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- PDB-8cbe: SARS-CoV-2 Delta-RBD complexed with BA.4/5-2 and Beta-49 Fabs -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 8cbe
タイトルSARS-CoV-2 Delta-RBD complexed with BA.4/5-2 and Beta-49 Fabs
要素
  • BA.4/5-2 heavy chain
  • BA.4/5-2 light chain
  • Beta-49 heavy chain
  • Beta-49 light chain
  • Spike protein S1
キーワードVIRAL PROTEIN / SARS-CoV-2 / BA.4 mAb / BA.5 mAb / RBD / BA.4/5-1 / BA.4/5-2 / BA.4/5-5 / Beta-49 / 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 / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
類似検索 - ドメイン・相同性
Spike glycoprotein
類似検索 - 構成要素
生物種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: 3.16 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: Nat Commun / 年: 2024
タイトル: Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4/5 infection.
著者: Liu, C. / Das, R. / Dijokaite-Guraliuc, A. / Zhou, D. / Mentzer, A.J. / Supasa, P. / Selvaraj, M. / Duyvesteyn, H.M.E. / Ritter, T.G. / Temperton, N. / Klenerman, P. / Dunachie, S.J. / ...著者: Liu, C. / Das, R. / Dijokaite-Guraliuc, A. / Zhou, D. / Mentzer, A.J. / Supasa, P. / Selvaraj, M. / Duyvesteyn, H.M.E. / Ritter, T.G. / Temperton, N. / Klenerman, P. / Dunachie, S.J. / Paterson, N.G. / Williams, M.A. / Hall, D.R. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
履歴
登録2023年1月25日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年2月7日Provider: repository / タイプ: Initial release
改定 1.12024年5月8日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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: BA.4/5-2 heavy chain
L: BA.4/5-2 light chain
E: Spike protein S1
B: Beta-49 light chain
A: Beta-49 heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)118,4136
ポリマ－117,6815
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 area12200 Å2
ΔGint-60 kcal/mol
Surface area45950 Å2
手法PISA
単位格子
Length a, b, c (Å)179.861, 147.022, 52.197
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 HLBA

#1: 抗体 BA.4/5-2 heavy chain


分子量: 24359.309 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 BA.4/5-2 light chain


分子量: 23387.990 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 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)
#5: 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)

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タンパク質 / 糖 , 2種, 2分子 E

#3: 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

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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: 2.93 Å3/Da / 溶媒含有率: 58.05 %
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 and 18% (w/v) PEG 20000

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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: I04 / 波長: 0.95373 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2022年11月25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: 0.95373 Å / 相対比: 1
反射解像度: 3.16→60 Å / Num. obs: 24651 / % possible obs: 100 % / 冗長度: 13.3 % / Biso Wilson estimate: 101.13 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.345 / Rpim(I) all: 0.098 / Net I/σ(I): 6.1
反射 シェル解像度: 3.16→3.21 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1210 / CC1/2: 0.322 / % 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
GDA1.20.1_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
開始モデル: 7Q0G

7q0g


解像度: 3.16→56.92 Å / SU ML: 0.4584 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 26.8599
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2657 1206 4.91 %
Rwork0.2262 23351 -
obs0.2282 24557 99.78 %
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: 102.96 Å2
精密化ステップサイクル: LAST / 解像度: 3.16→56.92 Å
タンパク質核酸リガンド溶媒全体
原子数8085 0 49 0 8134
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00238328
X-RAY DIFFRACTIONf_angle_d0.517811327
X-RAY DIFFRACTIONf_chiral_restr0.04251277
X-RAY DIFFRACTIONf_plane_restr0.00461451
X-RAY DIFFRACTIONf_dihedral_angle_d11.55122987
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.290.34941220.34192549X-RAY DIFFRACTION99.11
3.29-3.440.34241100.3172552X-RAY DIFFRACTION99.92
3.44-3.620.30291350.28782534X-RAY DIFFRACTION99.93
3.62-3.840.30191410.27532572X-RAY DIFFRACTION100
3.84-4.140.29991410.24722541X-RAY DIFFRACTION100
4.14-4.560.26551270.20252612X-RAY DIFFRACTION99.96
4.56-5.220.251400.192616X-RAY DIFFRACTION99.93
5.22-6.570.2691490.21182613X-RAY DIFFRACTION100
6.57-56.920.21451410.19632762X-RAY DIFFRACTION99.21
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)
16.63825066280.561794064715-3.342703763685.79269740766-3.594985721743.59628684948-0.223780235649-0.2287758736451.26834390972-0.0153437085309-0.06395236488561.05709351473-0.789851109880.225208114156-0.120443097820.7732258152060.147026593287-0.05645087716060.53675709095-0.04906617110240.480023387826-9.07257.755-16.727
24.67027099852.877407483940.7182678119097.82205227454-2.095172067923.66382453722-0.5414593794050.8723051886130.8945464441720.3331801948621.423901710911.722335242060.03413272484620.0721523587497-0.2513072621240.874188747120.1046854105740.1182543020041.17367680134-0.1317287165170.999577891086-19.48250.776-13.911
33.261984755161.978401443290.4824259257077.2221338715-3.565807699654.00499843338-0.0289450608752-0.45682861624-0.375401969240.896635512186-0.455798476004-0.0786741671358-0.945676165132-0.259458529190.3077017813010.836246174252-0.0968571958390.01589972286491.02433598837-0.1572154561770.824241573245-7.7546.418-8.41
40.8793199269471.704277564630.7754742093146.34863854198-2.160906169153.64123026829-0.0203172689607-0.533702636987-0.2366004401830.2948512491310.6408578649150.675586946504-0.7225752516840.230668545342-0.1711831826711.187439485960.1635507190110.01929208280680.871586867677-0.2102673423730.953117696624-14.02854.326-7.015
56.183920343674.9878107515-1.414297409366.28243364098-3.403973065762.95713478348-0.712526199272-0.3532326611840.345393242239-0.1555911994210.06495609014430.347754654827-0.6478858288990.1531311809920.1500627948750.746368478774-0.0307902792770.1280227231971.04843318288-0.1972215565460.789877790559-3.85652.231-13.247
60.346983760621-0.446723636507-0.8229139550131.08402356963-1.350343880881.46054278704-0.1712829795070.544211377138-0.117998521269-0.06036457781990.03441287372220.1718501386840.102590156397-0.4586667592790.05346226774740.878544062282-0.184682807268-0.0640381679550.989353310045-0.1827545947950.78190438949-0.17351.532-25.162
74.44592550293-1.14937106188-2.214676093254.007313942251.572801938364.000100011110.67036801210.4896282606820.291626682073-0.447946278564-1.030683042640.0603309844709-0.840315109177-0.7382516842740.2060459669871.101683321690.0587660254199-0.09105369832220.8839646581460.01050300472620.7190831274648.39458.173-35.982
82.819494575220.209399649659-1.160724479434.681898135470.4457950291374.993475371660.6223191948841.099998577290.182445563027-0.678692360146-0.4696562935580.266945741166-0.364956690082-0.5092758828860.1191523463850.9356715343180.193535813442-0.1585560535571.007404283880.01408001667490.7108319656528.75559.57-43.608
92.696322974180.633674342367-2.580226414774.481437443111.307083387369.118250964281.254493974880.7949060029031.28866618011-0.215309323741-1.01877568751-0.210216255425-1.727575960470.4340873527560.1591566809591.35031174916-0.0535363930746-0.1315932010171.179856210130.204030698510.66484176249112.06666.751-44.944
106.86284214522-1.8032934846-1.887394241243.07150931701-3.454745533177.20083831961-0.3515735544270.0840303121476-0.87242136726-0.054292685182-0.9476456744710.5013463127951.198487277070.746929314260.6802160917990.823852999702-0.1686206509050.0591523336020.825603755586-0.06346074169330.8516785406953.99929.889-22.002
113.70788085677-0.544574884855-2.882807535962.93623323356-1.048321299166.42849281275-0.138173703870.136865284151-0.480847068908-0.0122783692635-0.3092236196140.3974078475230.724982371134-0.3547797643270.3441477987410.753739510885-0.1893516461490.1384533520450.823818035848-0.2319089163550.818990313635-3.38431.736-20.909
124.224433293443.42991971195-1.769529297128.823738410362.530929909741.609115608510.1754374972470.310125570587-0.00745142164031-0.303789040818-0.2397706495840.3045940121490.1760119340640.178836857406-0.0512871690530.9251656416450.0338132755517-0.0664506093940.9663845075890.06801436143380.68746274286221.03953.722-35.799
136.490730276811.429860453260.3734106618537.936592035350.9790273660423.25194994719-0.1034873222521.21674383065-0.7051599187340.3356193328990.5234345868240.324390589288-0.336793454050.611763062409-0.1823765212250.959908115715-0.03367627182440.04660379403031.04667289659-0.1322504463270.74377959129216.75947.449-32.584
144.6666988707-1.00687320191.343551166986.742491902721.117287649273.64721061409-0.03534636358860.4011362078471.026634458830.3511808320470.542587437694-1.28864732601-0.03562023345480.959446585764-0.284749855250.828811682779-0.1706965888680.03911431496611.078883871610.004613721881760.74861735912227.85458.539-32.601
156.792606452082.107302491923.234844545685.334391276014.788034896846.23374625576-0.3205445648970.5938807641170.0926804421117-0.1339183872330.602868790443-0.6718344198510.3499534326390.559864532162-0.4704706683090.6777491078660.0528432757720.008035609746751.159826464450.06212186082890.58868625136728.85448.224-38.94
162.35810735798-1.23802654829-1.270690377091.1093132127-2.452385234795.304742148120.141366246675-0.04467630808040.09426924231740.1838989639840.07338683977430.3238097229550.7524478122320.0088765180557-0.3600245477831.26131239513-0.2794967603270.07412998180741.08817177031-0.426125181460.995194567077-23.7029.6829.968
172.000864479541.958688012432.012231647886.36551648077-0.5282189173795.112146582760.107957995609-0.08097536055240.1035235597580.588121129585-0.146186768169-0.491698970753-0.2513768057730.3218917100720.02551007537550.896201144313-0.1523410741580.2428838288561.04454052443-0.4011615560121.15117179185-16.4218.3567.509
182.22555472802-1.33073666459-0.3684931415825.300688048640.8744205742072.834492969810.490691471322-0.1412903219650.3511742618890.0460616363737-0.97006512320.301624428446-0.158309897682-0.2933034853420.1930504302560.646018138804-0.09408883210330.2272860095530.960374960577-0.2679259121530.980529319799-25.10724.542-4.279
192.53056628621-0.9189080425390.7570430311572.95798674088-1.566560985274.482500268880.06002742661220.2997975722590.077423209840.0437142071549-0.2232155541820.219719577839-0.07130859854950.0484121737534-0.08655351977550.783429437053-0.2215347811540.05324659077840.992020677757-0.3814299443611.13511721694-24.64424.345-5.674
206.659906901931.75639462567-0.8414527809757.234941728291.470765118236.444762841680.1400810401960.06783899243970.889862027987-0.441874659134-0.1450353575060.605804314383-0.323397192288-0.0381084588695-0.0454930335070.6684981685420.0121951761033-0.02809667864340.555566940452-0.1135383855230.893027835675-38.604-6.057-2.874
213.928152107592.340088988410.2092269530517.368788057731.596427831756.75791884873-0.113552126744-0.1995093099510.74071295375-0.0292082984197-0.063328329911.08038485911-0.27265472060.6284767532210.0316241253440.8118269805740.1204111339390.03565466739160.679063880473-0.1234489915440.885203598424-38.758-5.887-1.893
220.0757033330568-0.0277709539323-0.09941995788331.680995899093.267572026066.10664868974-0.7865406625690.4470559932590.406032141099-1.09817944647-0.3793525936582.02070855935-0.239119961999-0.5567235738660.8940482822851.04035895687-0.0363518115449-0.1872942664380.70296450579-0.006491741321350.974013718218-45.545-20.068-16.874
232.178411246431.96973720369-0.09073942284717.55743223118-1.380264654443.6726364099-0.165869131921-0.0182597818388-0.01364508772030.5404676226390.3630443429990.327041332993-0.120541362836-0.108252525732-0.2223910637760.8470513442170.09051382506750.05276846983140.8637966262920.02559395945570.616442488253-47.253-41.003-10.705
242.145068588661.35308264032-0.224549902922.71269593473-2.342119270215.27190235622-0.650648809132-0.4547946409650.197947981495-0.6900821505641.52257525531.17431277480.924637725548-0.353970723299-0.3126302035191.028737828210.002106349316710.03108065203651.11096359966-0.03989861580241.0676991733-50.495-44.887-19.73
254.852288438723.800279791924.218200542447.946185508613.812566317264.858826424590.126626245309-0.443044017386-1.07958816791.03532835248-0.226479836068-1.259284998910.5816605950250.2981232896230.1489475460620.928899057162-0.110836390207-0.06503120555531.21080541306-0.1637884184810.749170400857-29.067-23.6915.111
263.683588440141.097736638912.706934204587.590550972390.1581149571313.951748307530.689384715473-0.9047475802750.3714555802940.959488363614-0.6098029558340.337018663171-0.174794294051-0.484061525992-0.08988047441880.859459342686-0.2298727252990.08687952995591.02907635426-0.2913789773790.833952120468-31.887-13.65114.332
274.785925860610.3385669417422.048456838028.509786390280.2471570032033.69001645211-0.4437506592790.6197769337281.685113458762.132908537110.0482769798481-0.00352335677326-0.4358191855830.319138227383-0.1108943438681.13071800042-0.202490928980.161438593641.34441225225-0.3622221720850.906685675314-36.257-11.53422.57
280.9724897972460.3736083024530.503045214348.989233032122.308948889871.08347939255-0.199763436217-0.438525779220.2328477864070.347191967195-0.2452339458670.3286209775180.703658812123-0.3267809902860.259214951891.13222941282-0.3292616824330.03326219955331.01080273398-0.1666914991620.701758949414-33.019-18.61917.212
291.691465373441.75348002646-1.224790800252.397134392710.3409561587861.1818379076-0.0828197658141-0.1282667977460.04455433076121.233631732480.593735106119-0.08697462694750.03381300037670.582106879638-0.4634794643490.849922163067-0.08286275778-0.0053095283040.905999440273-0.08161422240880.71159969634-30.877-20.5339.976
307.615063347941.38660821919-0.9136324126332.833484021444.41234815037.66327856939-0.9276460876941.58226908001-0.172946089997-0.652942499380.146461470653-0.0703223303052-3.394277570150.692207554874-0.05512023510730.9842923857090.0646316904165-0.1936541041550.957599638524-0.008367061523450.68593091395-36.419-46.043-14.22
315.249214344670.0937273647560.9930736966161.271247428272.272758681856.643424933590.4794193575480.116512968875-0.0467967496790.2329793387490.0733632067576-0.2306046677760.01397270979010.0836640913335-0.5365407023650.8530054425180.1032499902540.005032002725930.7028015582390.07633943022320.625610545795-34.429-37.432-4.96
326.404403675331.76268209814-0.9161950483963.647280437462.839190069872.52266271389-0.6550629152131.07600678846-0.7329076741210.3368134286030.08695268201540.2714586260031.59726511377-3.37102804947-0.3858897369520.9089983321210.07330205358790.1761740735360.870150061090.06159323025450.741180577557-34.631-39.021-13.443
336.826222653195.272660928363.04176600653.769559189383.549000647774.338498786820.4468215182210.133510385542-0.9125399593091.168413094280.804460261507-0.7868870303951.117711207321.18152286605-1.04897311670.8837633561060.103638704586-0.1083835830530.8306678718270.04661062034570.73817914457-26.823-43.573-7.587
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:17 )H1 - 17
2X-RAY DIFFRACTION2( CHAIN H AND RESID 18:33 )H18 - 33
3X-RAY DIFFRACTION3( CHAIN H AND RESID 34:64 )H34 - 64
4X-RAY DIFFRACTION4( CHAIN H AND RESID 65:83 )H65 - 83
5X-RAY DIFFRACTION5( CHAIN H AND RESID 84:99 )H84 - 99
6X-RAY DIFFRACTION6( CHAIN H AND RESID 100:144 )H100 - 144
7X-RAY DIFFRACTION7( CHAIN H AND RESID 145:185 )H145 - 185
8X-RAY DIFFRACTION8( CHAIN H AND RESID 186:213 )H186 - 213
9X-RAY DIFFRACTION9( CHAIN H AND RESID 214:226 )H214 - 226
10X-RAY DIFFRACTION10( CHAIN L AND RESID 1:18 )L1 - 18
11X-RAY DIFFRACTION11( CHAIN L AND RESID 19:113 )L19 - 113
12X-RAY DIFFRACTION12( CHAIN L AND RESID 114:150 )L114 - 150
13X-RAY DIFFRACTION13( CHAIN L AND RESID 151:174 )L151 - 174
14X-RAY DIFFRACTION14( CHAIN L AND RESID 175:197 )L175 - 197
15X-RAY DIFFRACTION15( CHAIN L AND RESID 198:213 )L198 - 213
16X-RAY DIFFRACTION16( CHAIN E AND RESID 333:375 )E333 - 375
17X-RAY DIFFRACTION17( CHAIN E AND RESID 376:442 )E376 - 442
18X-RAY DIFFRACTION18( CHAIN E AND RESID 443:469 )E443 - 469
19X-RAY DIFFRACTION19( CHAIN E AND RESID 470:527 )E470 - 527
20X-RAY DIFFRACTION20( CHAIN B AND RESID 1:62 )B1 - 62
21X-RAY DIFFRACTION21( CHAIN B AND RESID 63:103 )B63 - 103
22X-RAY DIFFRACTION22( CHAIN B AND RESID 104:115 )B104 - 115
23X-RAY DIFFRACTION23( CHAIN B AND RESID 116:200 )B116 - 200
24X-RAY DIFFRACTION24( CHAIN B AND RESID 201:216 )B201 - 216
25X-RAY DIFFRACTION25( CHAIN A AND RESID 1:17 )A1 - 17
26X-RAY DIFFRACTION26( CHAIN A AND RESID 18:52 )A18 - 52
27X-RAY DIFFRACTION27( CHAIN A AND RESID 53:73 )A53 - 73
28X-RAY DIFFRACTION28( CHAIN A AND RESID 74:100 )A74 - 100
29X-RAY DIFFRACTION29( CHAIN A AND RESID 101:124 )A101 - 124
30X-RAY DIFFRACTION30( CHAIN A AND RESID 125:139 )A125 - 139
31X-RAY DIFFRACTION31( CHAIN A AND RESID 140:180 )A140 - 180
32X-RAY DIFFRACTION32( CHAIN A AND RESID 181:193 )A181 - 193
33X-RAY DIFFRACTION33( CHAIN A AND RESID 194:219 )A194 - 219

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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