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- PDB-8qrf: SARS-CoV-2 delta RBD complexed with XBB-6 and beta-49 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: 8qrf
タイトルSARS-CoV-2 delta RBD complexed with XBB-6 and beta-49 Fabs
要素
  • Beta-49 heavy chain
  • Beta-49 light chain
  • Spike protein S1
  • XBB-6 heavy chain
  • XBB-6 light chain
キーワードVIRAL PROTEIN / Viral protein/immune system / SARS-CoV-2 / RBD / XBB-6 / Beta-49 / BA.2.86 / XBB.1.5
機能・相同性
機能・相同性情報


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / 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
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)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.7 Å
データ登録者Zhou, D. / 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 Rep Med / 年: 2024
タイトル: A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity.
著者: Chang Liu / Daming Zhou / Aiste Dijokaite-Guraliuc / Piyada Supasa / Helen M E Duyvesteyn / Helen M Ginn / Muneeswaran Selvaraj / Alexander J Mentzer / Raksha Das / Thushan I de Silva / ...著者: Chang Liu / Daming Zhou / Aiste Dijokaite-Guraliuc / Piyada Supasa / Helen M E Duyvesteyn / Helen M Ginn / Muneeswaran Selvaraj / Alexander J Mentzer / Raksha Das / Thushan I de Silva / Thomas G Ritter / Megan Plowright / Thomas A H Newman / Lizzie Stafford / Barbara Kronsteiner / Nigel Temperton / Yuan Lui / Martin Fellermeyer / Philip Goulder / Paul Klenerman / Susanna J Dunachie / Michael I Barton / Mikhail A Kutuzov / Omer Dushek / / Elizabeth E Fry / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton /
要旨: BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible ...BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible for many infections in 2023. The global spread and plethora of mutations in BA.2.86 has caused concern that it may possess greater immune-evasive potential, leading to a new wave of infection. Here, we examine the ability of BA.2.86 to evade the antibody response to infection using a panel of vaccinated or naturally infected sera and find that it shows marginally less immune evasion than XBB.1.5. We locate BA.2.86 in the antigenic landscape of recent variants and look at its ability to escape panels of potent monoclonal antibodies generated against contemporary SARS-CoV-2 infections. We demonstrate, and provide a structural explanation for, increased affinity of BA.2.86 to ACE2, which may increase transmissibility.
履歴
登録2023年10月6日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年5月8日Provider: repository / タイプ: Initial release
改定 1.12024年5月22日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年6月5日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume
改定 1.32024年10月9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
E: Spike protein S1
B: Beta-49 light chain
A: Beta-49 heavy chain
H: XBB-6 heavy chain
L: XBB-6 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)117,9726
ポリマ－117,2405
非ポリマー7331
水00
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 area11650 Å2
ΔGint-58 kcal/mol
Surface area46650 Å2
手法PISA
単位格子
Length a, b, c (Å)189.106, 146.544, 51.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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要素

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抗体 , 4種, 4分子 BAHL

#2: 抗体 Beta-49 light chain


分子量: 23566.121 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 Beta-49 heavy chain


分子量: 23431.438 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 XBB-6 heavy chain


分子量: 24575.293 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)
#5: 抗体 XBB-6 light chain


分子量: 22730.949 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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タンパク質 / 糖 , 2種, 2分子 E

#1: タンパク質 Spike protein S1


分子量: 22935.734 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 (ウイルス)
遺伝子: S, 2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2
#6: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 732.682 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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詳細

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: 3.02 Å3/Da / 溶媒含有率: 59.31 %
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 citric acid pH 3.5 and 28% (w/v) PEG 8000

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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: 0.97627 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2023年9月17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: 0.97627 Å / 相対比: 1
反射解像度: 3.7→63 Å / Num. obs: 15935 / % possible obs: 100 % / 冗長度: 13.3 % / Biso Wilson estimate: 133.14 Å2 / CC1/2: 0.948 / Rmerge(I) obs: 0.78 / Rpim(I) all: 0.221 / Net I/σ(I): 4.8
反射 シェル解像度: 3.7→3.76 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 740 / CC1/2: 0.23

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解析

ソフトウェア
名称バージョン分類
GDA1.20.1_4487データ収集
PHENIX1.20.1_4487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 / 解像度: 3.7→57.92 Å / SU ML: 0.6943 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 38.6285
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.3169 828 5.26 %
Rwork0.272 14920 -
obs0.2745 15748 99.05 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 169.15 Å2
精密化ステップサイクル: LAST / 解像度: 3.7→57.92 Å
タンパク質核酸リガンド溶媒全体
原子数8044 0 49 0 8093
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00298296
X-RAY DIFFRACTIONf_angle_d0.594111302
X-RAY DIFFRACTIONf_chiral_restr0.04351274
X-RAY DIFFRACTIONf_plane_restr0.00621444
X-RAY DIFFRACTIONf_dihedral_angle_d11.68532943
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.930.42861310.39232349X-RAY DIFFRACTION95.38
3.93-4.240.38911330.3472427X-RAY DIFFRACTION99.61
4.24-4.660.31751190.29512497X-RAY DIFFRACTION99.62
4.66-5.340.34991300.27962479X-RAY DIFFRACTION99.92
5.34-6.720.33791440.27752516X-RAY DIFFRACTION99.85
6.72-57.920.26641710.21332652X-RAY DIFFRACTION99.89
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)
14.12257787768-0.80618238458-1.514720055038.383043963964.763716068823.948220763560.728052692344-0.117736539169-0.171185351008-2.693762448740.380851476462-0.562783703371-1.09105658092.04290475546-0.3599130647511.91523362618-0.131899554459-0.1850467955651.144007694380.09343240092961.243473254330.8768340825-7.04259914306-10.5656507391
27.72813503331.421806945970.3588849421619.837969241613.164243698151.049737274-0.3734897599760.5479129360960.763845413629-0.757048363698-0.279037533903-0.5375040686114.19719266504-0.2227783996630.3938606228421.93851264878-0.0453600262717-0.197617815541.263563237530.1100022200311.0568537966130.13640061290.401877938713-11.173904828
36.34405359391-5.94095124942.347507473215.52462458109-2.153443821750.8513623006850.9109881568580.281840948373-2.22477433865-1.19374534270.261904906692.840926813193.99929087562-3.730545904221.506600393412.85030972337-0.916782874825-0.1784039732371.780439928810.0816072550791.3126087366515.3621142874-8.0661104862-10.1068255209
44.944177056240.0362264889631-0.5990789916233.338834275251.54045793512.272567091960.450040931182-0.2071925564970.3385855537890.1282500254270.1201345706190.1222476613120.522333515736-0.71423779694-0.6025013881061.49895761057-0.263857961746-0.1766398021691.254798796680.3283108870511.090053394519.51183748835.0237543281-6.78590677033
50.1661791168470.422919779098-0.5389150643063.8781079442-5.491978037637.10771611660.00642758900494-0.424031093296-0.448629471385-0.982697943542-1.00475457592-2.186786626161.507512629970.0118335217577-0.4167127576761.69036553831-0.590061022717-0.07209927085181.51219033160.1549061065811.2164373820928.54032713188.334239061969.55958427608
62.50486124941-1.401268672610.8018642523763.44740143428-1.064905668086.45525138876-0.254776224213-0.7342822122810.1025128110171.34347106350.714812607489-0.06295014666170.733850994088-0.128113301449-1.558710627590.579047041771-0.0915462956508-0.3622396407221.194719284570.1538486481771.3374989664334.529135017619.45324339378.56899369455
77.02506142693-5.16847874306-3.347079320718.64123447004-0.5712263197393.683202919-3.464529601310.3538406460061.416620803420.0584761102322.936879960320.920730076499-1.142523553830.4959790786211.399075547522.03716163089-0.667663251431-0.6029450367211.794538733540.04747145761061.0748926099518.63109240051.4903945613.0582376563
86.50010365385-2.01083005988-1.918375238462.99330079938-1.173559577231.586696491540.6149482579011.339711393150.811883030003-1.669700852940.260983092821-0.6217924703992.07166542988-0.834392817659-1.074481505371.93603202728-0.332117405037-0.02507041795791.31681091750.3472798235981.3601525101224.05972979451.23770172278-15.539847334
93.62505224656-2.127747251171.681816607664.57340213064-1.032883621275.416546013651.58994710145-0.2184853741960.4436998300823.3961566703-0.888591354411-1.15003429366-0.8814092131821.63454230922-1.970479566561.70691542283-0.0227447802005-0.7278304321040.946707893767-0.2126392745681.920691074646.9765040653-23.43769433426.98444595165
104.588012571161.292996439442.75876677567.608187529671.395709749861.49706910844-0.786136599510.2382127628640.4163258173343.843789982770.259409692671-0.767299057652-0.606665071151-0.4540848700280.8009319121992.8493312857-0.605827957353-0.716624978081.394438066890.02417833586031.4990146563237.7847069866-18.87369304833.21894494489
116.21922952523-1.57642090612-0.01142786189687.891097007475.131109927643.47984468528-1.67644665993-1.76043352814-1.605116123173.54761895523-0.298904696959-0.1816862889250.380270308057-0.479152693419-1.149217484933.33328376065-0.350217147319-0.8751294229170.8434622096050.04753664823511.0447937210638.5641717052-25.37803575459.33379397315
124.20967935447-0.815256743710.4079171566121.388275351280.3807483703336.07133731879-0.965150008616-0.008864446445740.966066232580.4597965333030.435751833241-1.24566816633-1.33748231529-1.233268303910.8565555619821.360998475280.0180270462835-0.1733652631610.844698273573-0.2471856449911.1684145871242.9787254912-27.99496747074.3390082092
134.908030526351.50713097294-0.9391927535718.319525506750.8460558984431.048012868280.7791362284-0.108278054709-1.458260051141.370312485-1.049710790070.6928112745431.16012250026-1.129361226880.2171264303110.381716374530.2219598224740.1663328384731.61114481458-0.4284257685152.1489019471641.9740919959-64.80304597910.7070503507
145.03679186986-3.57553282786-0.7760985675225.56736190181-2.257199331487.73663322944-1.189993925910.249196870989-1.258473611481.01771185517-0.656596241471-0.141164193892-2.073283441310.684536374758-1.076725361670.8637122667480.4168594114120.08560210038480.879613343166-0.249653296961.227159282549.1040171707-51.604249215313.4519557717
150.67904283273-1.859908007690.2431280565577.578066911962.60942181066.515676213090.968042100881.06574948370.5808858521771.33142336353-0.7571343286491.357221588461.73505451751-0.9384699775070.2124341759581.035624993780.5879591282510.2944362840241.317733820330.24035127491.6417575545553.9703806688-56.4761078167.5482904779
164.044676416870.326733515837-0.2952889832394.11399101746-0.7437546522773.90262020775-0.790206602374-0.703919515608-1.09275418538-0.01371957271891.48919018852.89252001775-0.654585350723-1.874157715622.62047038691.129858132350.360788552503-0.03485947614411.60427569311-0.1642538292651.6504502681944.8792111153-53.456312992810.5613290512
176.49723047608-1.15289159381-1.675085001971.220642935951.036394007067.3701179267-1.59151559884-0.9113075388230.5827941511911.737792770470.251024384404-0.972094156472-0.874451311792-0.8034886010510.527832474941.499551050350.129474572972-0.1620113078461.01819521486-0.1014424975531.0034634139952.8326269914-59.637368971318.2457993777
189.07122753464-7.50840223152-4.364194685157.914424422114.692635746334.994110231892.144099958582.80448388902-0.586372277797-1.60212343986-2.43411274920.08374290786312.00883312777-1.109526577851.233281407061.70959333480.10878224986-0.4353092689112.06963439381-0.5569432362620.92191925109427.7681130866-38.2414507202-13.2819977876
191.42530131070.3002669133091.564267467266.073689305990.2870938795276.67311274940.06693134724051.573303068-0.105840255762-0.943653609233-0.0914347385742-0.1117884812630.1080851912721.99311505415-0.03746377613661.259621687020.262349689244-0.2364968873421.55531113548-0.07977974388511.0708702572232.9544175744-29.9027982539-16.0272451843
200.62601708698-1.831043579750.6809005048497.38199834916-1.794110496151.278168553340.573177279490.577544676393-0.886276822971-1.62247434148-1.32368456941.03436186921-0.509046006544-0.350921166372-0.1556128248651.56506462670.057972132966-0.1625244611241.36845967599-0.225692899221.1499496052730.5812912653-35.2975624874-8.46442550177
213.35447432019-1.071481859061.36809008814.749493072510.4167373599366.97776074539-0.5966004507960.929933216613-2.146633900130.353455481359-1.392217674752.956649974411.958211309720.253818181784-0.5332166640311.01703972192-0.05763153362060.4625604267361.46800183555-0.4783483919892.5482952692437.0802999033-60.145194833511.6120691628
220.336213434088-1.003152242520.3149811656183.979053641130.05356662478351.37169892543-0.08061076239640.381547290178-2.709745128141.47524959294-0.4142595254161.5207070258-0.00816809267811-0.1189181171281.030413879720.45817585930.241486710108-0.1877228765571.88209082949-0.4814408048443.1539345994229.6948378419-51.25118410989.05851391441
231.719132846690.4037664509370.5822284028770.910794238049-0.5385978006471.39587366356-0.0511839172431-1.26325000884-3.30174476971.29464099850.2321720435682.270361882471.2488139050.518981126784-0.218678791717-1.133334124751.917898241991.972730905570.324675469757-1.287156426342.1404483394338.2255209178-53.99132624628.14929538156
241.82698058897-1.99080334141.245292672826.18701259521-1.221553160934.2931395651-1.17206977272-1.20389197692-2.02737715611-0.3350493065091.523426127311.714566725640.330782615337-1.22557320111-0.2498788106640.277274134245-0.9365138241030.5406107585672.850355990260.09868859941052.386309161727.2224740628-59.06116870814.0026564372
254.08640974022-3.48138791351-2.66444615092.767547604772.398240910533.69784147581-2.020164908540.6574738217431.20830026907-0.2751860301680.8380631776342.290013782780.2772681812060.393467649618-0.3648633635481.10232582847-0.918598610563-0.4473206645641.162023197290.1760063353063.1565997547127.4675499548-60.81963171156.0876626631
266.11227448366-3.22593803975-5.169988561785.335257829012.488158208883.3692575854-1.403375770670.4526127783950.4482811112342.100459830030.850096240285-0.0509217688462-1.485970824270.0968571749165-0.3796498846571.617413772440.07657813538920.02283686171770.9224490040650.06104913461981.1459705050719.048663442640.851374028810.7997315745
278.990046964780.498492003096-6.085734986885.618361599512.329228080879.21124880335-0.09459822212763.951385557460.49783363044-1.317818335440.5851695652410.689275400352-0.00462223750485-0.890305467535-0.2731194610291.449022212860.08921299373590.2238661060661.417428462870.6613600539581.522542316615.153142965935.24647871661.02206825441
283.375918685371.69909923882-0.3200023404881.628461294510.4809853678080.8382725229160.2563745492491.240507045532.88953932041-2.219497119080.518793254409-0.356459148507-1.004525245420.127700082679-0.3708601682821.264446784430.0347619117737-0.1224625301791.444155757910.6433536479351.8954678023217.584072632443.54582357124.4502526602
291.30558180826-1.90714639342-0.6782249770729.92549706513.89217232153-0.1022280992050.4162474263120.167800673658-0.0841555435456-1.116450041490.179724385357-0.320079322537-0.0601263475006-0.884294629287-0.4142373778581.245474898830.304656865288-0.08804969539451.232649711180.3277079630071.3119412406616.04811899337.384022420412.7757878296
300.981256530883-0.963520839923-0.5837051354922.32731854197-1.555703243491.977211859560.451363428144-0.3041835799351.29759851309-0.352783906614-0.711542771071-0.316602715531-1.910694630590.6358131741040.0001700537247881.699245343520.331245544790.02179784098772.385660091030.1835644333162.040931344452.9028223411360.219897692336.3105985225
310.6422363833240.02617051006640.9142547328661.32102201782-2.128265891693.06919845610.147009990636-0.1546566155190.008246326375431.23149513638-0.3681411804011.56472816714-0.157478841882-0.337944907652-2.78805920938E-51.3922702323-0.1954092469250.389482767431.08666757640.08802995096411.60604546378.3661427281222.629434171919.1600613283
320.257670944665-0.385844722931-0.2884332057290.1716276350230.7485684227151.85582498945-0.9287386891040.2688027859150.08383086144961.583530993460.04765080547250.227746328914-2.366631398840.862438973908-0.01274178181251.52066887374-0.062700192470.3532168557931.111507033680.4369238203661.293297259328.985647307922.773045936823.0477966833
331.552163228710.9092876173471.085203703641.141883662041.925684315863.11797103019-1.07266605296-0.8571705935170.652239185447-0.4504475615530.2768228118230.2960329998711.79931034966-0.952747534939-0.0001867147479712.608676664140.1159654535230.3534617580732.006563147770.09737315236541.80958925133-11.168087459451.900379677734.7223580711
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 'E' and (resid 330 through 349 )EA330 - 3491 - 20
22chain 'E' and (resid 350 through 364 )EA350 - 36421 - 35
33chain 'E' and (resid 365 through 375 )EA365 - 37536 - 46
44chain 'E' and (resid 376 through 442 )EA376 - 44247 - 113
55chain 'E' and (resid 443 through 459 )EA443 - 459114 - 130
66chain 'E' and (resid 460 through 494 )EA460 - 494131 - 165
77chain 'E' and (resid 495 through 506 )EA495 - 506166 - 177
88chain 'E' and (resid 507 through 527 )EA507 - 527178 - 198
99chain 'B' and (resid 1 through 18 )BB1 - 181 - 18
1010chain 'B' and (resid 19 through 76 )BB19 - 7619 - 76
1111chain 'B' and (resid 77 through 91 )BB77 - 9177 - 91
1212chain 'B' and (resid 92 through 115 )BB92 - 11592 - 115
1313chain 'B' and (resid 116 through 130 )BB116 - 130116 - 130
1414chain 'B' and (resid 131 through 152 )BB131 - 152131 - 152
1515chain 'B' and (resid 153 through 165 )BB153 - 165153 - 165
1616chain 'B' and (resid 166 through 190 )BB166 - 190166 - 190
1717chain 'B' and (resid 191 through 216 )BB191 - 216191 - 216
1818chain 'A' and (resid 1 through 17 )AC1 - 171 - 17
1919chain 'A' and (resid 18 through 100 )AC18 - 10018 - 100
2020chain 'A' and (resid 101 through 124 )AC101 - 124101 - 124
2121chain 'A' and (resid 125 through 150 )AC125 - 150125 - 146
2222chain 'A' and (resid 151 through 170 )AC151 - 170147 - 166
2323chain 'A' and (resid 171 through 193 )AC171 - 193167 - 189
2424chain 'A' and (resid 194 through 205 )AC194 - 205190 - 201
2525chain 'A' and (resid 206 through 219 )AC206 - 219202 - 215
2626chain 'H' and (resid 1 through 44 )HD1 - 441 - 44
2727chain 'H' and (resid 45 through 70 )HD45 - 7045 - 70
2828chain 'H' and (resid 71 through 91 )HD71 - 9171 - 91
2929chain 'H' and (resid 92 through 131 )HD92 - 13192 - 131
3030chain 'H' and (resid 132 through 226 )HD132 - 226132 - 220
3131chain 'L' and (resid 3 through 51 )LE3 - 511 - 49
3232chain 'L' and (resid 52 through 117 )LE52 - 11750 - 115
3333chain 'L' and (resid 118 through 214 )LE118 - 214116 - 212

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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