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- PDB-7zfb: SARS-CoV-2 Omicron RBD in complex with nanobody C1, Omi-18 and Om... -

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基本情報

登録情報
データベース: PDB / ID: 7zfb
タイトルSARS-CoV-2 Omicron RBD in complex with nanobody C1, Omi-18 and Omi-31 Fabs
要素
  • Nanobody C1
  • Omi-18 heavy chain
  • Omi-18 light chain
  • Omi-31 heavy chain
  • Omi-31 light chain
  • Spike protein S1
キーワードVIRAL PROTEIN (ウイルスタンパク質) / SARS-CoV-2 (SARSコロナウイルス2) / Omicron (Ο) / BA.1 (SARSコロナウイルス2-オミクロン株) / BA.2 (SARSコロナウイルス2-オミクロン株) / RBD / antibody (抗体) / Fab / Omi-18 / Omi-31 / VIRAL PROTEIN/IMMUNE SYSTEM (ウイルス性)
機能・相同性
機能・相同性情報


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / 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 / エンベロープ (ウイルス) / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / 生体膜 / identical protein binding / 細胞膜
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
類似検索 - ドメイン・相同性
スパイクタンパク質
類似検索 - 構成要素
生物種Lama glama (ラマ)
Severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.08 Å
データ登録者Zhou, D. / Huo, J. / Ren, J. / Stuart, D.I.
資金援助 英国, 2件
組織認可番号国
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 英国
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 英国
引用ジャーナル: Cell / 年: 2022
タイトル: Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
著者: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / ...著者: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / Donal Skelly / Thomas G Ritter / Ali Amini / Sagida Bibi / Sandra Adele / Sile Ann Johnson / Bede Constantinides / Hermione Webster / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / Derrick Crook / Andrew J Pollard / Teresa Lambe / Philip Goulder / / Neil G Paterson / Mark A Williams / David R Hall / Juthathip Mongkolsapaya / Elizabeth E Fry / Wanwisa Dejnirattisai / Jingshan Ren / David I Stuart / Gavin R Screaton /
要旨: Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA. ...Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site; however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focused in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains, and many show broad reactivity with variants of concern.
履歴
登録2022年4月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年6月1日Provider: repository / タイプ: Initial release
改定 1.12022年6月15日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22022年6月22日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32022年6月29日Group: Derived calculations
カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen
改定 1.42024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
M: Nanobody C1
N: Nanobody C1
E: Spike protein S1
A: Omi-31 heavy chain
B: Omi-31 light chain
H: Omi-18 heavy chain
L: Omi-18 light chain
C: Omi-31 heavy chain
D: Omi-31 light chain
K: Omi-18 light chain
J: Omi-18 heavy chain
F: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)263,66014
ポリマ－263,21712
非ポリマー4422
水0
1
M: Nanobody C1
E: Spike protein S1
A: Omi-31 heavy chain
B: Omi-31 light chain
H: Omi-18 heavy chain
L: Omi-18 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)131,8307
ポリマ－131,6096
非ポリマー2211
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
N: Nanobody C1
C: Omi-31 heavy chain
D: Omi-31 light chain
K: Omi-18 light chain
J: Omi-18 heavy chain
F: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)131,8307
ポリマ－131,6096
非ポリマー2211
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)111.188, 135.092, 112.244
Angle α, β, γ (deg.)90.000, 101.663, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and resid 2 through 228)
d_2ens_1(chain "C" and resid 2 through 228)
d_1ens_2(chain "B" and (resid 2 through 8 or resid 10 through 213))
d_2ens_2(chain "D" and (resid 2 through 8 or resid 10 through 213))
d_1ens_3(chain "E" and (resid 333 or resid 336 through 345...
d_2ens_3(chain "F" and (resid 333 or resid 336 through 345...
d_1ens_4(chain "H" and (resid 2 through 101 or resid 103 through 219))
d_2ens_4(chain "J" and (resid 2 through 101 or resid 103 through 219))
d_1ens_5(chain "K" and (resid 4 through 93 or resid 95 through 110 or resid 112 through 210))
d_2ens_5(chain "L" and (resid 4 through 93 or resid 95 through 110 or resid 112 through 210))
d_1ens_6(chain "M" and (resid 1 through 10 or resid 12 through 16 or resid 18 through 123))
d_2ens_6(chain "N" and (resid 1 through 10 or resid 12 through 16 or resid 18 through 123))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALPROE2 - 228
d_21ens_1VALPROI2 - 228
d_11ens_2SERPROF1 - 7
d_12ens_2ALATHRF9 - 212
d_21ens_2SERPROJ2 - 8
d_22ens_2ALATHRJ10 - 213
d_11ens_3THRTHRC1
d_12ens_3CYSTHRC4 - 13
d_13ens_3PHELEUC15 - 186
d_14ens_3ALALYSC188 - 195
d_21ens_3THRTHRM1
d_22ens_3CYSTHRM4 - 13
d_23ens_3PHELEUM15 - 186
d_24ens_3ALALYSM188 - 195
d_11ens_4VALVALG2 - 101
d_12ens_4GLYSERG103 - 215
d_21ens_4VALVALL2 - 101
d_22ens_4GLYSERL103 - 215
d_11ens_5LEUSERK1 - 90
d_12ens_5ASPPROK92 - 107
d_13ens_5ALATHRK109 - 207
d_21ens_5LEUSERH2 - 91
d_22ens_5ASPPROH93 - 108
d_23ens_5ALATHRH110 - 208
d_11ens_6GLNGLYA1 - 10
d_12ens_6VALGLYA12 - 16
d_13ens_6LEUSERA18 - 123
d_21ens_6GLNGLYB1 - 10
d_22ens_6VALGLYB12 - 16
d_23ens_6LEUSERB18 - 123

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6

NCS oper:
IDCodeMatrixベクター
1given(0.989362252517, -0.00710497518369, 0.145299183145), (-0.0236057168667, -0.99340997299, 0.112157905182), (0.14354477847, -0.114394689087, -0.983010046583)41.1858663078, -30.2040844966, 109.194955384
2given(0.990065328712, -0.0114525319188, 0.14014094475), (-0.029316972643, -0.991586261973, 0.126084099637), (0.137517853378, -0.128940003796, -0.982070931971)41.2334056799, -31.6491434166, 108.348848006
3given(0.985234963438, -0.00764819762888, 0.171036755969), (-0.0113004688417, -0.999728229751, 0.0203903418889), (0.170834323902, -0.022022073277, -0.985053634106)39.0538769455, -22.5961525554, 111.830677374
4given(0.983065789383, -0.0107897037193, 0.18293505962), (-0.0449561437492, -0.981959289291, 0.18367062725), (0.177653029481, -0.188784365001, -0.96581564734)37.2974396041, -37.9185437938, 108.480482195
5given(0.995067520597, -0.018642500834, 0.0974324720783), (-0.00518545392357, -0.990614995676, -0.1365834595), (0.0990643251642, 0.135404532805, -0.985825477443)-56.8684448669, -18.5746049929, 108.389235926
6given(0.978160364615, 0.0413798938521, 0.203690955816), (0.031396961304, -0.998153337233, 0.0520014056757), (0.205466619959, -0.0444704368785, -0.977653235215)37.9893375604, -23.8694611639, 111.317648733

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要素

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抗体 , 5種, 10分子 MNACBDHJLK

#1: 抗体 Nanobody C1


分子量: 14659.114 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Lama glama (ラマ) / 発現宿主: Escherichia coli (大腸菌)
#3: 抗体 Omi-31 heavy chain


分子量: 24802.873 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)
#4: 抗体 Omi-31 light chain


分子量: 22780.051 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)
#5: 抗体 Omi-18 heavy chain


分子量: 23376.338 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)
#6: 抗体 Omi-18 light chain


分子量: 22833.049 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)

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タンパク質 / 糖 , 2種, 4分子 EF

#2: タンパク質 Spike protein S1 / SARS-CoV-2 Omicron Spike protein


分子量: 23157.164 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 (SARSコロナウイルス2)
遺伝子: S, 2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2
#7: 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 / N-アセチルグルコサミン


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

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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: 3.14 Å3/Da / 溶媒含有率: 60.78 %
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: 0.2 M Ammonium sulfate, 0.1 M MES pH 6.5, 20 % 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: I04 / 波長: 0.9795 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2022年3月4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: 0.9795 Å / 相対比: 1
反射解像度: 3.08→87 Å / Num. obs: 60199 / % possible obs: 100 % / 冗長度: 14.1 % / Biso Wilson estimate: 110.19 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.264 / Rpim(I) all: 0.073 / Net I/σ(I): 5.4
反射 シェル解像度: 3.08→3.13 Å / Mean I/σ(I) obs: 0.2 / Num. unique obs: 2994 / CC1/2: 0.286

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解析

ソフトウェア
名称バージョン分類
GDA1.19_4092データ収集
PHENIX1.19_4092精密化
xia2データ削減
xia2データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7QNW

7qnw


解像度: 3.08→70.56 Å / SU ML: 0.667 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 42.3168
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.3078 2718 5.08 %
Rwork0.2605 50808 -
obs0.2629 53526 88.98 %
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: 176.96 Å2
精密化ステップサイクル: LAST / 解像度: 3.08→70.56 Å
タンパク質核酸リガンド溶媒全体
原子数17886 0 28 0 17914
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.004318388
X-RAY DIFFRACTIONf_angle_d0.679225095
X-RAY DIFFRACTIONf_chiral_restr0.04662817
X-RAY DIFFRACTIONf_plane_restr0.00563234
X-RAY DIFFRACTIONf_dihedral_angle_d11.83386501
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS0.454023083923
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.629717147132
ens_3d_2FX-RAY DIFFRACTIONTorsion NCS0.382073151381
ens_4d_2JX-RAY DIFFRACTIONTorsion NCS1.79906369486
ens_5d_2LX-RAY DIFFRACTIONTorsion NCS1.78073507061
ens_6d_2NX-RAY DIFFRACTIONTorsion NCS0.288777081828
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.140.4748200.4781291X-RAY DIFFRACTION9.87
3.14-3.20.4826290.4377586X-RAY DIFFRACTION19.71
3.2-3.260.47381380.47322121X-RAY DIFFRACTION71.69
3.26-3.330.50621780.48332834X-RAY DIFFRACTION96.05
3.33-3.410.49441630.48932963X-RAY DIFFRACTION99.08
3.41-3.50.46261440.46483011X-RAY DIFFRACTION99.12
3.5-3.590.47791450.40082966X-RAY DIFFRACTION99.3
3.59-3.70.37821420.36422980X-RAY DIFFRACTION98.99
3.7-3.820.37741710.33512992X-RAY DIFFRACTION99.75
3.82-3.950.39031730.30092969X-RAY DIFFRACTION99.56
3.95-4.110.32681710.28432956X-RAY DIFFRACTION99.52
4.11-4.30.33431500.26233024X-RAY DIFFRACTION99.72
4.3-4.520.24821550.21132975X-RAY DIFFRACTION99.65
4.52-4.810.2391520.2113020X-RAY DIFFRACTION99.84
4.81-5.180.2491230.20733042X-RAY DIFFRACTION99.75
5.18-5.70.28511640.22193006X-RAY DIFFRACTION99.94
5.7-6.520.2831530.23443028X-RAY DIFFRACTION99.66
6.52-8.220.26591790.23923007X-RAY DIFFRACTION99.81
8.22-70.560.25321680.18873037X-RAY DIFFRACTION98.34
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)
18.45886879207-5.61397698895-1.632921327637.46015841869-0.4468323843344.955602289470.005899912106261.07205758511-0.180964766958-2.310557782740.444954970961-2.12563659735-0.405866380245-0.947240256452-0.2525273070160.957237563340.250663558110.3908961240641.44797382283-0.1199297346532.50684582693-19.4049521724-1.743552380557.12544026396
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36.537301504560.08162864905323.657175225356.67452421541.683759729783.34629499023-1.100913106722.91003197511.91124683944-1.67566969757-0.7454612891131.32588533421-0.703482602295-1.750219547090.871125287770.8616018689420.451495185179-0.04570274114822.304325010270.9498695012092.63638273243-27.03489870777.673749127444.19356896379
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506.02498112081-1.46646707806-0.9038426311683.395510848431.697806087941.011789484060.106191626010.6259829483290.8705082658731.095058014890.1164903696651.81778927341-0.608376657044-0.45692283631-0.2751640330670.9508399698080.09951041674980.3138578351860.9198641688650.1974728163781.47556061169-44.5348992091-18.229235721182.6918962047
514.06994915296-1.138529821842.239769807670.7851350846790.1644423371035.752229896642.415323471171.48653909349-0.127669417819-1.032860149120.861402727065-0.2881482362071.65538025722-0.376036602414-2.21759833831.67050260738-0.199185408939-0.2497245403151.870746817550.4810798383973.77247519958-88.4203339704-20.908104363693.1848766813
524.97456398766-0.6945682641841.201399648892.022956421641.435384605772.907196100270.289547357338-1.510047103990.8144438481220.388748147301-0.235078487568-0.342774619049-0.3762789509810.122833014294-0.09971616342631.529452588590.1425156386910.6077267192761.413904070730.3985779148373.12108674964-77.1397604722-16.941702544896.2218403397
532.05470205666-1.56726696844-0.1709915265194.927971547051.05153105113.927429430770.1185564845710.688482640607-0.3407528478150.11090817957-0.5064687432881.532524876070.0789453087406-0.5321364523030.454045364020.8313271171060.1297822080360.1112435500560.8333763587970.2690362091721.30395815173-48.3295576513-37.220948612775.2746153899
540.99069449751-2.19632388254-0.662924036825.417934779390.08994200148865.45069797796-0.7332284262770.698546510937-0.2920670576260.394837353178-0.3528861220421.04674272651.11793771223-0.952225594628-0.2287628372030.9304515271190.4339438996810.02293208565220.4852463587421.41777748852-0.250804816044-47.6005169207-35.285655793974.0564813359
553.58342845701-0.37808282787-4.25516976510.06774082401590.511490448035.095922175670.585730272035-0.5440388471111.829672990870.122198247394-0.2537108914541.58104115342-0.0865068323406-1.3922917476-0.7751758103640.886163638920.04216786290950.005886024749611.501025150360.2167751112282.2479968814-71.9699486438-35.181968113279.9134074856
566.716955091981.24268995085-0.9293134536120.972126986041.657766240234.52747098142-0.2582190838420.7555695367970.6647576402180.5397160162470.1878288904162.34579511146-0.53920639324-1.36118143496-0.07596838083831.206236389920.4012689601140.3833534391341.85756662360.7554854261552.96218267445-83.3703356049-20.717216696380.6271439976
573.97410131465-1.55232451540.5875548827522.504753020521.442728380264.24756663615-0.264754795469-0.752478463053-0.3648354102420.9860940192580.3337391515130.1441456274930.1740793642990.498454173833-0.301143376621.05501709653-0.2219857810280.3090685671171.03949894939-0.1977750549411.5649616993-1.422105282-12.228555117297.2479173732
583.7415619285-1.33418198919-0.6859333330644.382422055961.108524437812.549182341120.407637458610.398671057020.04024972487720.7905106597560.242333127783-0.352675940357-0.2578309293660.654208907941-0.2378230365421.08417619163-0.1379997887020.4109626472531.04637538016-0.2422853715531.91154767896-2.58804120929-9.3912220848791.6079900199
594.155341881741.36415857447-1.578443369810.8054379676110.5631881960193.361746672180.2288431873631.746294623940.3441891931650.392188103233-0.306416940736-0.2522382990030.0734730641958-1.13864723282-0.406776787661.37768489568-0.1829892854480.05003590156591.956274471290.2665874211191.306266128217.854302956522.4606439713103.547026895
605.792512591041.65502131457-1.554408088573.665246411520.7623324626257.488876573720.0915155677542-0.602055264335-1.26310214449-1.35344706554-0.650940661822-0.9947816795360.168084723789-0.4324690895260.4441059943521.4294941168-0.3465368795330.1616615710020.7823124196020.008554305491851.733303698744.763081882222.6470622199108.863772937
610.930882048008-0.572419992631-0.3767840825810.4266405715720.2098836166810.153918271222-1.11968655983-1.43471121619-0.592901764604-0.577086412997-0.0457575991656-0.6477114143440.2839568482380.01139276927190.6339140403291.83289126004-0.1357043551380.2083663859071.85722003494-0.1890191641421.80373490209-0.93592303877728.2476133891117.853040001
627.309795134980.386944193620.1894004116610.867768740753-1.652604653683.44635499226-0.832633855767-0.909635931812-0.8463454511750.1480672048661.40837038024-0.729305461342-0.1676800934990.6078829989030.448763304371.45027937249-0.2498654013090.2780001069471.23759879029-0.6132663855310.9359962423222.5849535824526.7534635195109.218023569
636.637332725631.12921559942-2.024658724491.277453586521.425303228753.61134085340.246757312218-1.45382118181-0.736354343394-0.834777045650.414112525944-1.470852343260.1416202817371.040164290380.2865766936871.93464407829-0.316987811186-0.02068862332591.14285412946-0.1632745932752.4467659103711.396144316327.8765904814111.146034276
642.19166483031-0.463799051071-2.213165987550.1039159341610.5608686331266.37234856552-0.4925126217290.03382800150241.4229211727-0.281624761409-0.07712574247580.792576663443-0.0268763163711-0.9807874467690.6227509358541.46263328648-0.298449285180.9212737174931.00763530201-0.07831685321282.41833335502-23.58706790528.7256483475395.0927252164
658.37770260676-2.81459313875-0.9381716453295.754816745123.951887318282.79600890040.09714250407520.2004222396630.251180298233-0.05548147719330.02265255560790.902054298133-0.558422287498-0.537194323036-0.3194598049621.19701104191-0.207276585040.6096215611141.108104641670.1776754117431.90195174313-23.3490434157-1.7600568137694.1878847565
662.353768336730.5431528371540.5762108915144.46016497288-0.6564566015430.2472048003320.862001677927-0.246104478930.53284276279-0.727443768004-0.4423146341570.149221618152-0.985806484959-0.6821760167760.1022660289111.41548316103-0.1713599295280.6935251597321.16940562190.06358151235391.70666649281-17.13512992385.1348147157693.8401394251
674.65604198893-1.235251569382.009706730521.5073548970.004467920878441.89521061895-1.578815107951.35604363228-1.10652438657-0.2649083541770.67030350450.1896876851970.336865290602-0.2543853384820.9272669591271.79632228951-0.4520464208350.3925870736691.02181550989-0.1334591270691.31322498637-3.143501024624.517564519297.0571143665
680.160233530124-0.5167915294280.2395372056562.59769036211-2.106122291892.69887598687-1.209128306853.10959391467-0.567402349801-0.5493657391481.554007054220.490770237481-1.06368363449-0.797729801801-0.5273500030061.62857782908-0.5129724375320.2659733277832.28597372672-0.07141021925062.27602608238-9.1632439052130.175034602692.5936372422
692.468737824593.76601319969-1.353894965576.13671571764-2.648268650426.279410680030.495948246720.930528465455-1.085192179740.9229720137040.6812574336881.61766655526-0.486100354147-0.273026629353-0.3619142844220.9661611370380.03449966311950.4419866211310.71513477455-0.1639807541052.216438391515.62341674674-5.4030394304415.545993537
705.64858431274-0.6894238946620.9375516955622.382590470280.6719554843220.9914605152420.8211153079320.6462016531240.02022115194510.935602681623-0.2535044792192.22469954003-0.986266014371-0.8228351549930.123740041615-0.150247101385-0.9583064476381.20843148068-0.1790855051730.2544647447652.7801780473510.42469729171.6582930109723.6066194003
712.953768505992.132932208263.023789703725.967622311541.743823786774.668727531590.52444723541-0.120392343896-1.46410032381.17802123980.444821103957-0.732891558913-0.00841895695010.542340939731-0.08056699912141.08055891830.09949630850760.5640014454340.738989389240.5513366275982.4800322770814.5019940062-5.6015623442930.0920132722
722.96373189615-1.409977038912.046015501320.804800091859-1.112923694622.72380868031-0.5640712251641.9913859361-1.92845269814-1.898483919980.182017919341-0.3469931744650.9751317801831.685697451340.8673144854331.09884776316-0.052093388810.9928362468721.2849345628-0.8415554967251.994829030218.2835744067-6.5802353629617.9907116527
736.48645771516-1.27308569356-0.03336174571081.483294452851.95345898622.966598800960.172258698307-1.1016319656-1.835668819171.797933384660.6413416358360.1344310351310.596660249949-0.1617129580980.07134384291011.18447610071-0.1955177415750.5576478553890.5232158557940.01695991261543.08279360384.19450051578-10.224005383323.4298912303
740.810959193903-0.235414797211-0.3507338502323.159008299260.3404493438571.770631451370.0398373041113-0.0366281236829-1.04364367882-0.1430097612550.28496084562-0.000883455949594-0.2581545222840.275927346242-0.3185928294810.716926751193-0.006328391915770.3745212979080.804757644435-0.1316627873781.793314648769.045058905291.885921749524.6196496506
757.330969080695.00075391488-0.9463175333943.58338160619-1.851221883798.436602558710.726433427708-1.620203321670.1589119188841.22127372006-0.5255024220781.12745883712-2.01713501105-0.214991091522-1.028113759411.49078356440.1833609686850.06963993631451.76207629097-0.03819265963771.67435803817-32.60132248793.054792081827.20538479804
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 'C' and (resid 150 through 172 )CI150 - 172150 - 172
22chain 'C' and (resid 173 through 192 )CI173 - 192173 - 192
33chain 'C' and (resid 193 through 203 )CI193 - 203193 - 203
44chain 'C' and (resid 204 through 228 )CI204 - 228204 - 228
55chain 'D' and (resid 1 through 23 )DJ1 - 231 - 23
66chain 'D' and (resid 24 through 101 )DJ24 - 10124 - 101
77chain 'D' and (resid 102 through 122 )DJ102 - 122102 - 122
88chain 'D' and (resid 123 through 165 )DJ123 - 165123 - 165
99chain 'D' and (resid 166 through 213 )DJ166 - 213166 - 213
1010chain 'K' and (resid 4 through 17 )KK4 - 171 - 14
1111chain 'K' and (resid 18 through 31 )KK18 - 3115 - 28
1212chain 'K' and (resid 32 through 89 )KK32 - 8929 - 86
1313chain 'K' and (resid 90 through 119 )KK90 - 11987 - 116
1414chain 'K' and (resid 120 through 130 )KK120 - 130117 - 127
1515chain 'K' and (resid 131 through 151 )KK131 - 151128 - 148
1616chain 'K' and (resid 152 through 172 )KK152 - 172149 - 169
1717chain 'K' and (resid 173 through 210 )KK173 - 210170 - 207
1818chain 'J' and (resid 1 through 110 )JL1 - 1101 - 110
1919chain 'J' and (resid 111 through 219 )JL111 - 219111 - 215
2020chain 'F' and (resid 333 through 353 )FM333 - 3531 - 21
2121chain 'F' and (resid 354 through 375 )FM354 - 37522 - 43
2222chain 'F' and (resid 376 through 516 )FM376 - 51644 - 184
2323chain 'F' and (resid 517 through 527 )FM517 - 527185 - 195
2424chain 'M' and (resid 1 through 7 )MA1 - 71 - 7
2525chain 'M' and (resid 8 through 17 )MA8 - 178 - 17
2626chain 'M' and (resid 18 through 24 )MA18 - 2418 - 24
2727chain 'M' and (resid 25 through 39 )MA25 - 3925 - 39
2828chain 'M' and (resid 40 through 52 )MA40 - 5240 - 52
2929chain 'M' and (resid 53 through 60 )MA53 - 6053 - 60
3030chain 'M' and (resid 61 through 73 )MA61 - 7361 - 73
3131chain 'M' and (resid 74 through 91 )MA74 - 9174 - 91
3232chain 'M' and (resid 92 through 99 )MA92 - 9992 - 99
3333chain 'M' and (resid 100 through 107 )MA100 - 107100 - 107
3434chain 'M' and (resid 108 through 123 )MA108 - 123108 - 123
3535chain 'N' and (resid 1 through 17 )NB1 - 171 - 17
3636chain 'N' and (resid 18 through 24 )NB18 - 2418 - 24
3737chain 'N' and (resid 25 through 39 )NB25 - 3925 - 39
3838chain 'N' and (resid 40 through 52 )NB40 - 5240 - 52
3939chain 'N' and (resid 53 through 60 )NB53 - 6053 - 60
4040chain 'N' and (resid 61 through 73 )NB61 - 7361 - 73
4141chain 'N' and (resid 74 through 91 )NB74 - 9174 - 91
4242chain 'N' and (resid 92 through 107 )NB92 - 10792 - 107
4343chain 'N' and (resid 108 through 124 )NB108 - 124108 - 124
4444chain 'E' and (resid 333 through 353 )EC333 - 3531 - 21
4545chain 'E' and (resid 354 through 375 )EC354 - 37522 - 43
4646chain 'E' and (resid 376 through 516 )EC376 - 51644 - 184
4747chain 'E' and (resid 517 through 527 )EC517 - 527185 - 195
4848chain 'A' and (resid 1 through 23 )AE1 - 231 - 23
4949chain 'A' and (resid 24 through 67 )AE24 - 6724 - 67
5050chain 'A' and (resid 68 through 134 )AE68 - 13468 - 134
5151chain 'A' and (resid 135 through 149 )AE135 - 149135 - 149
5252chain 'A' and (resid 150 through 228 )AE150 - 228150 - 228
5353chain 'B' and (resid 2 through 62 )BF2 - 621 - 61
5454chain 'B' and (resid 63 through 101 )BF63 - 10162 - 100
5555chain 'B' and (resid 102 through 122 )BF102 - 122101 - 121
5656chain 'B' and (resid 123 through 213 )BF123 - 213122 - 212
5757chain 'H' and (resid 1 through 39 )HG1 - 391 - 39
5858chain 'H' and (resid 40 through 113 )HG40 - 11340 - 113
5959chain 'H' and (resid 114 through 138 )HG114 - 138114 - 134
6060chain 'H' and (resid 139 through 158 )HG139 - 158135 - 154
6161chain 'H' and (resid 159 through 169 )HG159 - 169155 - 165
6262chain 'H' and (resid 170 through 204 )HG170 - 204166 - 200
6363chain 'H' and (resid 205 through 219 )HG205 - 219201 - 215
6464chain 'L' and (resid 3 through 17 )LH3 - 171 - 15
6565chain 'L' and (resid 18 through 89 )LH18 - 8916 - 87
6666chain 'L' and (resid 90 through 114 )LH90 - 11488 - 112
6767chain 'L' and (resid 115 through 188 )LH115 - 188113 - 186
6868chain 'L' and (resid 189 through 210 )LH189 - 210187 - 208
6969chain 'C' and (resid 1 through 23 )CI1 - 231 - 23
7070chain 'C' and (resid 24 through 52 )CI24 - 5224 - 52
7171chain 'C' and (resid 53 through 67 )CI53 - 6753 - 67
7272chain 'C' and (resid 68 through 77 )CI68 - 7768 - 77
7373chain 'C' and (resid 78 through 91 )CI78 - 9178 - 91
7474chain 'C' and (resid 92 through 134 )CI92 - 13492 - 134
7575chain 'C' and (resid 135 through 149 )CI135 - 149135 - 149

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万見について

-
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