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- PDB-7zf3: SARS-CoV-2 Omicron RBD in complex with Omi-3 and EY6A Fabs -

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データを開く


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基本情報

登録情報
データベース: PDB / ID: 7zf3
タイトルSARS-CoV-2 Omicron RBD in complex with Omi-3 and EY6A Fabs
要素
  • EY6A heavy chain
  • EY6A light chain
  • Omi-3 heavy chain
  • Omi-3 light chain
  • Spike protein S1
キーワードVIRAL PROTEIN (ウイルスタンパク質) / SARS-CoV-2 (SARSコロナウイルス2) / Omicron (Ο) / RBD / antibody (抗体) / Fab / Omi-3 / EY6A / VIRAL PROTEIN/IMMUNE SYSTEM (ウイルス性)
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 / 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 / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / 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 / エンベロープ (ウイルス) / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / 生体膜 / identical protein binding / 細胞膜
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
2-プロパノール / スパイクタンパク質
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.15 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

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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: EY6A heavy chain
L: EY6A light chain
A: Omi-3 heavy chain
B: Omi-3 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)118,38111
ポリマ－117,8935
非ポリマー4896
水0
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: homology
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area12720 Å2
ΔGint-52 kcal/mol
Surface area45030 Å2
手法PISA
単位格子
Length a, b, c (Å)87.517, 119.889, 134.019
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

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要素

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タンパク質 , 1種, 1分子 E

#5: タンパク質 Spike protein S1 / SARS-CoV-2 Omicron Spike protein / RBD / Spike protein receptor binding domain


分子量: 23157.164 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2)
遺伝子: S, 2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2

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抗体 , 4種, 4分子 HLAB

#1: 抗体 EY6A heavy chain


分子量: 24318.260 Da / 分子数: 1 / 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 EY6A light chain


分子量: 23315.855 Da / 分子数: 1 / 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: 抗体 Omi-3 heavy chain


分子量: 23634.482 Da / 分子数: 1 / 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)
#4: 抗体 Omi-3 light chain


分子量: 23466.943 Da / 分子数: 1 / 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)

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非ポリマー , 2種, 6分子

#6: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル / グリセリン


分子量: 92.094 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C3H8O3
#7: 化合物 ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / 2-プロパノ-ル / 2-プロパノール


分子量: 60.095 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O / コメント: alkaloid*YM

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詳細

研究の焦点であるリガンドがあるかN

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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: 2.98 Å3/Da / 溶媒含有率: 58.75 %
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 citrate tribasic dihydrate pH 5.0, 30% (v/v) Jeffamine ED-2001 pH 7.0

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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: 3.15→74 Å / Num. obs: 252075 / % possible obs: 100 % / 冗長度: 13.7 % / Biso Wilson estimate: 77.01 Å2 / CC1/2: 0.955 / Rmerge(I) obs: 0.491 / Rpim(I) all: 0.136 / Net I/σ(I): 5
反射 シェル解像度: 3.15→3.2 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1209 / CC1/2: 0.33 / % possible all: 99.2

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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: 7QNW

7qnw


解像度: 3.15→73.28 Å / SU ML: 0.4714 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 25.4111
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2661 1232 4.93 %
Rwork0.2076 23770 -
obs0.2104 25002 99.87 %
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: 77.91 Å2
精密化ステップサイクル: LAST / 解像度: 3.15→73.28 Å
タンパク質核酸リガンド溶媒全体
原子数8074 0 32 0 8106
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00238296
X-RAY DIFFRACTIONf_angle_d0.498711278
X-RAY DIFFRACTIONf_chiral_restr0.04231256
X-RAY DIFFRACTIONf_plane_restr0.00451445
X-RAY DIFFRACTIONf_dihedral_angle_d10.86952955
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.280.35641410.31212576X-RAY DIFFRACTION99.41
3.28-3.430.33671190.29062594X-RAY DIFFRACTION99.71
3.43-3.610.34731270.25082612X-RAY DIFFRACTION99.89
3.61-3.830.30011510.24562602X-RAY DIFFRACTION99.93
3.83-4.130.25551350.2092616X-RAY DIFFRACTION100
4.13-4.540.22451230.1722638X-RAY DIFFRACTION99.96
4.54-5.20.22041360.16372665X-RAY DIFFRACTION100
5.2-6.550.23651380.19312669X-RAY DIFFRACTION99.96
6.55-73.280.26161620.19052798X-RAY DIFFRACTION99.97
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)
12.546687909211.20818395658-0.7496379992313.98375332063-2.308431885485.7233060052-0.186703473858-0.1792470700460.2163704889550.0636050176283-0.18272882211-1.28028122170.3405903008350.5959192541070.1913348738050.6168362451390.0925622126236-0.03992269490370.753186305271-0.1271812972730.7542572365555.21794996573-44.42475663465.89039929677
22.45869603169-0.578532472842-1.001021613013.88459671645-0.6744762562365.373536693370.195670357194-0.134144623405-0.1520882697880.2940428251430.318885050249-0.08811782052120.3688732917730.426370605308-0.6101761612020.564028847984-0.00208791863694-0.09201456536730.732008915868-0.05582055275150.5890718682240.14431127397-40.876520357211.9982880677
31.219879936090.774603604461-0.5354552339314.73642791958-0.4911796490750.939589516970.09564887139350.1981080632240.1266967813920.6407221214850.0589910912487-0.1546709096350.1571787689650.0919061998252-0.113820796560.57486589818-0.00670041179105-0.100317526050.6557439299260.009469534372040.592416691106-8.06451181825-52.24769044754.94404973432
43.757996838040.8834503251090.9367137124283.21644644079-1.180865911210.489357886496-0.01964726109490.493047381772-0.0002787721460060.2406644291710.0691472036128-0.007860325978380.04834942324880.4953844941650.1451064572690.8605133049530.0857922249239-0.02574647203870.532730362297-0.005444769934930.547706893888-16.3644217076-69.53919816720.0990587657725
54.953979436394.360831913723.002136262199.387145592796.02774931514.884764281880.5401199641091.08912954507-0.7905132513850.879714654027-0.165809082369-1.339916970131.534024302890.901913403909-0.3751504760940.9405932242390.131941982609-0.01035668731880.8565013007240.1023711681350.799838781006-12.5922593968-78.218421899-2.03303365729
63.805164310412.210783513151.18113139438.771094815747.616400975956.8860986222-0.3638623048380.5939760534440.2944251235810.840238343618-0.673096933011.552658455671.879674964120.1784939335750.7029638342680.608352668069-0.1467065527510.1218126367720.594412839975-0.00881975528920.691742051581-23.3647879894-38.560007111-1.88528837643
75.603007388614.038035361792.204027386672.77584781970.9390110586048.69304695873-0.1948774367760.4676231363440.538348042055-0.429568274655-0.01528134992750.314286756967-0.31718208294-0.2321358639440.2354297217040.535679806765-0.000927058078703-0.04834802903180.385161057628-0.001218974625330.529468506483-15.2162185795-32.6051738691-3.12827940269
80.8392627638351.649966799071.553762126374.771367040311.924431022640.4621651420430.1477169234110.0240156759743-0.07100457099320.1770667944590.08816751838190.1503732623530.4295913063940.130683688954-0.1172123705620.60033798936-0.07529614240770.04178556856870.556431637672-0.02995010789420.571895513645-18.7863875807-41.3297769241-3.14326038968
95.10938955276-1.905269795780.3679673740544.66921192323-1.409754958725.162789750730.0928564298461-0.49634647915-0.271907415169-0.27457313354-0.1806700310970.1868240748740.6807128297880.0303708884789-0.006321923887760.718008930833-0.01327062872820.1128749268980.5020474760160.06265769109820.676344894039-27.8835603316-68.76147592364.71976204318
101.5247646121.131058809762.394789124036.51994063431-2.000173176666.412874789580.062266331649-0.254117867381-0.1430799027931.04156733762-0.259422224007-0.133101718675-0.725969711722-0.1790261924330.2734577803380.5925302918360.09014384889540.09712603815560.598462730953-0.0156712254880.54702865861-26.7527449408-61.43601231672.80817920815
112.08357527765-2.731666767940.3469204536685.38674704878-1.529312134574.20197967996-0.78618388449-0.719739864412-0.05777327514570.6993570792521.234222684370.1945287746840.613904630174-1.40128601875-0.7348635188011.06981260744-0.0912975548087-0.006389664497130.6851626202910.1243936618590.77401681861-30.3591486447-70.87760260110.8493338774
121.584543004720.3560715344391.409802837263.12057470493-2.302819360717.067036184630.275229313125-0.747147287705-0.1204829459891.152120505650.9483438057310.90264847513-0.511005251064-1.85114849481-1.052276225130.646625190455-0.1997236527070.002657123625010.9162556008150.1773193808981.13129782457-37.7104234852-69.31886560022.46843303266
135.553501382012.000231356793.755277110482.75292458086-0.7465956201454.622433611240.5911498287410.345254032590.537254880558-0.528144298133-0.8850114876220.5880055826670.150031771456-1.373201004220.1861548292440.361175273119-0.08547599359740.01783806424350.7534276809850.05771673134830.518969002983-51.1736808957-28.745920189125.669894963
144.221487904383.008123586140.1739509779023.876969264550.4498040265026.05471184314-0.1250911474380.4514239226510.0245949635383-0.1586109235580.2377826517110.2703469558930.279782184855-0.0342235546344-0.1254904433980.6131273088140.04761792225850.03850340359310.5437669730090.004032556808780.458359578892-39.5409240068-26.367420067526.5921747407
155.145857117372.26224286689-2.522212231921.08911588103-0.4317316304914.60690398895-0.3420720515360.8497300835030.0409903648980.4731581125950.5144503268660.5994109425010.742397831155-0.908589577479-0.06200506337360.7093503140390.03152590398140.01823836080980.8126970081870.1114085366260.340903018612-44.9147741406-29.091785580921.5203423362
168.739683027378.019432028752.425943347537.190986312192.195835044438.02475886462-0.02910881472870.3543629899090.101750502205-0.321506384438-0.1147031809290.867537342283-0.2369883833150.5604784208290.205580994310.4908336442240.06545247429940.09540416456170.56605359120.07175024342280.740184097404-41.0924318776-25.075169971935.8390623789
176.72349731960.2256672752-2.489354309965.054953223682.285382750771.995306072-0.5009293317831.1835885615-0.649177126775-1.805703064980.7263862153720.458614943249-0.141083992668-0.7002621275970.1150066816651.0936978537-0.05934513614450.08891447727890.8095290273550.1015474395450.433223360627-57.7347105325-40.222481267123.4858828206
186.54261360601-0.398744341943-3.723283454222.352460623-2.552042985545.33598183936-1.69115492151-0.893886827587-0.187444061488-0.550655229638-1.096002977730.318029951242.26015041197-1.516811756791.100643496340.638021032593-0.1637560298950.1315411409580.877493437994-0.1406116225030.871140178225-76.6804309339-41.867669681243.3934019249
196.60777568790.0301515663937-2.240781445240.743412594322-2.334346014047.401425038280.687697364538-0.569861665670.114910022413-0.242587191309-0.0955510497608-0.549605197781-1.998044155690.145602443988-0.9570361879440.9350246849930.02852246403320.1454317550140.723844505437-0.1135307332130.715615607186-66.6857171233-39.18849487335.4736629673
202.963563718810.7818650556560.2882014547814.57539891531-1.093093832950.3755567790981.5860763398-0.2940472459470.7080285071250.765261658055-0.6496455991790.291299316485-1.91802400876-0.3316558476430.5833700538761.510560024880.09227878073580.67701081180.441594611054-0.0525557003461.45399761078-66.6209005257-31.147913731445.7928915467
215.052943985160.5959648377761.965416050249.66693845648-0.6726544002940.840017467834-0.4140411916610.452994490558-0.636858339617-0.8850901962511.786765843641.663410315560.1585527945481.02605776591.635989960340.6402552985170.05275375420730.1963641097920.6852425761630.02140709930790.590899285401-62.1709769348-48.209563436333.2173115055
225.642720849420.6485714993991.919192236083.652041667644.026044388148.22029289971-0.0187932065588-0.4396053963470.7711343070711.36521337392-0.4714968987180.561995920445-0.0337970019217-1.379292522480.05191504386330.983868771304-0.008263885347720.2856631512840.513317481038-0.1540131532910.786345091461-73.2250488092-35.811880644445.969379256
233.182799676230.617019785925-2.299871829071.60963653072.049001252125.371262073340.3385276559750.89029748011.280714494880.4235137057680.2426050168910.166809169232-2.47000017838-1.39137057537-0.5418321843471.587198936060.2614467766750.2519751552410.8914746893210.1203688515660.850321941-71.7183653796-33.143526963333.8076993088
245.00313625018-0.06818592326820.3045433451853.67778279721-0.7098753809362.44161212374-0.34741014246-0.845437243479-0.6072387234740.6397133047830.122643672174-0.4705749006571.493608526790.6195008498210.08566301699411.06245727563-0.0139157243953-0.01895516880870.609383954952-0.0392301453960.507024311914-36.5829950767-40.542343037550.5716620254
255.764300203320.5515343363270.02900932690174.76433973528-0.7191038342943.719090229380.0950511150686-0.73549203335-0.1915689458250.320529061867-0.0585503203359-0.3149894196230.2211138444910.261766110851-0.0981930289890.789322039495-0.04652359011070.06354534749950.6919918464650.01394347485460.491840894974-34.4892007955-30.391489007648.1763626194
261.84889188930.8637156781792.624773130412.68877251165-2.070312657857.32477433230.09129938170690.1039934838170.561649093419-0.06382371489320.1818600526670.3315353657960.0163600598468-0.251539422013-0.4990922573340.849053048297-0.02435447226130.01894396260040.6338745937430.01584991279710.520949813924-38.1421160992-33.355890181144.9315871404
273.602682622541.084333251120.1275951605510.2739897777160.05512228338980.3053701828750.491916689976-0.184906012791-0.2800232969750.0719610452107-0.2975220786640.06573657248010.5484133409590.0728217951183-0.06892586442950.856210050645-0.09233352273860.2325551414870.57725651088-0.02794951236130.656819377424-58.5644451694-44.669178712354.3738424605
286.483916418372.11558343772.057306098170.9057447370240.5941937504734.51460330055-0.516913106671-0.1046488006141.203155472650.258998085055-0.2561484570560.885490379414-0.196904939245-0.9040321893630.1385478158280.842907216261-0.01976270438780.1215675608580.7668314386750.04027131433690.770481397992-74.2588981918-47.644407266840.1357419517
296.322489300221.642503671523.077881740473.027775456830.8891667197652.169484849730.1177600922050.302649918953-0.4032071919620.2777130932150.0939501097786-0.205221780915-0.02768645400560.452025670455-0.1136284927130.73416354483-0.002366645950290.1442945662420.5352012521620.004798726176830.52819908743-62.9366168264-51.78341992148.1165813239
307.371728717391.176887483220.2896093389141.52299437555-0.481490894835.036482644190.5363733557850.706934987975-1.94356177505-0.634830207171-0.236076778866-0.5710032611440.411630872830.0190453730744-0.05111619305180.874916533872-0.07843031241990.1239802156930.63836877777-0.1444587733180.591470587832-72.7242244654-54.055650157239.0169421757
314.456157263220.5107999666022.178940763010.8557517685460.8785064368444.365522552520.02831881703870.203092273090.4124618257440.223350026905-0.2789682675570.3690553208070.03695836394640.28917584662-0.1470484052480.758788370724-0.1687644657840.01764187604990.5880999315080.06607527834780.689333483656-73.4516638791-56.005528926351.3392741476
325.262490432660.184841729473-0.901602865762.857467443080.9145039660866.463002183140.113264442797-0.295350623642-0.7402182704520.509748312886-0.03579791502510.003835177953150.6560613583680.3920938783-0.339846227940.778945972254-0.1510528915080.05711534148980.618464684209-0.1459031755990.610492993447-2.11657554522-13.176142940629.4680024311
336.18330278784-0.57385302031-6.777103167326.327409640350.6664265686787.49715898051-0.145732411453-0.630817107965-0.08536760797940.138850933770.1333891169670.1942272131110.01985519474410.6077530003830.07311486379260.453522514664-0.0232875853208-0.1688618949340.634655173522-0.09910264781740.613375703454-0.437136037923-19.823614909821.295042012
343.48736934472-0.926299526513-3.141137310252.4886772232-1.422832238844.817825669720.155962879761-0.384045981023-0.08982247015290.212549486888-0.0736162578088-0.5324198524250.3863801173320.431580365282-0.08906371035920.591365333494-0.0384349184059-0.009393451418690.631017460153-0.111353203470.588089171059-6.93031888206-19.303752462219.7104493825
359.41566104416-2.06279515759-2.149968726974.846359176290.1067121302356.449357706650.0694116617403-0.1644166175760.550882579311-0.706446035108-0.227195449124-0.405345274225-0.125349133012-0.5915522107260.02667533188630.547128135905-0.0343085787999-0.08353754526430.4589795613640.03227407035150.459432883822-15.741863535-19.830263333722.2138494506
362.34819259172-1.84210364183.919807506316.81025219984-1.122569503967.05640165898-0.310732715447-2.213531783911.295650273451.197005352490.250886240658-1.267732430690.04875413465430.354334967935-0.2032604408440.7193837129580.166412014214-0.09109059511071.27388942664-0.05863404351750.609791977379-10.2529156846-21.909490896543.4802351783
376.431469492180.7595778899631.56972701471-0.04353146811150.1942296415023.560522125980.148801636681-0.6086912912370.9410875474240.06208044075770.07138846503640.29988563141-0.706995242143-0.307847993699-0.2903113472920.7425154551220.05176047028030.1225961029750.478827117746-0.04944994301410.769707240103-28.6060656715-9.5380210661333.703364842
381.46193787921.728524204722.257596557113.278868856871.78405901298.038075303340.665415384351-0.135053936792-0.2858954417480.201747371083-0.0979963752221-0.1471837772391.56429263869-1.44364275991-0.6048619438860.871976807229-0.191175735097-0.2643141949740.8864638116190.3243435775720.715836228121-15.3285671317-27.581210513841.1082734895
396.521368295322.76175041313-4.430264614747.74357417061-3.976754990868.227158631490.304902998442-0.1858211510110.503923766372-0.4368342292840.2167591878440.624794488349-0.3318205468520.331025245635-0.08389530324150.4838637478810.0438470458271-0.02403251980680.531281448065-0.0274809748180.465186948979-3.72051831257-13.937603830717.5525005905
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 33 )HA1 - 331 - 33
22chain 'H' and (resid 34 through 99 )HA34 - 9934 - 99
33chain 'H' and (resid 100 through 142 )HA100 - 142100 - 137
44chain 'H' and (resid 143 through 196 )HA143 - 196138 - 191
55chain 'H' and (resid 197 through 222 )HA197 - 222192 - 217
66chain 'L' and (resid 1 through 18 )LB1 - 181 - 18
77chain 'L' and (resid 19 through 75 )LB19 - 7519 - 75
88chain 'L' and (resid 76 through 114 )LB76 - 11476 - 114
99chain 'L' and (resid 115 through 151 )LB115 - 151115 - 151
1010chain 'L' and (resid 152 through 173 )LB152 - 173152 - 173
1111chain 'L' and (resid 174 through 198 )LB174 - 198174 - 198
1212chain 'L' and (resid 199 through 214 )LB199 - 214199 - 214
1313chain 'A' and (resid 1 through 17 )AD1 - 171 - 17
1414chain 'A' and (resid 18 through 72 )AD18 - 7218 - 72
1515chain 'A' and (resid 73 through 90 )AD73 - 9073 - 90
1616chain 'A' and (resid 91 through 111 )AD91 - 11191 - 111
1717chain 'A' and (resid 112 through 124 )AD112 - 124112 - 124
1818chain 'A' and (resid 125 through 140 )AD125 - 140125 - 135
1919chain 'A' and (resid 141 through 159 )AD141 - 159136 - 154
2020chain 'A' and (resid 160 through 170 )AD160 - 170155 - 165
2121chain 'A' and (resid 171 through 180 )AD171 - 180166 - 175
2222chain 'A' and (resid 181 through 198 )AD181 - 198176 - 193
2323chain 'A' and (resid 199 through 218 )AD199 - 218194 - 213
2424chain 'B' and (resid 1 through 18 )BG1 - 181 - 18
2525chain 'B' and (resid 19 through 76 )BG19 - 7619 - 76
2626chain 'B' and (resid 77 through 103 )BG77 - 10377 - 103
2727chain 'B' and (resid 104 through 120 )BG104 - 120104 - 120
2828chain 'B' and (resid 121 through 141 )BG121 - 141121 - 141
2929chain 'B' and (resid 142 through 174 )BG142 - 174142 - 174
3030chain 'B' and (resid 175 through 190 )BG175 - 190175 - 190
3131chain 'B' and (resid 191 through 214 )BG191 - 214191 - 214
3232chain 'E' and (resid 333 through 353 )EI333 - 3531 - 21
3333chain 'E' and (resid 354 through 380 )EI354 - 38022 - 48
3434chain 'E' and (resid 381 through 409 )EI381 - 40949 - 77
3535chain 'E' and (resid 410 through 437 )EI410 - 43778 - 105
3636chain 'E' and (resid 438 through 451 )EI438 - 451106 - 119
3737chain 'E' and (resid 452 through 494 )EI452 - 494120 - 162
3838chain 'E' and (resid 495 through 506 )EI495 - 506163 - 174
3939chain 'E' and (resid 507 through 527 )EI507 - 527175 - 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