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- PDB-8hrd: Crystal structure of the receptor binding domain of SARS-CoV-2 De... -

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基本情報

登録情報
データベース: PDB / ID: 8hrd
タイトルCrystal structure of the receptor binding domain of SARS-CoV-2 Delta variant in complex with IMCAS74 Fab and W14 Fab
要素
  • IMCAS74 Fab heavy chain
  • IMCAS74 Fab light chain
  • Spike protein S1
  • W14 Fab heavy chain
  • W14 Fab light chain
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / membrane fusion / Attachment and Entry / 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: 2.86 Å
データ登録者Zhao, R.C. / Wu, L.L. / Han, P.
資金援助 中国, 1件
組織認可番号
Chinese Academy of SciencesXDB29010202 中国
引用ジャーナル: Proc.Natl.Acad.Sci.USA / : 2023
タイトル: Defining a de novo non-RBM antibody as RBD-8 and its synergistic rescue of immune-evaded antibodies to neutralize Omicron SARS-CoV-2.
著者: Rao, X. / Zhao, R. / Tong, Z. / Guo, S. / Peng, W. / Liu, K. / Li, S. / Wu, L. / Tong, J. / Chai, Y. / Han, P. / Wang, F. / Jia, P. / Li, Z. / Zhao, X. / Li, D. / Zhang, R. / Zhang, X. / Zou, ...著者: Rao, X. / Zhao, R. / Tong, Z. / Guo, S. / Peng, W. / Liu, K. / Li, S. / Wu, L. / Tong, J. / Chai, Y. / Han, P. / Wang, F. / Jia, P. / Li, Z. / Zhao, X. / Li, D. / Zhang, R. / Zhang, X. / Zou, W. / Li, W. / Wang, Q. / Gao, G.F. / Wu, Y. / Dai, L. / Gao, F.
履歴
登録2022年12月15日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02023年12月20日Provider: repository / タイプ: Initial release
改定 1.12023年12月27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.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
A: Spike protein S1
O: IMCAS74 Fab heavy chain
P: IMCAS74 Fab light chain
D: W14 Fab heavy chain
F: W14 Fab light chain
B: Spike protein S1
C: IMCAS74 Fab heavy chain
E: IMCAS74 Fab light chain
G: W14 Fab heavy chain
H: W14 Fab light chain
K: Spike protein S1
L: IMCAS74 Fab heavy chain
M: IMCAS74 Fab light chain
N: W14 Fab heavy chain
Q: W14 Fab light chain
T: Spike protein S1
W: IMCAS74 Fab heavy chain
X: IMCAS74 Fab light chain
Y: W14 Fab heavy chain
Z: W14 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)487,97324
ポリマ-487,08820
非ポリマー8854
1,820101
1
A: Spike protein S1
O: IMCAS74 Fab heavy chain
P: IMCAS74 Fab light chain
D: W14 Fab heavy chain
F: W14 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)121,9936
ポリマ-121,7725
非ポリマー2211
905
タイプ名称対称操作
identity operation1_555x,y,z1
2
B: Spike protein S1
C: IMCAS74 Fab heavy chain
E: IMCAS74 Fab light chain
G: W14 Fab heavy chain
H: W14 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)121,9936
ポリマ-121,7725
非ポリマー2211
905
タイプ名称対称操作
identity operation1_555x,y,z1
3
K: Spike protein S1
L: IMCAS74 Fab heavy chain
M: IMCAS74 Fab light chain
N: W14 Fab heavy chain
Q: W14 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)121,9936
ポリマ-121,7725
非ポリマー2211
905
タイプ名称対称操作
identity operation1_555x,y,z1
4
T: Spike protein S1
W: IMCAS74 Fab heavy chain
X: IMCAS74 Fab light chain
Y: W14 Fab heavy chain
Z: W14 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)121,9936
ポリマ-121,7725
非ポリマー2211
543
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)196.662, 270.048, 118.156
Angle α, β, γ (deg.)90.000, 107.850, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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要素

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抗体 , 4種, 16分子 OCLWPEMXDGNYFHQZ

#2: 抗体
IMCAS74 Fab heavy chain


分子量: 25335.576 Da / 分子数: 4 / 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
IMCAS74 Fab light chain


分子量: 22698.014 Da / 分子数: 4 / 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
W14 Fab heavy chain


分子量: 25102.082 Da / 分子数: 4 / 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
W14 Fab light chain


分子量: 23441.945 Da / 分子数: 4 / 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 / / 非ポリマー , 3種, 109分子 ABKT

#1: タンパク質
Spike protein S1


分子量: 25194.447 Da / 分子数: 4 / 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: 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: 4 / 由来タイプ: 合成 / : C8H15NO6 / タイプ: SUBJECT OF INVESTIGATION
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
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 101 / 由来タイプ: 天然 / : H2O

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詳細

研究の焦点であるリガンドがあるかY

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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: 3.2 Å3/Da / 溶媒含有率: 61.54 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.2 M Ammonium formate, 20% w/v Polyethylene glycol 3350

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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: SSRF / ビームライン: BL02U1 / 波長: 0.979183 Å
検出器タイプ: DECTRIS EIGER2 S 9M / 検出器: PIXEL / 日付: 2022年3月8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: 0.979183 Å / 相対比: 1
反射解像度: 2.86→112.47 Å / Num. obs: 134730 / % possible obs: 100 % / 冗長度: 7 % / Biso Wilson estimate: 59.11 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.9
反射 シェル解像度: 2.86→3.01 Å / Rmerge(I) obs: 0.822 / Num. unique obs: 19639 / CC1/2: 0.792

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解析

ソフトウェア
名称バージョン分類
PHENIXdev_4382精密化
PHENIXdev_4382精密化
XDSデータ削減
XDS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: 2.86→63.06 Å / SU ML: 0.3857 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 26.4286
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2439 3954 1.49 %
Rwork0.2122 133825 -
obs0.2126 133430 99.54 %
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: 64.57 Å2
精密化ステップサイクル: LAST / 解像度: 2.86→63.06 Å
タンパク質核酸リガンド溶媒全体
原子数32869 0 56 101 33026
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.003433783
X-RAY DIFFRACTIONf_angle_d0.700346032
X-RAY DIFFRACTIONf_chiral_restr0.04665127
X-RAY DIFFRACTIONf_plane_restr0.00585893
X-RAY DIFFRACTIONf_dihedral_angle_d5.58634699
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.890.38641410.35569387X-RAY DIFFRACTION99.45
2.89-2.930.33821410.34769352X-RAY DIFFRACTION99.51
2.93-2.970.33611410.33019371X-RAY DIFFRACTION99.48
2.97-3.010.33421400.31089369X-RAY DIFFRACTION99.62
3.01-3.050.33631420.30699340X-RAY DIFFRACTION99.58
3.05-3.10.26911420.28799425X-RAY DIFFRACTION99.68
3.1-3.150.32271430.28899345X-RAY DIFFRACTION99.6
3.15-3.20.30961410.27859393X-RAY DIFFRACTION99.69
3.2-3.250.30841390.27439342X-RAY DIFFRACTION99.81
3.25-3.310.35251420.27529394X-RAY DIFFRACTION99.7
3.31-3.380.31291430.2669439X-RAY DIFFRACTION99.73
3.38-3.450.33481410.27229335X-RAY DIFFRACTION99.62
3.45-3.520.24731440.2649377X-RAY DIFFRACTION99.61
3.52-3.60.28631390.24119329X-RAY DIFFRACTION99.51
3.6-3.690.27271440.23039420X-RAY DIFFRACTION99.75
3.69-3.790.29121390.22169362X-RAY DIFFRACTION99.64
3.79-3.90.28221430.21679364X-RAY DIFFRACTION99.56
3.9-4.030.28921400.20839338X-RAY DIFFRACTION99.59
4.03-4.170.23811430.19549469X-RAY DIFFRACTION99.8
4.17-4.340.20191410.17279338X-RAY DIFFRACTION99.71
4.34-4.540.18141410.16019395X-RAY DIFFRACTION99.67
4.54-4.780.17571430.14859366X-RAY DIFFRACTION99.65
4.78-5.080.16821420.15459347X-RAY DIFFRACTION99.68
5.08-5.470.17481410.16579351X-RAY DIFFRACTION99.57
5.47-6.020.22781400.17829413X-RAY DIFFRACTION99.52
6.02-6.890.20291430.1939342X-RAY DIFFRACTION99.35
6.89-8.680.21121370.18069343X-RAY DIFFRACTION99.44
8.68-63.060.1881380.16829192X-RAY DIFFRACTION97.56
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.93065625771-2.28973869486-2.133584412885.678161789522.339758989829.941282809820.1517817744590.408505322436-1.16924757898-0.703516003318-0.1719955314740.07815654849960.295071309637-0.260830496471-0.05581586079920.486115164443-0.0704495829232-0.04101387957350.344053349624-0.01271961650130.44684404185986.3321043875-3.05990614945-68.1068241141
25.69523168996-2.73603388836-3.296702588124.548909052312.747486288396.148246548210.1732123189260.662200359953-0.685855168538-0.288854457996-0.0360235983491-0.0659863945315-0.5020512132980.304628696685-0.1245173161450.7508699401390.001268484172910.002546584697980.388361005011-0.0424605212620.50414560313895.8044619717-5.93467640057-67.3260620343
34.8424894365-1.94886984020.7714283489384.66986684475-0.02776530194521.874555026850.3287760259770.690080860310.583105820336-0.666262229422-0.233668760565-0.513908126161-0.3101827435490.311041219513-0.06997611391090.471741559285-0.05791160826780.0561138090680.378356085940.05698653603130.37395511489692.24858466148.23595138552-65.1185051048
46.16115500937-0.092488678346-0.2385891225171.89518925849-0.5154990716641.356586103840.05091651334120.1666794249830.1354691160580.0176871559248-0.04943971388120.07527462714080.185902357557-0.1861503176020.002691175831710.367144991228-0.04648028048320.03937050101820.225725582468-0.02892485683890.22532525745580.51953894256.46780248497-60.1136350692
55.452776991410.280346861615-0.1570184171812.94410841394-0.4913761342452.20363385825-0.0474690406123-1.06901707875-0.1783280835060.8252158954810.1354462106620.1972259855240.110938232228-0.29989679701-0.08085931801330.629337663352-0.03210198984120.01155055879570.4574007372430.01654141680770.35894611477174.92227224433.09314529045-43.4222754804
64.512502630410.5292851796981.49193357550.859068762820.4031234988992.19908870508-0.277341334424-0.0452547234654-0.2490121582890.111010007440.193898451571-0.04729891955840.1834761491890.0668010490313-0.03599051643540.578302138711-0.01651137053840.05920698686270.2969270344360.05958079069540.31124652366187.92826182134.97359261784-65.7349736945
74.961445543343.24639041843-1.203495662425.62924116061-3.008841229465.51729207136-0.291327106885-1.1774733048-0.02135614106821.23788808030.136975190029-0.4242611017890.7436263473440.670267161430.1700576548660.8664683370680.129381445398-0.1676647187260.423570164996-0.06310450400320.42883260358100.513842132-16.6677553496-27.9581737225
84.39722155876-0.612970197639-0.6576494848014.83812632764-1.446331367768.42134439616-0.0473860422353-0.2042891543550.5445301575550.930973912969-0.081903785577-0.318343510537-0.641482993920.003898470338030.08686232115680.5281209926620.0369562525916-0.06969977983380.272303007999-0.07047597750680.38879501553999.2678144356-9.57353676492-39.2409549567
91.661355261990.396547822706-1.404848720634.89753356676-2.671220041265.76462496953-0.106864371564-0.318072972420.7306780173441.094987212290.2005288989560.284377973186-0.445806618222-0.0953222773152-0.2624562306330.8607114885640.0549741970829-0.004343537324920.379984234092-0.07368584412620.50408573036893.6985061584-9.28190473838-31.6956395029
102.250058712251.44485935102-1.723867133175.41578465446-4.93553018226.90656553323-0.219461515385-0.1708717328640.1429283935020.3793185229850.0302911502252-0.3433153694070.05739597635530.01036425139750.1060373483610.547966474450.0961623578647-0.0958471243450.323930260987-0.09987128782510.36209661858599.5022427542-14.3851066216-39.7931920202
112.818790349410.609472217508-0.7167243401446.60911219691-2.274302387172.24175181419-0.04196880746660.146442117888-0.03701039800180.02183851724460.09991373247310.272765508545-0.0446105492327-0.576184281808-0.09610951913070.387620607362-0.04079886544190.0295097026910.617370742505-0.05468975214720.2823716414394.0639525194-48.7522389849-19.9540171448
125.31541851537-0.5580762238421.902373548912.01914038581-2.365256880675.671720504150.3441692120610.556700366752-0.2796940929820.00312088534861-0.2104351706960.347970040498-0.578869093995-0.495243906646-0.2038712489040.443890194652-0.0010544734095-0.003451685963070.511767259387-0.03586689355360.27917317148694.3213986378-42.3810648824-23.4196231047
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1072.84077686976-0.4035242384050.6832126860496.41527060997-1.243701968555.980465986140.1735094128940.194913499958-0.629094625539-0.03098118340490.1553408183770.2182220910470.559294535683-0.17973823155-0.3157104067040.340456811641-0.0746366523365-0.04556300805570.386325904326-0.04552945588180.51452219422562.39794552140.969419771475-95.6957572736
1085.58436621989-5.92211989139-0.7993809524216.508254632170.1762826507334.44019881814-0.0245977826392-0.04399332401020.905952005271-0.01922629876470.2096374894820.0590435225803-1.07189427493-0.200034066376-0.1340709412710.9107542966220.00272495363835-0.01069799231650.4304729325810.07963582327450.58926987252859.820589193432.8525587736-79.2213328131
1099.472065926730.525983477339-1.886832559084.021815718431.400963554289.45694269501-0.402948035799-0.746547016141-0.1068985721560.5255346248360.2699847612210.499572922939-0.3818487164-0.4092323700680.2135347280160.6312428566970.05146049731950.05776619606580.3938352695190.0528668519640.46014186409952.488517174125.1815497256-74.8082070431
1108.06711527606-0.684154343643-1.608263043592.895625642352.583144421082.43562427681-0.830649361261-1.51785508125-0.3162562595041.404543960950.5894165515850.140594698392-0.1588587726940.1401689691560.2580888912210.8476250818640.1566025954750.06057638762850.6972711843160.08531374851580.51498386720757.647520079526.1562774409-66.9906777551
1119.21911979459-8.31823635963-8.246628371219.602931841157.875637706618.50062266896-0.965699945542-0.640446870455-1.011292375030.8579336183190.467113875970.827617713048-0.004680965651710.2537712462150.5015994055010.5635726041-0.01379171467910.0001056546652440.5368418882770.1491251974930.49326821891564.60704065626.6813084093-74.7474381916
1123.214805978663.50486095270.4511333361687.72483119447-0.3337859302899.80855210619-0.03179667671820.207841062680.6967359878280.666846503962-0.05073848741951.2751428552-1.20865060002-1.672667132160.1211373968930.7128956046550.1927823103360.09416719615920.6054638094950.07441344371210.63557341674548.068038502727.3712724287-77.187980821
1131.94545655903-1.12393665097-1.609538437042.710221200271.326791240715.72679064830.3473769827660.5600457933180.880655860485-0.336110654880.352762652891-0.362063126155-0.8665723250830.510591519729-0.5901787378020.528165389588-0.172624462350.05242747812620.435714110965-0.04739749797340.66325822507873.000240718522.9667630957-86.9357000671
1143.31721209568-1.33715586306-0.5891625861562.742929304581.095377766316.246044675380.2777232139510.456226951725-0.843168813619-0.5548612295980.0579940588457-0.02629166516221.13982707763-0.340367490405-0.1366254381240.72290779675-0.1877548468010.004606052349920.640349456789-0.09297082193020.71760581529369.6619781099-0.0279148381518-107.329760698
1152.17406958206-0.736229224845-1.435227625194.22920791453.004341581973.67282571541-0.1419216532520.5609266567070.369894672015-0.5240604516790.468145047214-0.118219206766-0.4789384017-0.123080647553-0.3406647388590.439690609624-0.144871515078-0.01112471250350.527703689434-0.07506842126490.65162515150973.394599620113.9672062123-102.678214602
1163.290057061910.4818487904741.750132314232.39460986145-0.5572994115772.0185501469-0.2011665944550.2157561883160.00372926271811-0.392033427590.000997214382105-0.264088231644-0.4142610673230.4122613645020.1981715961970.523022569863-0.1050047924780.07828139347960.5572433414260.03890083899450.55803143695670.462321949915.2203026152-99.9028907477
1173.90644555860.7277884898860.0588094921924.999782288312.781583223827.99311884982-0.001289117588840.907899073803-1.0313842784-1.135665615170.590660270962-0.0906167311985-0.183483529577-0.255459499633-0.4098446113780.560184671169-0.1400909197130.01144730018440.831450455643-0.09291328264050.55812383736668.27322133315.60879537677-114.252893418
1185.845417327893.783527075032.767060083714.841515318583.225552067182.86705553744-0.3287632764421.218176157750.198427667957-0.3916252152540.7517818292880.0589595214692-0.3412413863530.888983576509-0.4867717881190.551980449032-0.2054978135070.1386729153590.74624507588-0.09066908221020.65942486464280.261940929513.6619993864-107.122356959
1196.5290239211.891111669336.800370432022.087544037351.772378828157.09049709370.728751083122-0.0536905090777-0.939743686058-0.4843042227160.726275376536-1.506479651071.185349931281.39093766544-1.435258207750.608034494713-0.02137275684980.1306302338930.897017973324-0.25552604410.94883558048179.83446096341.71830922834-110.532215323
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 'A' and (resid 333 through 353 )AA333 - 3531 - 21
22chain 'A' and (resid 354 through 364 )AA354 - 36422 - 32
33chain 'A' and (resid 365 through 421 )AA365 - 42133 - 89
44chain 'A' and (resid 422 through 459 )AA422 - 45990 - 127
55chain 'A' and (resid 460 through 494 )AA460 - 494128 - 162
66chain 'A' and (resid 495 through 527 )AA495 - 527163 - 195
77chain 'O' and (resid 1 through 17 )OC1 - 171 - 17
88chain 'O' and (resid 18 through 60 )OC18 - 6018 - 60
99chain 'O' and (resid 61 through 91 )OC61 - 9161 - 91
1010chain 'O' and (resid 92 through 135 )OC92 - 13592 - 135
1111chain 'O' and (resid 136 through 173 )OC136 - 173136 - 173
1212chain 'O' and (resid 174 through 193 )OC174 - 193174 - 193
1313chain 'O' and (resid 194 through 219 )OC194 - 219194 - 219
1414chain 'O' and (resid 220 through 230 )OC220 - 230220 - 230
1515chain 'P' and (resid 1 through 23 )PD1 - 231 - 23
1616chain 'P' and (resid 24 through 35 )PD24 - 3524 - 35
1717chain 'P' and (resid 36 through 63 )PD36 - 6336 - 63
1818chain 'P' and (resid 64 through 94 )PD64 - 9464 - 94
1919chain 'P' and (resid 95 through 110 )PD95 - 11095 - 110
2020chain 'P' and (resid 111 through 125 )PD111 - 125111 - 125
2121chain 'P' and (resid 126 through 141 )PD126 - 141126 - 141
2222chain 'P' and (resid 142 through 154 )PD142 - 154142 - 154
2323chain 'P' and (resid 155 through 177 )PD155 - 177155 - 177
2424chain 'P' and (resid 178 through 191 )PD178 - 191178 - 191
2525chain 'P' and (resid 192 through 213 )PD192 - 213192 - 213
2626chain 'D' and (resid 1 through 124 )DE1 - 1241 - 124
2727chain 'D' and (resid 125 through 149 )DE125 - 149125 - 149
2828chain 'D' and (resid 150 through 229 )DE150 - 229150 - 229
2929chain 'F' and (resid 1 through 90 )FF1 - 901 - 90
3030chain 'F' and (resid 91 through 128 )FF91 - 12891 - 128
3131chain 'F' and (resid 129 through 150 )FF129 - 150129 - 150
3232chain 'F' and (resid 151 through 215 )FF151 - 215151 - 215
3333chain 'B' and (resid 333 through 353 )BG333 - 3531 - 21
3434chain 'B' and (resid 354 through 375 )BG354 - 37522 - 43
3535chain 'B' and (resid 376 through 393 )BG376 - 39344 - 61
3636chain 'B' and (resid 394 through 421 )BG394 - 42162 - 89
3737chain 'B' and (resid 422 through 459 )BG422 - 45990 - 127
3838chain 'B' and (resid 460 through 494 )BG460 - 494128 - 162
3939chain 'B' and (resid 495 through 506 )BG495 - 506163 - 174
4040chain 'B' and (resid 507 through 516 )BG507 - 516175 - 184
4141chain 'B' and (resid 517 through 527 )BG517 - 527185 - 195
4242chain 'C' and (resid 1 through 67 )CI1 - 671 - 67
4343chain 'C' and (resid 68 through 150 )CI68 - 15068 - 150
4444chain 'C' and (resid 151 through 230 )CI151 - 230151 - 230
4545chain 'E' and (resid 1 through 23 )EJ1 - 231 - 23
4646chain 'E' and (resid 24 through 77 )EJ24 - 7724 - 77
4747chain 'E' and (resid 78 through 109 )EJ78 - 10978 - 109
4848chain 'E' and (resid 110 through 154 )EJ110 - 154110 - 154
4949chain 'E' and (resid 155 through 177 )EJ155 - 177155 - 177
5050chain 'E' and (resid 178 through 191 )EJ178 - 191178 - 191
5151chain 'E' and (resid 192 through 213 )EJ192 - 213192 - 213
5252chain 'G' and (resid 1 through 33 )GK1 - 331 - 33
5353chain 'G' and (resid 34 through 92 )GK34 - 9234 - 92
5454chain 'G' and (resid 93 through 124 )GK93 - 12493 - 124
5555chain 'G' and (resid 125 through 149 )GK125 - 149125 - 149
5656chain 'G' and (resid 150 through 229 )GK150 - 229150 - 229
5757chain 'H' and (resid 1 through 38 )HL1 - 381 - 38
5858chain 'H' and (resid 39 through 90 )HL39 - 9039 - 90
5959chain 'H' and (resid 91 through 115 )HL91 - 11591 - 115
6060chain 'H' and (resid 116 through 215 )HL116 - 215116 - 215
6161chain 'K' and (resid 333 through 393 )KM333 - 3931 - 61
6262chain 'K' and (resid 394 through 409 )KM394 - 40962 - 77
6363chain 'K' and (resid 410 through 494 )KM410 - 49478 - 162
6464chain 'K' and (resid 495 through 527 )KM495 - 527163 - 195
6565chain 'L' and (resid 1 through 122 )LO1 - 1221 - 122
6666chain 'L' and (resid 123 through 158 )LO123 - 158123 - 153
6767chain 'L' and (resid 159 through 229 )LO159 - 229154 - 224
6868chain 'M' and (resid 1 through 110 )MP1 - 1101 - 110
6969chain 'M' and (resid 111 through 177 )MP111 - 177111 - 177
7070chain 'M' and (resid 178 through 210 )MP178 - 210178 - 210
7171chain 'N' and (resid 1 through 17 )NQ1 - 171 - 17
7272chain 'N' and (resid 18 through 104 )NQ18 - 10418 - 104
7373chain 'N' and (resid 105 through 124 )NQ105 - 124105 - 124
7474chain 'N' and (resid 125 through 149 )NQ125 - 149125 - 149
7575chain 'N' and (resid 150 through 229 )NQ150 - 229150 - 229
7676chain 'Q' and (resid 1 through 25 )QR1 - 251 - 25
7777chain 'Q' and (resid 26 through 38 )QR26 - 3826 - 38
7878chain 'Q' and (resid 39 through 61 )QR39 - 6139 - 61
7979chain 'Q' and (resid 62 through 90 )QR62 - 9062 - 90
8080chain 'Q' and (resid 91 through 113 )QR91 - 11391 - 113
8181chain 'Q' and (resid 114 through 150 )QR114 - 150114 - 150
8282chain 'Q' and (resid 151 through 163 )QR151 - 163151 - 163
8383chain 'Q' and (resid 164 through 198 )QR164 - 198164 - 198
8484chain 'Q' and (resid 199 through 215 )QR199 - 215199 - 215
8585chain 'T' and (resid 333 through 349 )TS333 - 3491 - 17
8686chain 'T' and (resid 350 through 364 )TS350 - 36418 - 32
8787chain 'T' and (resid 365 through 393 )TS365 - 39333 - 61
8888chain 'T' and (resid 394 through 409 )TS394 - 40962 - 77
8989chain 'T' and (resid 410 through 421 )TS410 - 42178 - 89
9090chain 'T' and (resid 422 through 442 )TS422 - 44290 - 110
9191chain 'T' and (resid 443 through 459 )TS443 - 459111 - 127
9292chain 'T' and (resid 460 through 479 )TS460 - 479128 - 147
9393chain 'T' and (resid 480 through 494 )TS480 - 494148 - 162
9494chain 'T' and (resid 495 through 506 )TS495 - 506163 - 174
9595chain 'T' and (resid 507 through 516 )TS507 - 516175 - 184
9696chain 'T' and (resid 517 through 527 )TS517 - 527185 - 195
9797chain 'W' and (resid 1 through 128 )WU1 - 1281 - 128
9898chain 'W' and (resid 129 through 230 )WU129 - 230129 - 230
9999chain 'X' and (resid 1 through 17 )XV1 - 171 - 17
100100chain 'X' and (resid 18 through 125 )XV18 - 12518 - 125
101101chain 'X' and (resid 126 through 143 )XV126 - 143126 - 143
102102chain 'X' and (resid 144 through 175 )XV144 - 175144 - 175
103103chain 'X' and (resid 176 through 210 )XV176 - 210176 - 210
104104chain 'Y' and (resid 1 through 104 )YW1 - 1041 - 104
105105chain 'Y' and (resid 105 through 139 )YW105 - 139105 - 139
106106chain 'Y' and (resid 140 through 158 )YW140 - 158140 - 158
107107chain 'Y' and (resid 159 through 229 )YW159 - 229159 - 229
108108chain 'Z' and (resid 1 through 25 )ZX1 - 251 - 25
109109chain 'Z' and (resid 26 through 48 )ZX26 - 4826 - 48
110110chain 'Z' and (resid 49 through 69 )ZX49 - 6949 - 69
111111chain 'Z' and (resid 70 through 83 )ZX70 - 8370 - 83
112112chain 'Z' and (resid 84 through 101 )ZX84 - 10184 - 101
113113chain 'Z' and (resid 102 through 113 )ZX102 - 113102 - 113
114114chain 'Z' and (resid 114 through 128 )ZX114 - 128114 - 128
115115chain 'Z' and (resid 129 through 150 )ZX129 - 150129 - 150
116116chain 'Z' and (resid 151 through 174 )ZX151 - 174151 - 174
117117chain 'Z' and (resid 175 through 188 )ZX175 - 188175 - 188
118118chain 'Z' and (resid 189 through 204 )ZX189 - 204189 - 204
119119chain 'Z' and (resid 205 through 215 )ZX205 - 215205 - 215

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万見について

-
お知らせ

-
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