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- PDB-8qzr: SARS-CoV-2 delta RBD complexed with BA.4/5-9 Fab -

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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: 8qzr
タイトルSARS-CoV-2 delta RBD complexed with BA.4/5-9 Fab
要素
  • BA.4/5-9 heavy chain
  • BA.4/5-9 light chain
  • Spike protein S1
キーワードVIRAL PROTEIN / Viral protein/immune system / SARS-CoV-2 / RBD / BA.4/5 mAbs / BA.4/5-9 mAb
機能・相同性
機能・相同性情報


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / 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 / symbiont entry into host cell / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 (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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, 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: 3.77 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10月29日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年4月3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
改定 1.22024年11月13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
L: BA.4/5-9 light chain
H: BA.4/5-9 heavy chain
A: BA.4/5-9 heavy chain
B: BA.4/5-9 light chain
C: Spike protein S1
E: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)141,51610
ポリマ－140,8816
非ポリマー6354
水00
1
L: BA.4/5-9 light chain
H: BA.4/5-9 heavy chain
C: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)70,7585
ポリマ－70,4413
非ポリマー3172
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: BA.4/5-9 heavy chain
B: BA.4/5-9 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)70,7585
ポリマ－70,4413
非ポリマー3172
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)251.576, 251.576, 251.576
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "C" and (resid 333 through 442 or resid 444 through 526 or resid 601))
d_2ens_1(chain "E" and (resid 333 through 442 or resid 444 through 601))
d_1ens_2(chain "H" and resid 2 through 120)
d_2ens_2(chain "A" and resid 2 through 120)
d_1ens_3(chain "L" and resid 1 through 108)
d_2ens_3(chain "B" and resid 1 through 108)

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1THRTHRASPASPCE333 - 4427 - 116
d_12ens_1LYSLYSGLYGLYCE444 - 526118 - 200
d_13ens_1NAGNAGNAGNAGCG601
d_21ens_1THRTHRASPASPEF333 - 4427 - 116
d_22ens_1LYSLYSGLYGLYEF444 - 526118 - 200
d_23ens_1NAGNAGNAGNAGEI601
d_11ens_2VALVALSERSERHB2 - 1202 - 120
d_21ens_2VALVALSERSERAC2 - 1202 - 120
d_11ens_3GLUGLULYSLYSLA1 - 1081 - 108
d_21ens_3GLUGLULYSLYSBD1 - 1081 - 108

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(0.122094542505, -0.983396555094, 0.134254005971), (-0.983349844496, -0.138198359726, -0.118001257194), (0.134595713233, -0.117611346383, -0.983896115035)-160.91799507, -161.595768667, 161.564821237
2given(0.104803477815, -0.986840535645, 0.123134025543), (-0.984607698256, -0.120377465974, -0.126716006172), (0.139871053376, -0.107958431325, -0.984266765432)-162.138031118, -160.116543594, 162.924232384
3given(0.12478950723, -0.983717673484, 0.12933335904), (-0.981704261251, -0.141313070711, -0.12762193968), (0.143820451699, -0.111041230727, -0.983354220386)-159.805970868, -161.415551306, 163.265041183

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要素

#1: 抗体 BA.4/5-9 light chain


分子量: 23619.143 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 BA.4/5-9 heavy chain


分子量: 23885.678 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


分子量: 22935.734 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
#5: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 2 / 由来タイプ: 合成 / 式: SO4
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: 4.71 Å3/Da / 溶媒含有率: 73.88 %
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 BIS-TRIS pH 6.5, 2% v/v Polyethylene glycol monomethyl ether 550, 1.8 M Ammonium sulfate

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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: 0.97624 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2023年7月1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: 0.97624 Å / 相対比: 1
反射解像度: 3.77→60 Å / Num. obs: 26729 / % possible obs: 100 % / 冗長度: 41.8 % / Biso Wilson estimate: 165.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.414 / Rpim(I) all: 0.065 / Net I/σ(I): 8
反射 シェル解像度: 3.77→3.84 Å / Num. unique obs: 1322 / CC1/2: 0.351 / % possible all: 100

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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: 3.77→59.3 Å / SU ML: 0.7085 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 36.1209
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2997 1319 4.94 %
Rwork0.2506 25375 -
obs0.2531 26694 99.87 %
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: 196.35 Å2
精密化ステップサイクル: LAST / 解像度: 3.77→59.3 Å
タンパク質核酸リガンド溶媒全体
原子数8665 0 38 0 8703
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0028928
X-RAY DIFFRACTIONf_angle_d0.524512133
X-RAY DIFFRACTIONf_chiral_restr0.04281311
X-RAY DIFFRACTIONf_plane_restr0.00431572
X-RAY DIFFRACTIONf_dihedral_angle_d11.37413183
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2ECX-RAY DIFFRACTIONTorsion NCS0.216400767085
ens_2d_2BHX-RAY DIFFRACTIONTorsion NCS0.437128439145
ens_3d_2ALX-RAY DIFFRACTIONTorsion NCS0.456092952279
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.77-3.930.35581450.36282771X-RAY DIFFRACTION99.66
3.93-4.10.3611450.30242824X-RAY DIFFRACTION100
4.1-4.320.36961480.29182775X-RAY DIFFRACTION100
4.32-4.590.32941620.28452775X-RAY DIFFRACTION99.97
4.59-4.940.34551530.26522810X-RAY DIFFRACTION99.83
4.95-5.440.30871190.27392842X-RAY DIFFRACTION99.97
5.44-6.230.33461400.28072843X-RAY DIFFRACTION100
6.23-7.840.29681590.24162814X-RAY DIFFRACTION99.9
7.85-59.30.23771480.19432921X-RAY DIFFRACTION99.55
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)
15.24272065835-5.96246492602-1.494572123359.53584472974-1.907727077824.30289246289-0.4928250581491.93633232089-1.6722081076-1.237704157710.8922007468662.103732978680.930185753521-1.58564457522-0.8466400065741.4670074988-0.0938107121271-0.2106916765321.976860120950.5800605416341.77639333162-129.827292841-85.203101687657.4254571898
26.17606831431-6.28976091335-0.1626687793428.128333602250.4411145674317.57648862107-0.3128489316290.3592296792910.03701389914310.436319143564-0.0649514535635-0.4036373475370.649427366743-0.0309757486360.0426935653241.22718673779-0.190172638918-0.04767166604691.475488747080.441370230592.10678911802-121.205734472-83.584921453863.2380398346
35.47158521183-3.63658529545-4.757137567995.252253880334.837654603795.02909372695-1.94811224965-1.53021674659-0.3264797195030.7250415037612.456565624793.182835675692.29552317658-2.078152315760.08112181276371.444957497970.1687562073340.1827827930431.80667083732-0.1328355502532.24329117845-129.37502093-76.452477612669.7419465411
49.18660236404-3.92880158217-0.5781079177668.30906423966-3.894939574127.73819906448-0.326347831749-0.124453588744-1.396646926980.3786235746371.369329651522.38499868479-0.242360852233-0.337589230544-0.7268896235781.16860686422-0.1087735253930.03736358227581.410398704510.2556935934811.87631424721-129.684148387-82.589966413163.9562750826
51.72753742186-1.503009813911.655475219923.92196281673-3.4844296993.08288167145-0.4947428670533.30041439062-1.196658559240.3345738357680.955750382022-2.42323008565-0.5916720724630.920580178696-0.03573130955331.27993310245-0.113253589661-0.2765323932921.64304542240.1584397514731.7756811279-113.236378955-77.249764050262.861766497
67.391584568181.898985587536.312457801641.836848650640.7786087819948.377833470321.138116023324.69751572898-5.06885740396-0.106951485453-0.519903739609-0.511909519905-0.2636147235974.28159702014-0.5066089321812.27598304717-0.288861710771-0.6382521632262.163414891430.2078400739822.43972490094-142.330663847-81.526363227650.6555775487
72.6251361097-1.035923550825.711502701435.53768922024-1.470428452667.875438869060.6610265357561.07178370748-1.36757622048-0.7168900517930.146936723948-0.1978802839591.454325477290.563402469644-0.506359618231.547645843510.2199878915880.1050266450381.990444669650.08023221239962.23329852945-140.479604103-68.853861350831.9450406773
82.85733388642-0.443334638098-2.521176014597.37189334020.05915663392592.258991316881.49666602467-3.2180568613-0.4665580451385.42303799393-1.19257336541-1.163006943090.001547657277882.32655854202-1.014280831262.22174826253-0.545042233102-0.4362441077572.16817547982-0.1865643177211.87865812268-143.842806664-73.416766195250.8195385472
93.70337071561-1.3602334607-1.017475534424.72923880813-3.333652579573.776737023190.2162048437890.271953864943-1.40072492612-0.556334458363-0.491990468903-3.164639854731.34497588443-0.8162413493930.150329794561.813988294980.306655764923-0.2342277356112.529832672790.321499635531.77540684838-138.165821473-63.686369137423.5675807246
105.885835285173.36541424732-2.896788865411.87307829666-1.617193866443.032557150852.13522833145-2.37669987412-0.115800563842-2.24216748345-1.732193104233.67128812005-0.2217959033781.63551874796-0.6034098776672.365256784560.71746910856-0.3869619716621.84921126436-0.1487296849342.42751303308-146.691552655-74.526923143927.8296917857
115.61578093965-2.447933662230.50046404857310.2066886127-1.116576330635.2684639407-0.3471508141490.1330185211940.2207713156260.07173928768180.509194959933-0.7870440449740.4231218779690.621719443155-0.08752412291541.259816885960.0442099069199-0.1424984759431.571782502810.01220090643711.76039553498-114.776335153-61.003308881362.5418620097
125.24494475959-0.909708832983.633199618651.949441802430.8200797499221.565210002720.2474848681280.1041273594840.272447257659-0.323772207275-0.187617082893-0.650774849854-0.257497124719-0.309767735458-0.408965855111.404291246940.0802475156453-0.01590233576021.731974158850.2036768796061.41557022611-126.493479995-62.058880336852.5674009836
136.78336821986-2.2173843843-0.7434924161685.34831260795-3.814934390354.163192123520.145541530694-0.209258602535-0.5104911115880.443036742719-0.944076058185-0.314084922673-0.0199830605439-0.2309053209360.6094718859271.09214949409-0.0970499964251-0.1814954605061.977973933690.2730197506451.55654259479-144.331130034-56.934427914541.7531604023
144.551237953980.1954120670052.362836362653.342349572181.247693458825.648441053910.595954021084-0.7250014298810.4731472794760.59697429843-0.2760207511280.688254060342-0.0731945385177-0.968280812486-0.3025786602691.461491992360.07151000753530.337731200671.1567367427-0.3511627380481.6168206384-105.901501092-45.842970932893.0314313998
157.36778365169-4.920357451767.852747405274.68169640679-6.934940056931.99614238812-2.305158695661.78809805576-1.73798638865-0.383720905225-7.870815319763.09155089932-1.47009002598-1.236420303613.889770158162.19358413855-0.8283575523960.7148119255923.69881101934-1.276049699723.75727427483-118.003421662-30.1757042648111.698232808
162.99027070758-1.109055587392.52008544370.389055456901-0.9874800321363.023409566911.75248954037-2.11176509999-0.851097538595-4.525254782940.896969593667-0.006592779610832.26345838409-4.41706213555-2.03887422442.9732533074-1.03760773550.1874702067623.272034856880.2964525987463.88508901826-116.326437909-15.9017783314105.019957874
171.955299462757.179222477851.970316511236.625469517345.169314576691.984388185435.07111265452-3.617343889493.021179816993.05309778405-1.130054026821.23864290847-1.46113363818-1.33428436341-2.277372013974.575306950460.4391902008371.293346154773.57253233438-0.5426460732473.20463167032-110.12723957-29.9768177486114.313403202
188.158243979-1.16911902830.6970133663894.212798975233.220617245049.28728714483-2.707871066573.00243500372-2.8948854809-3.559891301542.303532084720.5793744988441.99529210449-1.135033057670.3935356874073.31866498841-1.055740800331.024936641982.68856787399-0.8054824606184.00759939989-122.582854509-25.4136809906108.309037154
194.82723956171-2.90153685478-2.206182188376.65453237638-4.531346382528.683162902340.766961699236-1.6125314063.072409267434.35917729189-0.8823973198711.85920960003-1.693678093540.2387684172930.7372207759041.36644082245-0.01550620207250.07987116083161.390264514-0.1605204200422.00962029349-83.8523502112-30.474318709897.2100367433
208.8669969388-0.751951783660.6247826592066.233397450051.888932758455.59447270008-0.135134257004-0.01234176075241.54153951808-0.102668055613-0.2104540714910.369681150249-1.24957561770.3910888016030.763883138551.91509701757-0.4169964983530.183099413730.883275277566-0.2495440527141.60640356195-90.5426667172-37.010455282390.4196795963
213.76762002366-4.134286504375.841780065674.54691347403-6.070027377248.315654675061.614176466791.564718456240.9283421185761.18760042572-1.740225674040.787828650588-0.03515529314810.9540996913080.0935726183141.54062798004-0.3030099938330.03396852568361.61716945683-0.1518578390041.64950030653-84.1235494519-33.732821659385.5060971873
222.16344263831-1.30368304436-0.3477188199832.751543548352.445363145352.627764226911.05025017525-1.746151975142.091061628495.10024810165-1.521846132560.643830048028-5.262105938910.7945662239151.663888937483.371031674130.344658378884-0.0005717388757381.924467507530.0594260519892.96563227534-90.8935012157-20.517931049489.1390627938
236.60235376184-5.0533950173-2.590676849394.08629285332.487535733021.52427749288-0.294492454779-0.127651626262-1.00401162513.44349387269-0.8201681614391.13146915075-0.6118362910280.1899556194961.250436353941.747668633920.06335125110170.1145125541071.46101235731-0.0453976144371.48913855919-90.2123862925-43.08897994693.9996058315
246.099086996455.48834940552-0.4955699594318.47602868996-5.742333867167.771415715711.79471897193-6.479422615141.895746916143.64749381831-1.29813625305-0.1809614706850.917276615682-3.03277819549-0.2504228735732.97795504777-0.904112689150.1972272226562.45503431811-1.128476421432.26626318975-91.3766147156-17.5826621981101.206880726
257.646580300110.773756390865-6.999459429160.215634810037-0.8993297105346.631643565432.32798928661-6.247314511788.297439393110.917096448276-3.225337265271.51908461594-2.848059874394.4405688712.625521421353.673254269890.142924156358-0.7177833079182.80969510246-0.3089516650062.9587830706-96.2556436654-18.0001019649109.222144816
262.00177305973-0.9174055459475.359188069110.094697161434-0.7092259015515.015187896552.633834729941.466403572886.67686463972.33604553845-2.495082482780.913250382891-4.587957544233.44901850136-0.2565377361155.12710930126-0.3865005866810.5338000251262.28585260706-0.261625970442.84963150759-99.6515049714-15.4866503813101.626164716
279.26837251657-1.96281775581-2.723338158758.21420150916-5.225567924624.531951848830.147835696506-0.2696289610450.8168629633782.55755590566-1.543421639530.530869139676-1.900789022271.359634580931.124222265081.5780187882-0.2882540215310.2008639862761.05263521635-0.02193116543061.71777152339-108.562878205-80.167901637699.7884720946
287.23811384307-2.05809620081-2.860663242859.94036307599-5.000405347324.95333195151-0.338792266699-0.5252035413132.717866250432.50173618531-1.0626296095-0.448619959847-0.327158943936-5.02716052360.7832769205991.99069866334-0.4340763329960.2446040605822.34578330227-0.6376702696430.812649560362-106.262528841-88.9055803194102.641565417
295.21718658855-2.557896369195.485906774516.79617117077-5.82648035587.53552218845-2.41373995018-0.8488527379952.537403963443.07013134506-0.03234186423032.19554129131-2.263868277270.4069276392561.943690400471.453161517610.1043594821380.7476672768432.15691790323-0.03679753370952.46544893091-122.336736834-86.8724283365101.655657014
300.548234576241-1.85250669623.281138585928.23918506746-4.09366249797.7416098977-0.111542452772-0.2715606068970.2580309836710.4499009498570.3717247315651.144024508440.148987760313-1.481512992170.05228828731521.275674623970.1327849481930.1900580916741.49199702935-0.233962760621.61191810363-114.524186335-87.060392680590.2117085527
316.924148576280.660406605367-7.094006668475.238274426941.912359610967.805913545040.990951692614-0.9531043949511.7413555553-0.4122035642440.790968003472-1.71828477251-0.8939188159570.78926975342-1.979875058091.256741420680.09380000982190.3116637291811.232803901040.1705815576071.59606020762-108.625596906-70.924711721182.7605948796
324.114130910150.776339229822-4.463833549384.53732839646-0.8065975420694.600282561460.707552118822-1.11109484882.01946583768-1.79135564288-0.8723476911162.662871794212.316233753412.067018383880.5040944169211.190384624150.01402458407680.05299704433721.270928163870.2224155036631.52223981543-101.861403079-85.02045371582.4006956627
337.707388750154.08023604785-4.792840609154.05653859966-3.859381577946.334032519740.2743633440310.225608013501-0.885955572554-1.26542828646-1.647364231760.07630418517-1.685402314314.598488764172.106715498321.641308558850.3391321111630.522009935511.894919441430.06615825907641.08097359931-96.2406728975-72.660259089968.5110580942
346.92547200731-2.18125080685-0.2790503721682.84933776388-4.134344589766.716375748631.69750144560.9981820079710.9699810154931.76663226614-0.05897896248340.502295749204-0.755403644365-0.848043354336-1.557845300521.29632505983-0.1368813235170.02356682646811.03998617418-0.2356558608321.91904556029-108.963677446-68.172754979477.8877729338
354.16180322595-4.79841844689-0.3464355131459.12692644093-0.293751308995.740539078352.85572133007-0.725548563376-1.12367004546-4.51812473331-2.78486538758-0.6381103069381.1376783175-0.3360744237730.2955614942681.21705784-0.55317540509-0.2668118508971.415116645340.08134369086811.86123060932-111.497171277-95.431880285397.1239115432
367.10544068137-4.72961174761-1.812036867273.042738550061.702075977612.19276899709-0.8804907421761.402150727420.732003827511-0.4892903559120.02096379269961.47965080493-0.452760041293-0.2360196915850.8700338743251.44754972858-0.273161175331-0.06124502637761.270579446710.08753509438441.79677643895-81.9807257993-55.49095212358.1856430064
372.350426700164.3699665508-5.360219144034.606542153681.981416326497.709863618010.1527526207721.749016580070.980966212826-0.8260707676510.5766853893143.09163190485-0.447473866661-1.44952658678-0.3072882406621.71515312559-0.155457380172-0.1366274300481.871984102290.3293517505211.5813175633-74.6639043026-49.174487700756.0276230798
385.32560070545-2.59754293886-1.154456936021.04878921701-0.9027064513127.206315750460.2331309895970.1241796082880.4996505867010.165047030676-0.4340940943280.556156156706-1.09194785206-0.01424959640090.3535070733131.322723948120.0123358899507-0.04200256964881.22906954215-0.1021620055061.64789523907-77.1574686086-47.611458131967.6221542231
395.324175144420.6109010157451.107335298725.1520221702-5.243535863215.222666978680.7890532992390.639391087546-1.395637072350.920447917930.8503155102760.652247414292-0.5574278769621.09110185538-1.395659169091.33685091745-0.114707525010.01024076332021.534773821260.1235828459771.93139131613-93.3552718375-54.729582655673.8375463782
402.419521181941.6790926982-4.077765857282.44468101708-2.531498651686.82660798875-0.643078019773-2.381699366210.437180269954-0.4819291530740.716556257351-0.6807570400251.007261544743.447176294440.1951173014931.13004232459-0.2777512429460.1798669632511.92177260169-0.1155047734921.7759533917-78.6140244815-59.421919964876.8446293338
417.203201383215.13104738291-4.03141133375.64783958079-5.168814806474.863869854821.80582510298-0.2003419224690.259353026006-3.13882528112-1.32002916074-0.409931415514-0.8576900168870.1246804273351.993751108051.78963767270.1399393113840.1046817264391.723082038180.3277866333090.833339554921-92.1049690972-64.980352718789.8196278672
429.17624731002-4.51258105004-2.507896021162.69697413888-1.207328449666.41152052261.52739500715-0.5811598930680.8243958730390.6591905846140.5606933691471.5222854722-0.8448950804760.135550665491-2.172277119681.02803923432-0.201749370920.01434518119381.06483503022-0.04186517380932.20453184435-96.7469937092-54.233103877778.2773941326
431.95802200171-2.35109563434-3.010681355760.4892658531452.687403894862.89616147795-0.879200162948-2.459742892420.7196006066390.00560119188920.999817870535-1.01377331070.06988583149980.254918418081-0.09102325892011.56156522925-0.1287618144640.01785896278960.67296651929-0.2079940548961.8947526548-67.6346293541-50.217996570362.2028355445
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 'L' and (resid 1 through 18 )LA1 - 181 - 18
22chain 'L' and (resid 19 through 38 )LA19 - 3819 - 38
33chain 'L' and (resid 39 through 61 )LA39 - 6139 - 61
44chain 'L' and (resid 62 through 90 )LA62 - 9062 - 90
55chain 'L' and (resid 91 through 102 )LA91 - 10291 - 102
66chain 'L' and (resid 103 through 114 )LA103 - 114103 - 114
77chain 'L' and (resid 115 through 164 )LA115 - 164115 - 164
88chain 'L' and (resid 165 through 175 )LA165 - 175165 - 175
99chain 'L' and (resid 176 through 191 )LA176 - 191176 - 191
1010chain 'L' and (resid 192 through 215 )LA192 - 215192 - 215
1111chain 'H' and (resid 2 through 83 )HB2 - 831 - 82
1212chain 'H' and (resid 84 through 141 )HB84 - 14183 - 137
1313chain 'H' and (resid 142 through 223 )HB142 - 223138 - 219
1414chain 'A' and (resid 2 through 123 )AC2 - 1231 - 122
1515chain 'A' and (resid 124 through 156 )AC124 - 156123 - 132
1616chain 'A' and (resid 157 through 172 )AC157 - 172133 - 142
1717chain 'A' and (resid 173 through 182 )AC173 - 182143 - 152
1818chain 'A' and (resid 183 through 216 )AC183 - 216153 - 165
1919chain 'B' and (resid 1 through 25 )BD1 - 251 - 25
2020chain 'B' and (resid 26 through 48 )BD26 - 4826 - 48
2121chain 'B' and (resid 49 through 75 )BD49 - 7549 - 75
2222chain 'B' and (resid 76 through 83 )BD76 - 8376 - 83
2323chain 'B' and (resid 84 through 102 )BD84 - 10284 - 102
2424chain 'B' and (resid 103 through 138 )BD103 - 138103 - 112
2525chain 'B' and (resid 139 through 165 )BD139 - 165113 - 122
2626chain 'B' and (resid 166 through 175 )BD166 - 175123 - 132
2727chain 'C' and (resid 333 through 353 )CE333 - 3531 - 21
2828chain 'C' and (resid 354 through 364 )CE354 - 36422 - 32
2929chain 'C' and (resid 365 through 375 )CE365 - 37533 - 43
3030chain 'C' and (resid 376 through 442 )CE376 - 44244 - 110
3131chain 'C' and (resid 443 through 459 )CE443 - 459111 - 127
3232chain 'C' and (resid 460 through 469 )CE460 - 469128 - 137
3333chain 'C' and (resid 470 through 479 )CE470 - 479138 - 147
3434chain 'C' and (resid 480 through 506 )CE480 - 506148 - 174
3535chain 'C' and (resid 507 through 526 )CE507 - 526175 - 194
3636chain 'E' and (resid 333 through 353 )EI333 - 3531 - 21
3737chain 'E' and (resid 354 through 375 )EI354 - 37522 - 43
3838chain 'E' and (resid 376 through 442 )EI376 - 44244 - 110
3939chain 'E' and (resid 443 through 459 )EI443 - 459111 - 127
4040chain 'E' and (resid 460 through 469 )EI460 - 469128 - 137
4141chain 'E' and (resid 470 through 479 )EI470 - 479138 - 147
4242chain 'E' and (resid 480 through 506 )EI480 - 506148 - 174
4343chain 'E' and (resid 507 through 526 )EI507 - 526175 - 194

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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