens_2d_2LX-RAY DIFFRACTIONTorsion NCS0.335946563156
ens_3d_2EX-RAY DIFFRACTIONTorsion NCS0.499780582906
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.380.36931460.3512605X-RAY DIFFRACTION98.43
3.38-3.530.33111310.30152725X-RAY DIFFRACTION99.93
3.53-3.720.31481350.27712702X-RAY DIFFRACTION99.89
3.72-3.950.28751400.26192706X-RAY DIFFRACTION99.93
3.95-4.250.30481300.23662714X-RAY DIFFRACTION100
4.25-4.680.23261320.18462701X-RAY DIFFRACTION100
4.68-5.360.23451440.18472723X-RAY DIFFRACTION99.97
5.36-6.750.24431330.21062742X-RAY DIFFRACTION99.97
6.75-62.270.22071140.18122820X-RAY DIFFRACTION99.69
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)
14.326755107312.355614624380.3869593691814.302372451481.825109268923.16819146668-0.0658023116561-0.3086174337170.1444565632570.213946687945-0.006865279062230.1981012719470.106181839485-0.2419748096010.07935955127420.635472715378-0.0445040750317-0.0497062151940.7079278343610.01552847016150.64448743083151.7827117547-6.727521485632.56180515164
23.437604329924.04995878534-0.3952300507974.2126710811-0.4856605452971.57165466979-0.106918436647-0.666132837591-0.7416094905820.351740404712-0.7280595721570.410630533652-0.12618016341-1.21485993171-0.6494733341870.5656466619420.0305088830827-0.05572932989561.028654370820.05177996433580.64019444744954.91443254527.1476005409635.804117814
37.05679913320.946247898501-0.1755228498995.242285996121.970900623982.14399307756-0.52602204009-0.0749618156738-0.5516020317180.4506521860910.225771711241-0.1462779275630.70090644117-0.4190287803090.350871726860.755167182194-0.115285076825-0.05290731427650.7514839071050.08318532360710.65560970848350.86442173282.2904637270735.7195558756
43.743279398790.939332035641.067194671777.16250475295-1.473591886032.32252247287-0.679046905933-1.58234432845-0.979077586361.007179745120.6505469552050.01710897258020.5074167607441.829494027950.3026324966070.8368739103960.100028068417-0.1008478046261.059933779160.1746247415040.71007682529856.24757586950.21408603729643.7688825745
52.496183317640.7879302043161.160786419853.76167420821-0.8885264082395.177276479440.372300627519-0.9322915548290.5584971375780.376889424817-0.2100899589620.741736259591-0.887980071391-0.346272238142-0.262457841220.8659521707080.0291234493161-0.04369730773240.738886023585-0.1523476397110.97716849664529.39263170944.969340442712.1586458173
62.462156191550.581455203546-0.1253710455373.18410852156-1.50349327153.48002805431-0.252812342488-0.5515123010131.15478172367-0.174583274404-0.09296025409190.7671397819420.111501806754-0.511092074489-0.2413774100640.5660418279330.02363440657390.1176085545410.941506328706-0.1136560066020.91484878255531.23699963512.233047589783.05560276747
73.001828794450.3587231268740.4986845481914.29232960924-0.9305554575745.35986111137-0.275822525140.877459008331-0.2878382377090.1836448037860.2839977151380.5429121780651.33261839947-0.507756281358-0.1887916962130.623776286657-0.1119003521440.009155710380691.08241162165-0.2083001901720.89573595661131.469048341-9.354773540817.96598494883
84.085189210121.41031787417-0.8119936343011.902909472050.5267728363752.89597135150.940435501927-0.642155027061-0.1585182445420.865931839404-0.6813890828280.03258470444930.303479673216-0.299284037327-0.2084309294260.858748172341-0.202919676447-0.09638323806541.27711024062-0.3171954533070.94847374565627.5114901931-2.0283258196910.0939097913
93.50086888317-0.3991444801043.582145776280.78385122146-0.03459121111343.802270193860.1608358624560.985842564251.057641678670.01033036537940.251691467929-0.440384652847-0.181082245237-0.50985715272-0.01451669642720.949736538593-0.123948918309-0.06396826839590.953322784552-0.0257946286990.84340885079539.18502905393.17873306894-0.746990154771
101.027197666070.5976713139370.7827859766470.6909476345560.3119173631910.648675861476-0.8442338727470.908624553147-0.5211408961690.407654186075-0.423490599351-0.09344086599980.405172095395-2.109069169951.055567712520.933006985642-0.352993095130.1972986327541.53375425763-0.3458729806850.80376414474328.6605860764.5266229514428.7694621664
116.14235987802-0.379081702438-0.408590402264.334047315191.546915273465.378145407650.158364870243-1.37417200858-0.355456604738-0.3343241324570.491866367112-0.1913155213440.3209986125140.843171892877-0.8756338116410.6755238693680.0823509252127-0.1417576021850.615769721905-0.04823533916890.8505191011754.453542578813.958995560141.3313334795
123.879060743550.6316982041180.6682629434373.837456448070.6776973751095.60156814266-0.3038757831410.458387840873-0.193687508916-0.216829353850.2414505620990.0929454314716-0.970424801045-0.547163306430.101390693170.7014781837580.069055019452-0.08561602148570.9838760571590.1147492867880.5289288083942.628634499616.803474080132.8773338205
135.214237800891.86210714092-0.8520751810933.06740420462.897459152694.25046277851-0.2287628581020.3428997939540.3452959480010.4694773796820.211635622981.25954908176-0.390717754156-0.9699293993830.06104597237281.07098083706-0.08638581599960.3245422102541.03665118110.1922961853670.87943912179840.31102496565.9694092502629.5844926974
147.40129270377-0.0511047346806-0.1246163167026.636347808761.210295876574.87012236785-0.348243118104-0.8208704988570.935876351727-0.3719804579780.298734673073-0.559608797232-0.9458254200750.3215252384340.03045761682150.686168378117-0.108467075865-0.03569924963130.718465995972-0.01026196208520.5950667667750.537633508621.26109290235.7915552657
154.779352581544.935902304194.626001036395.139356202614.832787544234.46241154991-0.120941828839-0.7794543670373.03308769693-0.10351160419-0.877473768931.14068086349-0.917576536285-0.1695717760011.033174328310.812200680583-0.0516005194822-0.06070335243681.17318590498-0.01144898057060.89562716650640.653819940720.976139531140.7147508071
167.331985502973.1742629047-5.118289760812.63101778354-0.9910780361374.288902575780.12908136805-0.1128392078220.619398171313-0.201203475912-0.2564821001670.770435885418-0.234082302308-0.08822435498070.2584188545441.183018364950.231192742394-0.1576769485840.8900294942810.03546069904030.66477805652234.78117785642.56675650272-36.4459484332
171.54063939710.926912036879-0.2585248010424.38100563568-1.541919182444.225645326630.2816023411230.2096679396250.0161142176256-0.208553547706-0.196079381837-0.03555955021280.1472173234360.130458383651-0.07255623336960.5582434854310.044982959681-0.03587897653480.7800784427710.04561709597020.63234003218438.7540281588-4.15786579441-23.5618823506
182.442858371783.024066804631.318054548494.128521048550.0682279832447.93192756389-0.1544520218281.013370003890.01538289622-1.116371970580.0475844439090.432032400855-0.5754224896380.139506290843-0.0672859995130.571236888256-0.0230996729032-0.09844405307820.6742778680140.1555202326950.72970433952396.215144343820.4736490025-13.4414222503
192.260145927171.149444516441.094939060713.601084750341.629381933396.65040628632-0.1820539369980.1889338421360.0976867186927-0.059223015540.221276517770.0956808091763-0.1248049583120.473312848241-0.120639571640.4592580570630.1138679507870.03612786003360.687833618129-0.004439449145270.64027543163396.015855031317.9433091282-2.40488966233
202.0640850839-1.58725904615-2.219588234010.839617035412.02508955057.32040700039-0.2142488797330.2207841859250.229592292410.1607523913940.3305953496620.01188026564930.7105228826580.168969300361-0.1947633320810.801973358395-0.0405511983198-0.1125266594930.584629089242-0.06139274686610.82796024467790.59013847616.0978915776-6.21192384273
216.90884973142-4.03921647770.5055816062934.60160512995-0.5399887903757.90985997408-0.4290577312431.907579540040.523490289264-0.5650832580740.2135298805220.7157026004-1.056744686590.963727589353-0.03798023173010.8187213240280.05038783873940.0400570034010.5652104250710.1018625026290.66245553445988.30534448494.58584240083-36.2957333001
228.515755931690.9165390281160.4934068413912.296933191.151646193422.49495321702-1.046086951581.044664269061.61653995243-0.5415349512230.494419168829-0.42319957169-1.01695837276-0.9067124552850.2919068905250.7060586705480.0214303180725-0.06301887683470.8226613173550.01254600818790.66272053342583.74120577519.78529181075-36.4043151902
237.42956768459-1.26071567675-2.09635465593.938192753052.00219359093.60732562728-0.4852955710760.08958884136550.538725121514-0.9718263349930.05789309145650.490714537773-0.504363461902-0.03868565019760.4182054562660.7564585653340.0880707842329-0.06012204099080.7154289188470.2567674252220.68941937339979.33531049237.19742580624-34.4737342681
243.74344135529-3.72247335333-2.283710804126.22425108672-0.8805509347055.478634291110.39317660626-0.236442017218-0.611118322626-1.38238638984-0.0568971091993-0.454030263834-0.386315940021-1.19386394871-0.212130835540.564245970474-0.353731599281-0.08007836335591.005872750510.3911240116231.1876390264482.150565103213.2159019977-42.9155525521
256.576403338591.777652893711.467101171993.153837901674.048847614675.23007918286-0.2395126248541.165340387970.028079401789-0.5188049632550.271674166437-0.3885136501840.341006910475-0.6444665954260.2912418841581.330116921860.0534143652008-0.001400715372451.118533620680.234835231260.62351951743884.06794528557.50979594912-47.0104461925
262.325554932151.05189564682.959866247173.27755616496-1.389981913646.82198355054-0.2415603393970.520188387825-0.631770297788-0.2808270584970.4482901259730.165590121312-0.2599598703830.251066690234-0.3559785907370.534960075150.1908764285430.07112779050510.612794796666-0.1724609776651.1024290289170.62283670055.12988661819-5.31875974725
274.02067603892.88798819962-0.7022032619326.314354225961.136521673362.171570432870.2992634162560.390200500413-0.02780904383520.0481826322656-0.4024137482520.00327176368299-0.0777639362555-0.5033342288330.2200191014540.463294468648-0.04962237223850.1146362339150.721967625682-0.04237579097030.66908312129674.732794698613.75493227960.232703192808
285.804397397261.594907303771.07244090333.762290925151.160927443162.765065507120.1243989514520.5773033491870.688121662793-0.307156196287-0.001893721361470.2118952912740.0506583199707-0.10165259838-0.1540123376680.7811804430040.04227213653440.01595558321920.8698083993150.01454802209030.65321672203569.51981728911.9754639143-2.54168379459
290.939451661759-1.929812450712.671700811844.34310645749-5.125571964488.502898109070.001240846033870.3201758495720.6245085142290.12956366682-0.968051697866-0.3339744083652.09817670610.2935550391930.6124644991860.662940263240.03136861905870.06543055385380.4900908169310.002565447842350.93608451600884.84931492177.3875252492.92043320402
304.13570799190.1941799735372.132296459674.061518391552.853114208637.0615458418-0.09312186781970.7007913091191.29480543979-0.00822456888734-0.26079410185-0.27525070041.048064621870.2069029147270.6517412382860.8897516324870.151630579274-0.1220155741450.647487764873-0.02932427462820.7977283918163.56062298095.40863814031-20.2848253221
315.34120270603-0.355219142035-0.5998914623993.977459050173.130402480152.35776288054-0.219830537649-0.172478773419-0.396252142548-0.1324572583690.06062559028390.2421786423470.144283089646-0.0991865073222-0.3288736582670.8442742183190.0673099526876-0.07154567948190.7516861919090.168119181970.67391813366477.9087785253-1.87746165789-35.1299004538
324.40018356351-1.322323945710.1943756857657.272828045882.75652895962.412077374950.571024294406-0.910579555887-1.668896924410.5571387249550.4273221559260.7522255499451.129112291620.491125894194-0.290536079731.050195200660.216295886772-0.2773643259641.059249785910.2139405941470.89560928584577.9947472365-14.2840393606-30.2859558125
333.55286920485-4.43422521105-0.8839093748096.688356870473.647167430424.144704341250.589489476034-1.64294916933-0.380341161102-1.329986030380.5059361729040.480622919560.2890896441-0.197766486327-0.9610195395870.9160332886980.0320331378443-0.1266161407480.775051479040.1237108831780.92324484380774.03296831684.32399822323-25.5432825135
348.3538949157-0.260356938793-1.342553399834.31785332669-0.2246470496142.321049143080.390982771202-0.24028515103-0.676357978402-0.455061458236-0.395705601460.02496059771060.00356319517406-0.479338368825-0.04665346554770.7306827830650.0179406757886-0.08202481397390.9017932985790.08242446731280.51836461205177.5287240932-10.6654116723-35.5509359562
357.81023598515-1.51851350458-2.476948226478.48758243665-4.121021502055.65351558606-0.241036716831-0.837739755692-0.3484532934960.9350029336340.04831077996570.4978439015-0.1312305345981.052395936750.1474708400611.08409973156-0.103496371066-0.180484130990.837299126933-0.009853332879980.74689628993490.265326373512.046025818537.8543545494
364.06629590625-3.863735285740.5909773315333.67422332097-0.6907645048636.30102478059-0.805147639058-0.184309818681-0.5323891587581.093998009170.372237015070.508577090624-0.06609859955410.04768868091240.4554128206721.22509430226-0.02019692162520.08811729231161.024352711280.09893090669830.863793082856100.6675852593.8809909987137.1734640951
373.93444245868-2.303116312321.572786841064.535673084050.5558275886235.637631084660.1205909454230.264655422159-0.2654148558420.0730738863231-0.366597075472-0.42571794232-0.1345911839960.03953615508490.1489567383170.744361094332-0.1552366199830.05809256858950.8693876370190.07488874038360.55848773882394.512041623610.343989988124.6526107213
380.946809366085-1.54154357220.3464347381582.53334790672-0.2203618409364.713980825880.0657785984933-0.155976348594-0.1065966148360.128847897282-0.1000132058710.156131699935-0.32022662886-0.0496022482193-0.02527044446750.579847871818-0.0510271618827-0.05132107975340.578888106084-0.01200854767710.65222028035386.415350438519.689337559719.4895885553
399.46991426235-8.972538272542.908768960068.52255629904-2.643279243668.108726573870.540558336647-1.17871260872-1.551330617251.33972118193-2.192748818170.159723548329-0.8370785950392.468729845721.565821207011.30272745894-0.156695558374-0.1116569627911.331304238550.4792827715271.61130966445110.45226404512.464750222343.3541756229
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 113 )HA1 - 1131 - 113
22chain 'H' and (resid 114 through 138 )HA114 - 138114 - 138
33chain 'H' and (resid 139 through 192 )HA139 - 192139 - 192
44chain 'H' and (resid 193 through 220 )HA193 - 220193 - 220
55chain 'L' and (resid 1 through 18 )LB1 - 181 - 18
66chain 'L' and (resid 19 through 38 )LB19 - 3819 - 38
77chain 'L' and (resid 39 through 61 )LB39 - 6139 - 61
88chain 'L' and (resid 62 through 89 )LB62 - 8962 - 89
99chain 'L' and (resid 90 through 104 )LB90 - 10490 - 104
1010chain 'L' and (resid 105 through 115 )LB105 - 115105 - 115
1111chain 'L' and (resid 116 through 130 )LB116 - 130116 - 130
1212chain 'L' and (resid 131 through 157 )LB131 - 157131 - 157
1313chain 'L' and (resid 158 through 176 )LB158 - 176158 - 176
1414chain 'L' and (resid 177 through 200 )LB177 - 200177 - 200
1515chain 'L' and (resid 201 through 215 )LB201 - 215201 - 215
1616chain 'E' and (resid 333 through 379 )EC333 - 3791 - 47
1717chain 'E' and (resid 380 through 527 )EC380 - 52748 - 195
1818chain 'A' and (resid 1 through 17 )AE1 - 171 - 17
1919chain 'A' and (resid 18 through 82 )AE18 - 8218 - 82
2020chain 'A' and (resid 83 through 113 )AE83 - 11383 - 113
2121chain 'A' and (resid 114 through 138 )AE114 - 138114 - 134
2222chain 'A' and (resid 139 through 161 )AE139 - 161135 - 157
2323chain 'A' and (resid 162 through 192 )AE162 - 192158 - 188
2424chain 'A' and (resid 193 through 207 )AE193 - 207189 - 203
2525chain 'A' and (resid 208 through 220 )AE208 - 220204 - 216
2626chain 'B' and (resid 1 through 18 )BF1 - 181 - 18
2727chain 'B' and (resid 19 through 61 )BF19 - 6119 - 61
2828chain 'B' and (resid 62 through 89 )BF62 - 8962 - 89
2929chain 'B' and (resid 90 through 104 )BF90 - 10490 - 104
3030chain 'B' and (resid 105 through 115 )BF105 - 115105 - 115
3131chain 'B' and (resid 116 through 146 )BF116 - 146116 - 146
3232chain 'B' and (resid 147 through 157 )BF147 - 157147 - 157
3333chain 'B' and (resid 158 through 176 )BF158 - 176158 - 176
3434chain 'B' and (resid 177 through 215 )BF177 - 215177 - 215
3535chain 'C' and (resid 333 through 353 )CG333 - 3531 - 21
3636chain 'C' and (resid 354 through 393 )CG354 - 39322 - 61
3737chain 'C' and (resid 394 through 442 )CG394 - 44262 - 110
3838chain 'C' and (resid 443 through 516 )CG443 - 516111 - 184
3939chain 'C' and (resid 517 through 527 )CG517 - 527185 - 195

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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