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- PDB-7zfe: SARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1 -

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基本情報

登録情報
データベース: PDB / ID: 7zfe
タイトルSARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1
要素
  • Nanobody C1
  • Omi-32 heavy chain
  • Omi-32 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-32 / VIRALPROTEIN/IMMUNE SYSTEM
機能・相同性
機能・相同性情報


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / 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: 3.25 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
Z: Nanobody C1
C: Spike protein S1
M: Omi-32 heavy chain
N: Omi-32 light chain
K: Omi-32 light chain
X: Nanobody C1
W: Nanobody C1
E: Spike protein S1
J: Omi-32 heavy chain
H: Omi-32 heavy chain
L: Omi-32 light chain
F: Omi-32 heavy chain
G: Omi-32 light chain
B: Spike protein S1
A: Spike protein S1
Y: Nanobody C1


分子量 (理論値)分子数
合計 (水以外)340,01616
ポリマ－340,01616
非ポリマー00
水0
1
Z: Nanobody C1
E: Spike protein S1
H: Omi-32 heavy chain
L: Omi-32 light chain


分子量 (理論値)分子数
合計 (水以外)85,0044
ポリマ－85,0044
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Spike protein S1
M: Omi-32 heavy chain
N: Omi-32 light chain
Y: Nanobody C1


分子量 (理論値)分子数
合計 (水以外)85,0044
ポリマ－85,0044
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
K: Omi-32 light chain
W: Nanobody C1
J: Omi-32 heavy chain
A: Spike protein S1


分子量 (理論値)分子数
合計 (水以外)85,0044
ポリマ－85,0044
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
X: Nanobody C1
F: Omi-32 heavy chain
G: Omi-32 light chain
B: Spike protein S1


分子量 (理論値)分子数
合計 (水以外)85,0044
ポリマ－85,0044
非ポリマー00
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)98.489, 159.908, 133.271
Angle α, β, γ (deg.)90.000, 106.765, 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 336 through 345 or resid 347...
d_2ens_1(chain "B" and (resid 336 through 345 or resid 347...
d_3ens_1(chain "C" and (resid 336 through 345 or resid 347...
d_4ens_1(chain "E" and (resid 336 through 345 or resid 347...
d_1ens_2(chain "F" and (resid 1 through 107 or (resid 108...
d_2ens_2(chain "H" and (resid 1 through 212 or resid 214 through 217))
d_3ens_2(chain "J" and (resid 1 through 107 or (resid 108...
d_4ens_2(chain "M" and (resid 1 through 107 or (resid 108...
d_1ens_3chain "G"
d_2ens_3chain "K"
d_3ens_3chain "L"
d_4ens_3chain "N"
d_1ens_4(chain "W" and (resid 1 through 10 or resid 12 through 16 or resid 18 through 124))
d_2ens_4(chain "X" and (resid 1 through 10 or resid 12 through 16 or resid 18 through 124))
d_3ens_4(chain "Y" and (resid 1 through 10 or resid 12 through 16 or resid 18 through 124))
d_4ens_4(chain "Z" and (resid 1 through 10 or resid 12 through 16 or resid 18 through 124))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDEnd auth comp-IDAuth asym-IDAuth seq-ID
d_11ens_1CYSTHRA1 - 10
d_12ens_1PHEILEA12 - 23
d_13ens_1TYRPHEA34 - 42
d_14ens_1CYSGLYA44 - 81
d_15ens_1ILEGLUA83 - 181
d_21ens_1CYSTHRB - N2 - 11
d_22ens_1PHEILEB - N13 - 24
d_23ens_1TYRPHEB - N35 - 43
d_24ens_1CYSGLYB - N45 - 82
d_25ens_1ILEGLUB - N84 - 182
d_31ens_1CYSTHRC1 - 10
d_32ens_1PHEILEC12 - 23
d_33ens_1TYRPHEC34 - 42
d_34ens_1CYSGLYC44 - 81
d_35ens_1ILEGLUC83 - 181
d_41ens_1CYSTHRE2 - 11
d_42ens_1PHEPHEE13 - 33
d_43ens_1CYSGLYE35 - 72
d_44ens_1ILEGLUE74 - 172
d_11ens_2GLULYSF1 - 212
d_12ens_2VALLYSF214 - 217
d_21ens_2GLULYSH1 - 212
d_22ens_2VALLYSH214 - 217
d_31ens_2GLULYSJ1 - 212
d_32ens_2VALLYSJ214 - 217
d_41ens_2GLULYSM1 - 212
d_42ens_2VALLYSM214 - 217
d_11ens_3ALACYSG1 - 216
d_21ens_3ALACYSK1 - 216
d_31ens_3ALACYSL1 - 216
d_41ens_3ALACYSN1 - 216
d_11ens_4GLNGLYW1 - 10
d_12ens_4VALGLYW12 - 16
d_13ens_4LEUSERW18 - 124
d_21ens_4GLNGLYX1 - 10
d_22ens_4VALGLYX12 - 16
d_23ens_4LEUSERX18 - 124
d_31ens_4GLNGLYY1 - 10
d_32ens_4VALGLYY12 - 16
d_33ens_4LEUSERY18 - 124
d_41ens_4GLNGLYZ1 - 10
d_42ens_4VALGLYZ12 - 16
d_43ens_4LEUSERZ18 - 124

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixベクター
1given(-0.876131242639, 0.0194208728767, -0.481681300622), (0.0536051157303, 0.996916395408, -0.0573078714848), (0.479083017065, -0.0760297985219, -0.874470658454)-9.13498448396, 14.6010033074, -40.520027617
2given(0.817294377968, -0.00177313315746, 0.5762176288), (-0.0135908669705, -0.999776391382, 0.016200480566), (0.576060055963, -0.021071858826, -0.817135722319)12.4196002206, 45.5444031536, -34.6798879691
3given(-0.457027406252, -0.0273893627669, -0.889030805283), (-0.0654819879231, -0.995777283069, 0.064340592022), (-0.887038927665, 0.0876209183434, 0.453303998963)-40.9703072509, 30.4475334986, 63.9611625157
4given(0.816757666164, 0.00885471323242, 0.576912912679), (0.0179541150479, -0.999788068345, -0.0100731398768), (0.576701451806, 0.0185852750235, -0.816743547901)-11.0157414166, 44.0273986113, 34.4800704975
5given(-0.897508300714, 0.065696616297, 0.43607660423), (0.0442899424397, 0.997269809277, -0.0590874648557), (-0.438767878437, -0.0337176824755, -0.897967631232)11.2313527498, -18.4795098323, -41.7673026892
6given(-0.98961337675, 0.0232819576907, -0.141856670632), (-0.0298870027216, -0.998557322399, 0.0446098750542), (-0.140613411967, 0.04838619979, 0.988881511631)-1.97963062974, 62.9202855303, 5.3578896472
7given(-0.890181974003, 0.0355360730039, 0.454217173471), (0.0308489521879, 0.999366828483, -0.017728064658), (-0.454559561894, -0.00176907972521, -0.890714586749)12.3174059225, -18.5296761096, -43.0321656888
8given(0.816047845613, 0.010435941278, 0.577890132118), (0.016062440439, -0.999860289971, -0.00462585618718), (0.577761119908, 0.0130572458031, -0.816101462231)-11.0784352064, 44.0536689065, 34.7619380054
9given(-0.992772637567, 0.0165606174937, -0.11886225661), (-0.01801778855, -0.999774989065, 0.0111951121084), (-0.118650113333, 0.0132558359819, 0.992847638572)-1.74054152376, 62.7357951982, 6.10610308423
10given(-0.864196725791, 0.0116707539108, -0.503018700086), (0.0505198583892, 0.99669149549, -0.0636695117558), (0.500611389244, -0.0804354170875, -0.86192713186)-10.3163748768, 14.1452506345, -39.5088340403
11given(0.81966541193, -0.00177565898758, 0.572839820126), (-0.0130130839801, -0.999794857159, 0.0155210580773), (0.572694746031, -0.0201764871489, -0.819520370238)12.3961533039, 45.6716961796, -34.7360405158
12given(-0.428542178083, -0.0274890444331, -0.903103512362), (-0.0697603053763, -0.995546696039, 0.0634056448552), (-0.900824678502, 0.0901727699578, 0.42471610537)-41.5949125066, 30.596076085, 61.9535406784

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要素

#1: 抗体
Nanobody C1


分子量: 14659.114 Da / 分子数: 4 / 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)
#2: タンパク質
Spike protein S1 / SARS-CoV-2 Omicron Spike protein


分子量: 23157.164 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 (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
#3: 抗体
Omi-32 heavy chain


分子量: 23711.529 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
Omi-32 light chain


分子量: 23476.111 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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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.96 Å3/Da / 溶媒含有率: 58.38 %
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: 0.15 M Lithium sulfate monohydrate, 0.1 M Citric acid pH 3.5, 18% w/v Polyethylene glycol 6,000

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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: 0.9762 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2022年2月28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: 0.9762 Å / 相対比: 1
反射解像度: 3.25→128 Å / Num. obs: 28305 / % possible obs: 87.8 % / 冗長度: 7.1 % / Biso Wilson estimate: 70.52 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.097 / Net I/σ(I): 6.6
反射 シェル解像度: 3.254→3.758 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1416 / CC1/2: 0.474

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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: 3.25→127.61 Å / SU ML: 0.5185 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 34.9018
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.293 1395 4.93 %
Rwork0.2366 26894 -
obs0.2395 28289 45.63 %
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: 98.73 Å2
精密化ステップサイクル: LAST / 解像度: 3.25→127.61 Å
タンパク質核酸リガンド溶媒全体
原子数22807 0 0 0 22807
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002323433
X-RAY DIFFRACTIONf_angle_d0.554731892
X-RAY DIFFRACTIONf_chiral_restr0.04183455
X-RAY DIFFRACTIONf_plane_restr0.0064139
X-RAY DIFFRACTIONf_dihedral_angle_d12.50568350
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS0.52145090378
ens_1d_3CX-RAY DIFFRACTIONTorsion NCS0.446824863348
ens_1d_4EX-RAY DIFFRACTIONTorsion NCS0.570702106277
ens_2d_2HX-RAY DIFFRACTIONTorsion NCS0.351064816078
ens_2d_3LX-RAY DIFFRACTIONTorsion NCS0.666504896505
ens_2d_4LX-RAY DIFFRACTIONTorsion NCS0.570183909918
ens_3d_2MX-RAY DIFFRACTIONTorsion NCS0.740445392855
ens_3d_3MX-RAY DIFFRACTIONTorsion NCS0.344293714891
ens_3d_4MX-RAY DIFFRACTIONTorsion NCS0.573231617797
ens_4d_2GX-RAY DIFFRACTIONTorsion NCS0.313198220678
ens_4d_3GX-RAY DIFFRACTIONTorsion NCS0.312234914284
ens_4d_4GX-RAY DIFFRACTIONTorsion NCS0.312565889387
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.370.413530.383581X-RAY DIFFRACTION1.37
3.37-3.510.452180.3371309X-RAY DIFFRACTION5.36
3.51-3.650.2707200.3263548X-RAY DIFFRACTION9.93
3.69-3.860.3941690.31471178X-RAY DIFFRACTION23.02
3.86-4.10.3193800.2621776X-RAY DIFFRACTION29.86
4.1-4.420.30921670.23523246X-RAY DIFFRACTION55.34
4.42-4.860.32662340.21033909X-RAY DIFFRACTION66.98
4.86-5.560.29722260.2194462X-RAY DIFFRACTION75.6
5.56-7.010.29972710.25835438X-RAY DIFFRACTION91.43
7.01-127.610.24893070.23115947X-RAY DIFFRACTION99.36
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)
15.90968563225-0.2276434146552.780854108775.90727614796-1.060160471723.572685572-0.584444359382-1.04727034654-1.298778226650.9344264225730.6683162594080.933158123908-0.234344396306-0.2129280611740.02559491989460.6512415960760.332163213517-0.1887241011090.9719586454130.3685486085231.22551928183-3.3789903334930.707256887270.3520115109
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942.27376940318-1.8853459198-2.860943044121.803520197152.141129083893.822231013690.143984581626-0.3046567230620.4008777605490.001404811180710.430847920356-0.42964742292-0.5473371545320.559797360199-0.4409071434632.07188096665-0.03601539633721.319075275350.779449118653-0.184461155811.84156069604-13.363921899931.6751751933-16.1062548148
951.804197935970.622994872387-0.05740792839661.78883426021-1.595662781931.58359859665-0.3657689250180.118873897116-0.634699026003-0.8454985066870.213181414118-0.1769246750710.5142533191680.03433554637340.8880355598042.20616435091-0.5346817656160.5540147082070.9701714600580.477395389351.69111882065-19.835047608132.8690078405-24.0344236156
961.05217469126-0.1516948800510.3979330657463.44813183349-2.852223695214.7608687556-0.8214727519370.42020829972-0.283928290943-0.66652349673-0.148571572714-0.5363834539670.1373276129420.7373241432840.4941727829772.322912425770.07889286405330.9802242998020.9563207726880.3673778066731.49860321657-14.762807527442.8546046049-21.2273401493
970.7348270870350.146579936871-0.6020396747382.491936368080.3705755859612.27634851135-0.6123965703520.215468421808-0.726988174353-0.835961094122-0.0538052954255-0.433508336888-0.001653582047730.0124137845963-0.2183601758921.86878094604-0.0195810667280.9647879982850.6037866736290.1807263526481.25185142703-26.022739961837.6368969757-14.7587508212
981.55178592672-0.715177926095-0.764793438130.32965053310.3523563748670.37736255581-0.3298170510891.46965591879-1.01528939619-1.37640473719-0.176181026164-0.4579655738280.739100718506-0.3702547573480.3312222066822.37621932065-0.266880302720.1366250665721.363913088680.1805074880370.834466882701-33.474542173843.4132168105-28.2789934921
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 'Z' and (resid 1 through 17 )ZA1 - 171 - 17
22chain 'Z' and (resid 18 through 52 )ZA18 - 5218 - 52
33chain 'Z' and (resid 53 through 73 )ZA53 - 7353 - 73
44chain 'Z' and (resid 74 through 107 )ZA74 - 10774 - 107
55chain 'Z' and (resid 108 through 124 )ZA108 - 124108 - 124
66chain 'C' and (resid 336 through 363 )CB336 - 3631 - 28
77chain 'C' and (resid 364 through 380 )CB364 - 38029 - 45
88chain 'C' and (resid 381 through 437 )CB381 - 43746 - 102
99chain 'C' and (resid 438 through 451 )CB438 - 451103 - 116
1010chain 'C' and (resid 452 through 517 )CB452 - 517117 - 182
1111chain 'M' and (resid 1 through 17 )MC1 - 171 - 17
1212chain 'M' and (resid 18 through 33 )MC18 - 3318 - 33
1313chain 'M' and (resid 34 through 60 )MC34 - 6034 - 60
1414chain 'M' and (resid 61 through 91 )MC61 - 9161 - 91
1515chain 'M' and (resid 92 through 109 )MC92 - 10992 - 109
1616chain 'M' and (resid 110 through 137 )MC110 - 137110 - 137
1717chain 'M' and (resid 138 through 160 )MC138 - 160138 - 160
1818chain 'M' and (resid 161 through 178 )MC161 - 178161 - 178
1919chain 'M' and (resid 179 through 217 )MC179 - 217179 - 217
2020chain 'N' and (resid 1 through 90 )ND1 - 901 - 90
2121chain 'N' and (resid 91 through 216 )ND91 - 21691 - 216
2222chain 'K' and (resid 1 through 18 )KE1 - 181 - 18
2323chain 'K' and (resid 19 through 30 )KE19 - 3019 - 30
2424chain 'K' and (resid 31 through 49 )KE31 - 4931 - 49
2525chain 'K' and (resid 50 through 62 )KE50 - 6250 - 62
2626chain 'K' and (resid 63 through 76 )KE63 - 7663 - 76
2727chain 'K' and (resid 77 through 115 )KE77 - 11577 - 115
2828chain 'K' and (resid 116 through 152 )KE116 - 152116 - 152
2929chain 'K' and (resid 153 through 200 )KE153 - 200153 - 200
3030chain 'K' and (resid 201 through 216 )KE201 - 216201 - 216
3131chain 'X' and (resid 1 through 24 )XF1 - 241 - 24
3232chain 'X' and (resid 25 through 32 )XF25 - 3225 - 32
3333chain 'X' and (resid 33 through 52 )XF33 - 5233 - 52
3434chain 'X' and (resid 53 through 60 )XF53 - 6053 - 60
3535chain 'X' and (resid 61 through 73 )XF61 - 7361 - 73
3636chain 'X' and (resid 74 through 83 )XF74 - 8374 - 83
3737chain 'X' and (resid 84 through 91 )XF84 - 9184 - 91
3838chain 'X' and (resid 92 through 107 )XF92 - 10792 - 107
3939chain 'X' and (resid 108 through 124 )XF108 - 124108 - 124
4040chain 'W' and (resid 1 through 17 )WG1 - 171 - 17
4141chain 'W' and (resid 18 through 39 )WG18 - 3918 - 39
4242chain 'W' and (resid 40 through 52 )WG40 - 5240 - 52
4343chain 'W' and (resid 53 through 73 )WG53 - 7353 - 73
4444chain 'W' and (resid 74 through 99 )WG74 - 9974 - 99
4545chain 'W' and (resid 100 through 117 )WG100 - 117100 - 117
4646chain 'W' and (resid 118 through 124 )WG118 - 124118 - 124
4747chain 'E' and (resid 335 through 353 )EH335 - 3531 - 19
4848chain 'E' and (resid 354 through 375 )EH354 - 37520 - 31
4949chain 'E' and (resid 376 through 393 )EH376 - 39332 - 49
5050chain 'E' and (resid 394 through 437 )EH394 - 43750 - 93
5151chain 'E' and (resid 438 through 451 )EH438 - 45194 - 107
5252chain 'E' and (resid 452 through 479 )EH452 - 479108 - 135
5353chain 'E' and (resid 480 through 494 )EH480 - 494136 - 150
5454chain 'E' and (resid 495 through 506 )EH495 - 506151 - 162
5555chain 'E' and (resid 507 through 516 )EH507 - 516163 - 172
5656chain 'J' and (resid 1 through 33 )JI1 - 331 - 33
5757chain 'J' and (resid 34 through 98 )JI34 - 9834 - 98
5858chain 'J' and (resid 99 through 122 )JI99 - 12299 - 122
5959chain 'J' and (resid 123 through 148 )JI123 - 148123 - 148
6060chain 'J' and (resid 149 through 178 )JI149 - 178149 - 178
6161chain 'J' and (resid 179 through 217 )JI179 - 217179 - 217
6262chain 'H' and (resid 1 through 60 )HJ1 - 601 - 60
6363chain 'H' and (resid 61 through 122 )HJ61 - 12261 - 122
6464chain 'H' and (resid 123 through 137 )HJ123 - 137123 - 137
6565chain 'H' and (resid 138 through 191 )HJ138 - 191138 - 191
6666chain 'H' and (resid 192 through 217 )HJ192 - 217192 - 217
6767chain 'L' and (resid 1 through 49 )LK1 - 491 - 49
6868chain 'L' and (resid 50 through 115 )LK50 - 11550 - 115
6969chain 'L' and (resid 116 through 130 )LK116 - 130116 - 130
7070chain 'L' and (resid 131 through 165 )LK131 - 165131 - 165
7171chain 'L' and (resid 166 through 190 )LK166 - 190166 - 190
7272chain 'L' and (resid 191 through 216 )LK191 - 216191 - 216
7373chain 'F' and (resid 1 through 122 )FL1 - 1221 - 122
7474chain 'F' and (resid 123 through 178 )FL123 - 178123 - 178
7575chain 'F' and (resid 179 through 217 )FL179 - 217179 - 217
7676chain 'G' and (resid 1 through 49 )GM1 - 491 - 49
7777chain 'G' and (resid 50 through 115 )GM50 - 11550 - 115
7878chain 'G' and (resid 116 through 165 )GM116 - 165116 - 165
7979chain 'G' and (resid 166 through 216 )GM166 - 216166 - 216
8080chain 'B' and (resid 335 through 353 )BN335 - 3531 - 19
8181chain 'B' and (resid 354 through 363 )BN354 - 36320 - 29
8282chain 'B' and (resid 364 through 380 )BN364 - 38030 - 46
8383chain 'B' and (resid 381 through 393 )BN381 - 39347 - 59
8484chain 'B' and (resid 394 through 437 )BN394 - 43760 - 103
8585chain 'B' and (resid 438 through 451 )BN438 - 451104 - 117
8686chain 'B' and (resid 452 through 494 )BN452 - 494118 - 160
8787chain 'B' and (resid 495 through 506 )BN495 - 506161 - 172
8888chain 'B' and (resid 507 through 517 )BN507 - 517173 - 183
8989chain 'A' and (resid 336 through 380 )AO336 - 3801 - 45
9090chain 'A' and (resid 381 through 518 )AO381 - 51846 - 183
9191chain 'Y' and (resid 1 through 24 )YP1 - 241 - 24
9292chain 'Y' and (resid 25 through 32 )YP25 - 3225 - 32
9393chain 'Y' and (resid 33 through 52 )YP33 - 5233 - 52
9494chain 'Y' and (resid 53 through 60 )YP53 - 6053 - 60
9595chain 'Y' and (resid 61 through 73 )YP61 - 7361 - 73
9696chain 'Y' and (resid 74 through 83 )YP74 - 8374 - 83
9797chain 'Y' and (resid 84 through 117 )YP84 - 11784 - 117
9898chain 'Y' and (resid 118 through 124 )YP118 - 124118 - 124

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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