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- PDB-7zfd: SARS-CoV-2 Omicron RBD in complex with Omi-25 Fab -

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基本情報

登録情報
データベース: PDB / ID: 7zfd
タイトルSARS-CoV-2 Omicron RBD in complex with Omi-25 Fab
要素
  • Omi-25 heavy chain
  • Omi-25 light chain
  • Spike protein S1
キーワードVIRAL PROTEIN / SARS-CoV-2 / Omicron / BA.1 / BA.2 / RBD / antibody / Fab / Omi-25 / VIRALPROTEIN/IMMUNE SYSTEM
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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 S1 subunit, receptor binding domain superfamily, 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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: 3.39 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
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 / : 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 1.32024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.42024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
H: Omi-25 heavy chain
E: Spike protein S1
L: Omi-25 light chain
A: Omi-25 heavy chain
F: Spike protein S1
B: Omi-25 light chain


分子量 (理論値)分子数
合計 (水以外)143,5716
ポリマ-143,5716
非ポリマー00
00
1
H: Omi-25 heavy chain
E: Spike protein S1
L: Omi-25 light chain


分子量 (理論値)分子数
合計 (水以外)71,7853
ポリマ-71,7853
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
2
A: Omi-25 heavy chain
F: Spike protein S1
B: Omi-25 light chain


分子量 (理論値)分子数
合計 (水以外)71,7853
ポリマ-71,7853
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)123.047, 123.047, 223.658
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-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 "E" and (resid 335 through 366 or resid 374 through 516 or resid 522 through 525))
d_2ens_1(chain "F" and resid 335 through 525)
d_1ens_2(chain "H" and (resid 1 through 186 or resid 188...
d_2ens_2(chain "A" and (resid 1 through 186 or resid 188...
d_1ens_3chain "L"
d_2ens_3chain "B"

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUSERB1 - 32
d_12ens_1PHEGLUB38 - 180
d_13ens_1ALACYSB182 - 185
d_21ens_1LEUCYSE3 - 181
d_11ens_2GLNTYRA1 - 186
d_12ens_2LEUALAA188 - 224
d_21ens_2GLNTYRD1 - 186
d_22ens_2LEUALAD188 - 224
d_11ens_3ALAGLUC1 - 213
d_21ens_3ALAGLUF1 - 213

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(0.517857927264, 0.422581494671, -0.743806458382), (0.384581232483, -0.891660826588, -0.238826811624), (-0.764146872526, -0.162375646851, -0.624270539524)-20.7411887641, -50.5380212738, -69.8320516368
2given(0.635808489132, 0.117118894237, -0.762909385025), (0.0391855522879, -0.992044028461, -0.11963752792), (-0.77085151465, 0.0461715302726, -0.635339383443)-24.3738025908, -49.3412739514, -66.7022101247
3given(0.811705477464, 0.170641930288, -0.558583520597), (0.109453341254, -0.983867314499, -0.141509976854), (-0.573719603939, 0.0537255906297, -0.817287817704)-18.6337039652, -48.3829744572, -73.5253939614

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要素

#1: 抗体 Omi-25 heavy chain


分子量: 24453.498 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: タンパク質 Spike protein S1 / SARS-CoV-2 Omicron Spike protein


分子量: 23880.939 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
#3: 抗体 Omi-25 light chain


分子量: 23450.975 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)
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: 2.95 Å3/Da / 溶媒含有率: 58.28 %
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: Proplex 1-31: 3.0 M Sodium formate, 0.1 M Tris pH 7.5

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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23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: 3.39→69 Å / Num. obs: 24618 / % possible obs: 100 % / 冗長度: 26.8 % / Biso Wilson estimate: 85.78 Å2 / CC1/2: 0.967 / Rpim(I) all: 0.233 / Net I/σ(I): 2.4
反射 シェル解像度: 3.39→3.45 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1194 / CC1/2: 0.314

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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
解像度: 3.39→68.67 Å / SU ML: 0.7316 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 37.5637
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.3377 1216 4.97 %
Rwork0.2856 23272 -
obs0.2882 24488 99.71 %
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: 97.91 Å2
精密化ステップサイクル: LAST / 解像度: 3.39→68.67 Å
タンパク質核酸リガンド溶媒全体
原子数9591 0 0 0 9591
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00219837
X-RAY DIFFRACTIONf_angle_d0.539913379
X-RAY DIFFRACTIONf_chiral_restr0.04241474
X-RAY DIFFRACTIONf_plane_restr0.00381721
X-RAY DIFFRACTIONf_dihedral_angle_d11.78723488
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2FX-RAY DIFFRACTIONTorsion NCS0.345606799463
ens_2d_2AX-RAY DIFFRACTIONTorsion NCS5.34038756937
ens_3d_2BX-RAY DIFFRACTIONTorsion NCS4.51754419324
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.39-3.530.41191320.38812503X-RAY DIFFRACTION98.91
3.53-3.690.40751340.35662531X-RAY DIFFRACTION99.85
3.69-3.880.40741300.34242552X-RAY DIFFRACTION99.7
3.88-4.130.40011460.33132536X-RAY DIFFRACTION99.89
4.13-4.440.3131150.27442566X-RAY DIFFRACTION99.74
4.44-4.890.30041400.24672559X-RAY DIFFRACTION99.48
4.89-5.60.33111450.25842594X-RAY DIFFRACTION99.85
5.6-7.050.32161300.28262636X-RAY DIFFRACTION100
7.05-68.670.28751440.24432795X-RAY DIFFRACTION99.97
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)
14.239563416881.66993281738-0.07199774368962.255114654250.634762019441.425932854550.655242905010.394579396050.2514229457910.2707095805830.056962576212-0.5944745052130.086065629636-0.2552511251621.264844992-0.0538912748272-0.2128354336190.2074845573440.337368839567-0.2252382018580.7285180944856.37081709966-8.81524565233-39.6700426952
25.83180532229-0.0851416334033-3.755716169045.14172705063.496591365028.09749747365-0.0516694437431.633862930250.624602870906-1.16563470329-0.464906004666-0.148086712782-0.172332997416-0.3836315301590.3601089574850.658877095878-0.106363753369-0.2210743979390.742834069947-0.009740825494490.623497607818-2.73247475721-7.8145417816-31.8255530971
31.731914780620.6141448208841.118238100933.47445151002-0.1228920191891.74360797312-0.06821099326660.497767779050.118029474323-0.6795745248420.385081399231-0.241595703749-0.3875719099060.92192889761-0.2117002565590.5969769839290.141351385539-0.01016708233790.5306064045440.000943871462520.6250649669812.23444980833-13.1619815048-34.2718436393
41.30724776396-0.7641056049290.462553404520.833472889216-0.6867406530181.1358535888-0.2458534941140.1389337076280.3862066424110.1073924750010.293454562957-0.7763339931530.2578469038220.456731341825-0.3008840247930.404579261231-0.1010773230790.1461355940890.767503771982-0.09479726289620.755225767681-4.072080830618.9161401946-48.1128469078
52.58000983759-0.000250755852665-1.162522573960.720859887019-0.6009311978351.004873421340.5957614447240.749877205334-0.2270352879630.0203441490584-0.00404262193996-0.446917808868-0.162228040813-0.732293478723-0.1934078426210.769025587608-0.3008962350760.09407135562410.4131187810830.1102239969890.614549731094-1.3068571227515.5957544492-43.2156245847
66.271900762381.296094392311.078856128581.16111021171.952506016265.662595269640.2058598052120.6312311244280.6728268315761.05357840792-0.5097856182350.279939151962-0.6265352337521.735335921680.3148123419950.99624708495-0.1539400578260.008067390083030.4339108713310.08037631451790.6142692619414.9013180531419.7765749209-46.9916267777
74.109450049751.16130748594-2.014059641.979455137830.7144825270532.059480657560.749748324387-1.55160241825-0.07393798682981.0924293024-0.100632356128-1.490420519631.271663576040.915146516256-0.6252247913951.805943758930.91794050755-0.4108243107071.58043994076-0.5882500167570.94632979632817.3185497396-21.774405159214.9117636234
82.950346108330.987051933276-0.1815273696053.990864485341.219274291461.980461747280.215807869932-0.0894535641859-0.0233288914170.3529938112520.1866491432090.2534433887460.3595085977480.2036022962-0.5457148918580.6292086754280.272498866567-0.06886802104350.798040903553-0.02638810375880.59852942732910.5626761761-20.1247702602-2.40886144043
92.330027994460.0553519530011-0.5923314320753.55496004985-0.1196829899662.06482763275-0.04806195329030.640558267028-0.3613131138021.02978364143-0.4812820533680.47201414126-0.140057964792-0.0868279954579-0.3020198201751.11764685973-0.0561002961323-0.3226378720561.52746005594-0.2404071445770.389722475853-6.418964555643.8506605269-14.9250335112
103.6156485182-1.20253102928-1.023481875525.4968662764-2.25451889285.685760718120.04197799670060.452993373866-0.7059854924660.940317657735-0.436292882448-0.616748688494-0.8049880091290.33651000635-0.1267571644950.7862596446480.02877274171-0.09631016926310.661066678194-0.07488462126740.507188490683-0.660595539493-3.1466039025-18.021063872
112.92062594343-0.828703958509-0.3926261540864.92455865302-0.7634993283023.3055927156-0.788785920239-1.44889130055-0.3584877683330.4957744509010.790881217731-1.37004178964-0.7546375995160.154551910229-0.2387817146570.9712820848760.0397568762291-0.04388106803881.04373316723-0.3000081347210.7472018764655.87284864256-2.98066592857-12.3852417337
123.575719321532.10846214942-1.279496232327.60302215745-2.439241336974.357669095710.948581149012-0.9717813762240.3881556782220.729122355881-0.107638979908-0.420639515175-0.8585757708740.3970379739580.2733057466320.704721769319-0.2219715422780.6137442020421.12030464041-0.6660016164110.677511704492.460428311887.98736166478-14.8390988184
131.85279055251-0.2544416054720.6721412224369.51099944793-0.287173598652.29439602764-0.4561340875440.04077908200130.1285458092950.7941146789130.619758437423-1.33714785317-0.0249505765469-0.2045727722880.3562481564920.824932300001-0.09927793511060.001526039301171.35227471629-0.08289103956790.653177675941-3.81286852072.95107332804-20.9146131752
142.16424971408-0.9586350908430.1171549909311.66752744563-0.08471898946530.396286084377-0.488110353544-0.990192789445-0.1293094762570.3080334000460.617225672821-0.3160087087220.08863110934670.1680385521810.300119120919-0.2657239200771.20430029319-0.1605575036110.434029665617-0.1832205613710.595011416793-5.7872643760327.2318516945-50.1685755111
154.24674600647-1.67315597062.57085932963.10201472953-0.9134861447513.678770374220.333625050846-1.74037441832-0.4456421196240.7768909598660.9658267283070.24600664855-0.161927129553-0.604896911455-0.221607973010.348950688320.254067782812-0.04852918602170.909004155427-0.3809873979190.585208444922-10.514221010226.8219039465-35.7271840848
163.30738079588-0.6379876803441.708662037534.26040842355-0.7665000768224.14411184410.365884081394-0.931719655049-0.381509203192-0.6096023613020.900583974660.433099974299-0.656859057869-0.861768333834-0.798110465210.558075233420.0007313185538010.03641540977590.494933041952-0.1834220952820.705559879692-11.961754725226.4051849542-40.7315109688
171.51285767488-0.3116915449480.2060045204023.369779222571.233596106220.51058810824-0.242192886576-0.2357304892020.07779956838290.4592446758260.143886937840.3907844567020.348255647134-0.1056301235750.4609304197121.04483800422-0.238972636729-0.255399572445-0.272853889916-0.2853872059890.505201243194-9.8505763448635.8430590331-37.1803290721
182.57749195841-0.8283287766340.4781492828414.299850364141.190094383371.19746779355-0.046519243935-0.01723989329330.204340746404-0.1443578685580.0451475844156-0.0753892096440.1259361998170.1748459139710.03186016102220.590857649989-0.0467593869473-0.1070654782560.5484104652750.05608470658770.6856991925222.59551066935-31.7394478209-45.8158277719
191.180990649430.283889645776-0.6326826045191.821411928770.1296619274191.538781223720.172628920659-0.335090515811-0.197540292259-0.005175999914520.2932207485440.5754618144830.166866258330.8269295107710.8433210697181.232620183490.175183442002-0.465883467882-0.0676330028554-0.07473576889690.5233760074014.57222344173-47.6130234667-44.2718751996
203.670149732031.71238903264-1.47369334190.87411572358-0.6130651321050.89822095753-0.500993514835-0.413145702637-0.4406571714050.8937835303950.52512012102-0.336276489658-1.013699273980.584907558735-0.09816154424110.7988410306160.204856696525-0.3199991047020.526578839874-0.1238748858180.93118186668914.9902640086-64.4149291383-37.1610837103
216.569056635411.81802585889-3.116032800583.8483117045-0.9592080451362.99438902776-0.3452480150081.618880362541.34287673642-2.464422805360.9020121670731.944090604220.425142844074-1.218438628190.7348391110451.924998455520.0437912879255-1.158274006850.4061503978070.1489639818621.92249454574-29.8872435951-22.6615832174-88.339130081
224.913817835681.25321388916-0.3767955761632.797022426020.4099585188823.04866506853-0.1411702316930.49696781935-1.57419403103-1.380000690990.1752555937961.095472348470.39420521809-0.876987039347-0.4614932880871.227874257960.160706242395-0.5075340051010.543104529770.02473819255851.20176814547-30.6597323718-33.5943195896-80.9829761089
233.898747297660.3675952759360.226325807782.7727247140.153469016611.261143201020.02356254007020.84518439118-0.986630578371-0.532795088120.5679526590460.251222692087-0.5977938997250.673001614677-0.3589744550010.994476889184-0.100449301594-0.1848459769230.753296865603-0.02700038737010.495910611224-22.1785453523-26.6380597619-71.5313697284
245.982493779180.3047745984420.538688471154.721872990291.155853124433.44252068232-0.3256333913110.629440496252-1.16883261608-0.6949575023660.5759531267310.146157376835-0.575849690486-0.127304809083-0.605112245420.76519185075-0.4026565014260.09373767542840.7676107985980.02866661082710.573872199886-18.8442049983-27.130301911-74.0605700942
252.16992994354-0.817827145436-1.06388568523.743186263361.885796130783.51459674680.301329792373-0.162307065762-1.02866189930.430896491910.350133706062-0.3116908494130.03204255557460.07110275193990.2597200202421.64626936683-0.439801924055-0.1618897435130.2211004854460.1896010125410.915886317423-12.2809641037-53.1095785653-56.5416977408
262.99522522084-0.0134494082035-0.8670934112025.1174139125-0.7178047646693.230723642770.0666856306594-0.5600068608380.3575244336860.2546465790170.206480256649-0.09381762443211.01691010170.822507191742-0.1342837418950.993291886237-0.411254669544-0.1237881947160.812795244749-0.1785184719250.46409469221-9.5097212116-43.964358605-57.7687623794
275.06111546692-0.368975515752-1.81678177027.77085568588-0.3341289305745.482165976820.152174621435-0.988308343072-0.357467531326-1.76819064736-0.7903611750350.2816006197910.7562470797290.4451460490690.1879849669491.114105073355.98106174192E-5-0.08980936802981.13246221201-0.02906114586490.609159240004-8.49058028222-47.0696412258-65.5365652564
280.7101490641830.7757809379011.215705680484.079605448091.727426088582.330399568440.236832340856-0.117798981432-0.248248388182-0.892778992492-0.365039517530.444050167534-0.0891144623663-0.924743329243-0.3129543572221.09976015322-0.1195719703130.1617111018170.4188547473240.1275909271630.573565580857-10.3723436424-40.5697460182-52.8941002649
293.24463995814-1.2809973274-0.02991487091316.857164779230.7597391336640.0819990089168-0.30328878333-0.2792491512140.777388073607-1.228746750580.191347929815-0.1071994802730.4911968169680.531688716638-0.2030646615671.469840988660.0229496618665-0.1814129434620.8574512901690.0716009954780.602862840756-4.64365788742-66.0811595308-54.55612321
302.317728281580.9472798148631.723950615712.765107650571.041890728161.30532533432-0.02491952119560.8897171779481.050122428420.7166777585950.245087476361-0.667036144005-0.1501614233510.3460749894150.06328828919650.7959622689360.168681008088-0.3266154516740.872460122831-0.1326403244390.7491970147388.75245337802-70.9076294273-27.3897093365
311.775646435211.237040097290.9876660564442.800114589293.3326091544.185971044240.4092621204550.06505641023420.4345171156110.2082912310830.5433576990180.779060337264-1.472967217430.4768996839420.5878542848541.13785453526-0.090856748299-0.1587835091680.3576798539260.01719348557720.562329006636-2.27390823171-69.1644467521-37.7695794089
321.05035533557-0.0223959791968-0.2909657509020.09577557993840.1476512508680.3108189594860.09599499858410.0634318253165-0.6574356893651.06710788814-0.7518309277160.1089179132360.525777418057-0.500857172451-0.06274217149221.12666780445-0.450544756692-0.03187068247560.627387356891-0.1538283577671.14215568556-5.18868384272-66.5517820363-29.3645287369
332.95167409815-1.898669967-1.085048855972.53728276411-1.05378192282.72070973234-0.02470812137770.0901444380714-0.0167477479773-0.255358076572-0.0958591932704-1.81200910452-0.3408351378260.4753462813580.1503642680460.721519822168-0.831967134176-0.1704062907550.892446214193-0.07114414479021.135729903533.25513069476-65.2832696232-51.6238575086
341.280408161730.787148998193-0.3516716947011.78992859451-0.07033309079770.1258806543880.404512289904-0.7434261913960.4248074588760.712628079973-0.45493725937-0.50117193010.161858495166-0.233268247157-0.09564900464750.993259993914-0.691377843187-0.1351472951960.5359690462460.08356676308950.852197421199-0.439465606799-70.5574661052-25.3709921921
350.466826403945-0.886705408259-0.2927789015883.227306967330.3830608254630.210599208702-0.207300703888-0.860659779817-0.326660240125-0.864312700121-0.003280975193471.063381457690.5047607735010.293257228133-0.1135943498040.970075978935-0.675069416666-0.2076210976051.423033054840.2875010266620.629880572287-3.60199489295-77.8573185526-34.9683119902
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 'H' and (resid 1 through 33 )HA1 - 331 - 33
22chain 'H' and (resid 34 through 51 )HA34 - 5134 - 51
33chain 'H' and (resid 52 through 119 )HA52 - 11952 - 119
44chain 'H' and (resid 120 through 144 )HA120 - 144120 - 144
55chain 'H' and (resid 145 through 185 )HA145 - 185145 - 185
66chain 'H' and (resid 186 through 224 )HA186 - 224186 - 224
77chain 'E' and (resid 335 through 393 )EB335 - 3931 - 57
88chain 'E' and (resid 394 through 525 )EB394 - 52558 - 185
99chain 'L' and (resid 1 through 18 )LC1 - 181 - 18
1010chain 'L' and (resid 19 through 48 )LC19 - 4819 - 48
1111chain 'L' and (resid 49 through 70 )LC49 - 7049 - 70
1212chain 'L' and (resid 71 through 84 )LC71 - 8471 - 84
1313chain 'L' and (resid 85 through 113 )LC85 - 11385 - 113
1414chain 'L' and (resid 114 through 128 )LC114 - 128114 - 128
1515chain 'L' and (resid 129 through 150 )LC129 - 150129 - 150
1616chain 'L' and (resid 151 through 197 )LC151 - 197151 - 197
1717chain 'L' and (resid 198 through 213 )LC198 - 213198 - 213
1818chain 'A' and (resid 1 through 99 )AD1 - 991 - 99
1919chain 'A' and (resid 100 through 144 )AD100 - 144100 - 144
2020chain 'A' and (resid 145 through 224 )AD145 - 224145 - 224
2121chain 'F' and (resid 333 through 374 )FE333 - 3741 - 35
2222chain 'F' and (resid 375 through 421 )FE375 - 42136 - 82
2323chain 'F' and (resid 422 through 479 )FE422 - 47983 - 140
2424chain 'F' and (resid 480 through 526 )FE480 - 526141 - 182
2525chain 'B' and (resid 1 through 18 )BF1 - 181 - 18
2626chain 'B' and (resid 19 through 48 )BF19 - 4819 - 48
2727chain 'B' and (resid 49 through 83 )BF49 - 8349 - 83
2828chain 'B' and (resid 84 through 101 )BF84 - 10184 - 101
2929chain 'B' and (resid 102 through 113 )BF102 - 113102 - 113
3030chain 'B' and (resid 114 through 128 )BF114 - 128114 - 128
3131chain 'B' and (resid 129 through 150 )BF129 - 150129 - 150
3232chain 'B' and (resid 151 through 163 )BF151 - 163151 - 163
3333chain 'B' and (resid 164 through 174 )BF164 - 174164 - 174
3434chain 'B' and (resid 175 through 197 )BF175 - 197175 - 197
3535chain 'B' and (resid 198 through 213 )BF198 - 213198 - 213

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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