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- PDB-6yla: Crystal structure of the SARS-CoV-2 receptor binding domain in co... -

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基本情報

登録情報
データベース: PDB / ID: 6yla
タイトルCrystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab
要素
  • Heavy Chain
  • Light chain
  • Spike glycoprotein
キーワードVIRAL PROTEIN / SARS-CoV-2 Spike protein / RBD / CR3022 / complex
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 / host extracellular space / viral translation / 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 / host extracellular space / viral translation / 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
MALONATE ION / 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: 2.42 Å
データ登録者Huo, J. / Zhao, Y. / Ren, J. / Zhou, D. / Ginn, H.M. / Fry, E.E. / Owens, R. / Stuart, D.I.
資金援助 英国, 1件
組織認可番号国
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 英国
引用ジャーナル: Cell Host Microbe / 年: 2020
タイトル: Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike.
著者: Jiandong Huo / Yuguang Zhao / Jingshan Ren / Daming Zhou / Helen M E Duyvesteyn / Helen M Ginn / Loic Carrique / Tomas Malinauskas / Reinis R Ruza / Pranav N M Shah / Tiong Kit Tan / Pramila ...著者: Jiandong Huo / Yuguang Zhao / Jingshan Ren / Daming Zhou / Helen M E Duyvesteyn / Helen M Ginn / Loic Carrique / Tomas Malinauskas / Reinis R Ruza / Pranav N M Shah / Tiong Kit Tan / Pramila Rijal / Naomi Coombes / Kevin R Bewley / Julia A Tree / Julika Radecke / Neil G Paterson / Piyada Supasa / Juthathip Mongkolsapaya / Gavin R Screaton / Miles Carroll / Alain Townsend / Elizabeth E Fry / Raymond J Owens / David I Stuart /
要旨: There are as yet no licensed therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric spike whose receptor binding domain (RBD) recognizes ...There are as yet no licensed therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2, initiating conformational changes that drive membrane fusion. We find that the monoclonal antibody CR3022 binds the RBD tightly, neutralizing SARS-CoV-2, and report the crystal structure at 2.4 Å of the Fab/RBD complex. Some crystals are suitable for screening for entry-blocking inhibitors. The highly conserved, structure-stabilizing CR3022 epitope is inaccessible in the prefusion spike, suggesting that CR3022 binding facilitates conversion to the fusion-incompetent post-fusion state. Cryogenic electron microscopy (cryo-EM) analysis confirms that incubation of spike with CR3022 Fab leads to destruction of the prefusion trimer. Presentation of this cryptic epitope in an RBD-based vaccine might advantageously focus immune responses. Binders at this epitope could be useful therapeutically, possibly in synergy with an antibody that blocks receptor attachment.
履歴
登録2020年4月6日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年4月15日Provider: repository / タイプ: Initial release
改定 1.12020年5月6日Group: Database references / Source and taxonomy / Structure summary
カテゴリ: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
改定 1.22020年7月29日Group: Data collection / Derived calculations / Structure summary
カテゴリ: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.32020年10月28日Group: Database references / Structure summary / カテゴリ: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.42024年1月24日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.52024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
E: Spike glycoprotein
H: Heavy Chain
L: Light chain
A: Spike glycoprotein
B: Heavy Chain
C: Light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,07738
ポリマ－145,4996
非ポリマー3,57932
水93752
1
E: Spike glycoprotein
H: Heavy Chain
L: Light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)74,56519
ポリマ－72,7493
非ポリマー1,81616
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Spike glycoprotein
B: Heavy Chain
C: Light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)74,51219
ポリマ－72,7493
非ポリマー1,76316
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)163.124, 163.124, 189.076
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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要素

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抗体 , 2種, 4分子 HBLC

#2: 抗体 Heavy Chain


分子量: 24455.520 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 Light chain


分子量: 24289.885 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, 5分子 EA

#1: タンパク質 Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


分子量: 24003.848 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
#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: 3 / 由来タイプ: 組換発現 / 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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非ポリマー , 5種, 81分子

#4: 化合物
ChemComp-DMS / DIMETHYL SULFOXIDE / 2-チアプロパン2-オキシド


分子量: 78.133 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C2H6OS / コメント: DMSO, 沈殿剤*YM
#5: 化合物
ChemComp-MLI / MALONATE ION / マロナ-ト


分子量: 102.046 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C3H2O4
#7: 化合物 ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / ペンタエチレングリコ-ル


分子量: 238.278 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H22O6 / コメント: 沈殿剤*YM
#8: 化合物 ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / ジエチレングリコ-ルモノメチルエ-テル


分子量: 120.147 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C5H12O3 / コメント: 阻害剤, 沈殿剤*YM
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 52 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 4.28 Å3/Da / 溶媒含有率: 71.23 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.1 M Sodium malonate, 0.1 M Tris pH 8.0 and 30% w/v Polyethylene glycol 1,000

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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: 2020年4月1日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9762 Å / 相対比: 1
反射解像度: 2.42→58.8 Å / Num. obs: 97407 / % possible obs: 100 % / 冗長度: 78.7 % / Biso Wilson estimate: 72.83 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.303 / Rpim(I) all: 0.034 / Net I/σ(I): 11.6
反射 シェル解像度: 2.42→2.46 Å / Num. unique obs: 4803 / CC1/2: 0.45

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
PHENIX1.17.1_3660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: 6M0J, 4KMT, 5I1D, 6YM0

6m0j

4kmt

5i1d

6ym0


解像度: 2.42→55.31 Å / SU ML: 0.5715 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 34.9087
Rfactor反射数%反射
Rfree0.2367 4837 5.14 %
Rwork0.2127 --
obs0.2139 94154 96.77 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 89.23 Å2
精密化ステップサイクル: LAST / 解像度: 2.42→55.31 Å
タンパク質核酸リガンド溶媒全体
原子数9947 0 87 52 10086
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00210255
X-RAY DIFFRACTIONf_angle_d0.521513909
X-RAY DIFFRACTIONf_chiral_restr0.04631525
X-RAY DIFFRACTIONf_plane_restr0.00431781
X-RAY DIFFRACTIONf_dihedral_angle_d17.76543695
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.450.5361340.524644X-RAY DIFFRACTION21.2
2.45-2.480.48131120.47272654X-RAY DIFFRACTION86.55
2.48-2.510.47961620.47282995X-RAY DIFFRACTION98.26
2.51-2.540.44661560.45412983X-RAY DIFFRACTION99.08
2.54-2.570.45441670.46043034X-RAY DIFFRACTION99.56
2.57-2.610.4151630.45353034X-RAY DIFFRACTION99.78
2.61-2.640.51421730.43653000X-RAY DIFFRACTION99.75
2.64-2.680.39941870.40893038X-RAY DIFFRACTION99.72
2.68-2.730.40921620.38383004X-RAY DIFFRACTION99.84
2.73-2.770.39981640.36343076X-RAY DIFFRACTION99.82
2.77-2.820.37781520.3433060X-RAY DIFFRACTION99.81
2.82-2.870.33761670.3263030X-RAY DIFFRACTION99.78
2.87-2.920.33151820.31543005X-RAY DIFFRACTION99.91
2.92-2.980.2931810.29833045X-RAY DIFFRACTION99.75
2.98-3.050.2991800.30123021X-RAY DIFFRACTION99.72
3.05-3.120.32411570.2873076X-RAY DIFFRACTION99.85
3.12-3.20.32961610.27643052X-RAY DIFFRACTION99.91
3.2-3.280.28721680.27233053X-RAY DIFFRACTION99.97
3.28-3.380.28351790.25143053X-RAY DIFFRACTION100
3.38-3.490.22911800.23173054X-RAY DIFFRACTION99.97
3.49-3.610.23291700.20833077X-RAY DIFFRACTION99.97
3.61-3.760.2341500.19873090X-RAY DIFFRACTION99.97
3.76-3.930.24991530.19623094X-RAY DIFFRACTION99.97
3.93-4.140.21351820.18483077X-RAY DIFFRACTION99.97
4.14-4.40.1971550.15493115X-RAY DIFFRACTION100
4.4-4.740.1591470.14343136X-RAY DIFFRACTION100
4.74-5.210.16581850.14183113X-RAY DIFFRACTION100
5.21-5.970.18831740.16133148X-RAY DIFFRACTION100
5.97-7.510.19871670.18083193X-RAY DIFFRACTION100
7.52-55.310.17541670.1633363X-RAY DIFFRACTION99.69
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)
10.5143076111421.13087323102-0.9604836893264.9933111997-4.240528454059.418709095620.07730088128150.170415423554-0.0923644422627-0.306640171870.1292228334610.2638854730080.563700704359-0.504630787835-0.207798455790.6147662862470.0235728412875-0.04051826131480.612212144850.04012611013420.617247448509-8.0313268056121.494121995526.5567069856
29.06311208456-2.57556798234-0.157368983263.97336589271.605494714711.86634535679-0.322139810831-0.395209171844-0.03546968376630.4111131366930.1017550229940.400442199113-0.3232768216450.1287117546240.2782247063840.762723827336-7.96949848874E-50.03959726689770.8021008060660.1096518138890.693548559194-1.8079491421129.603789463634.8585371332
34.26236936807-0.81232513823-0.4049992486754.89141649632-0.6055926706615.661463019490.1772759589530.09174812293620.166661518833-0.451805892677-0.2063798674710.0647454211198-0.2693978498140.297011410132-0.007785852130150.6594553243460.09561768159610.005905577849160.6114122068540.09852247698310.541414168524-3.8975631333534.396010158114.6074586009
42.74777970263-0.228615342776-0.5175418037563.76836304492-1.119455592365.796217956060.3678420647370.7430602381880.477219489541-0.714468881393-0.1304888303880.178945995646-0.543421763721-0.417406536254-0.4187706429311.081294418150.2624242609460.02792804744370.9466977314030.1784460791260.696135195754-13.529996593445.20512653053.89331587152
52.790236588670.898063825798-0.7049979511685.624764131-2.596326492367.366210674780.137010582269-0.1510236360820.06214261601160.1081545323880.0336484989012-0.0300046436665-0.2555748322470.408864499715-0.1355782973950.6394317616810.171539318956-0.08282241417670.6860163190270.06659422548680.648094028698-4.5760255594628.522208366122.4125345721
62.462166414120.03631502568731.511203038671.278056385820.6608129504312.80177684778-0.001693780644470.2816363616070.1470161731450.06437643148710.190473919945-0.232204938747-0.3355963724520.382705492444-0.1512316736880.601246002396-0.153978399870.04974494675890.6631221344740.04539517904680.57244575618520.86432086834.313112831835.603217413
73.040695936740.5328246137032.79164138560.7597237005890.8633502064232.09351330202-0.1060486138560.389743465730.1578015063340.01113752074080.202349725267-0.159655943866-0.4657806412460.481518990734-0.01843326600740.695650651236-0.1118373595080.06257016899240.7499953393620.09388726432080.65990865546325.054350213938.262949358238.1088983399
85.09124617209-0.585322187522-1.659608123612.004004173782.46639276473.13341468296-0.7079433471590.460815448711-0.8112975854910.186554208943-0.275744243347-0.4345382400991.55375948170.07924444150490.4984144047811.00687625124-0.2621328730730.03794092948980.743589272217-0.1164933309140.90247225001140.409262485736.770897255259.566112881
94.21272348478-0.609285096233-1.181545826453.938957787083.019612173687.99896504066-0.398199512948-0.00510816194315-0.7094618740761.11247448709-0.0399967745113-0.1486360438511.495335845290.2486115631510.4327737563811.01652124908-0.1846318642590.01619681109590.758779257185-0.04023594993040.92573250053441.900123531235.775393053963.0306021081
105.04798807465-0.5413341542122.060817314282.9359087235-0.8019621920276.401536306410.066136259822-0.3912586614380.3838762870490.233232676059-0.06672796170970.111766292667-0.505798327511-0.7186991192050.01144252172290.742294887293-0.04320901080630.07915730987780.669576257674-0.05526684957820.6496799469024.9875711472542.419125724350.4567249531
113.219705030970.9584292075911.399292921120.8093614144281.174884924522.018328874850.193862513241-0.5542026869140.3443718262420.068931980336-0.180969528942-0.0937784217894-0.0933118237083-0.342399713593-0.05569196568460.765442892038-0.1201937941610.04704004118970.47043827023-0.04143520649290.64802941542622.563109768244.114851465858.1616539632
128.226644726283.19748499356-3.045790469045.83338025683-1.023806985832.9294677468-0.0648117866050.1503290573590.4024368086280.799753471477-0.0858109283262-0.0642740087449-0.139739946564-0.4777757267460.1455451246560.779633062194-0.177411987701-0.08554028151710.702675382042-0.06301060006250.58517109557134.367682287151.368473128768.5337233059
135.135670976283.61583128605-1.131877724694.97463014864-0.09636898333512.65336059816-0.2085942787170.45903746949-0.2158203788530.1734157164370.2083611139720.08097232114370.0450890557509-0.4844588310.1564151128230.916654218729-0.069108789539-0.05026768543030.843454639223-0.03799842622520.71202614672631.778748248749.06913137965.9933974143
145.877661985732.28896005979-1.138369917864.129851095620.9003901966062.8584810249-0.119863028516-0.3462369971290.185788453190.3467919697160.0434835522034-0.4714677225880.1716758320460.225848510072-0.04346268845150.763849369663-0.114759018373-0.2056513026240.7128473545450.01372102013080.7217340472143.266289347454.609306888370.9621843778
150.2076485144950.756184383333-0.894028417995.45324705673-5.955359235856.933085752360.0844006771423-0.6333796034920.33580043474-0.475331308605-0.3272444830830.87906418922-0.341343886991-2.12683884297-0.6853010105260.966502645436-0.118195807188-0.1003307930271.10441248990.03311720384650.759585730668-4.4572561133320.964682044167.7400656299
164.215812308710.4944388794331.510649491741.080424932130.9741432990554.58131636682-0.022066685899-0.408464865879-0.157987835330.4969255867980.2134251921770.121619571405-0.17105686492-0.798863009224-0.153320234040.970712638631-0.291415217169-0.1061494983761.114094603780.2080873918180.550180439906-0.18051729602114.087178409774.8871624677
174.21050221646-2.574109057761.512170626881.79457670986-1.958707241745.904351987790.236072488464-0.08332703007211.037385938740.466814756604-0.737253601137-0.120693833779-0.7897591669590.4794083818180.1670368006140.764050864798-0.278664418881-0.1016258174461.100835177690.251462718980.787732253297.6219333222523.884801124464.5774928113
182.81923177210.77152287806-0.8502532214033.34977426369-0.2381145736043.85061516650.31212643256-0.255468390756-0.0983101048356-0.171485891806-0.4109284463090.1018101498310.523747202159-0.2261646546610.05117263643850.868216532089-0.230654049652-0.1452944900910.9794868717360.1586737148380.6417780025326.4699228308913.951031041258.9787126878
193.60538715975-1.199086074540.4485355903344.52111525791-0.2986736743385.20025987891-0.05090708806180.03090657753660.04116869587910.5864964900960.139625817791-0.208252230023-0.07617650403490.207698715593-0.06471351817251.00048610263-0.320498610172-0.1835168787160.9288752995030.211569417010.62683262357411.889434079512.16852475277.052756387
201.98664662793-0.8254008640990.8834930816141.75123043351-1.842755117155.81301762302-0.0954713438993-0.187998872699-0.1589541144090.4143846351470.135613829587-0.278360456150.3574364809310.203301598934-0.05248157762881.19863185665-0.306356381115-0.2162999138631.05989214640.1112781399970.67914481143312.2134074765.0001847969586.9637130387
215.40088551799-3.669716953251.394680039294.718498641820.7452565567053.944739682290.5579996731610.0952163864930.06387719805820.430177210745-0.462058089695-0.003300326486020.586878125423-0.117927379727-0.02007847976661.12188562331-0.340025091928-0.08428340814351.328091586980.05067940035610.694342149766-6.2568177689211.615440870555.9751820476
221.467906911430.0737660615156-0.3215224122741.140984007430.4323336823152.57300497770.197985870591-0.249707115052-0.2655390666130.1089875204450.0753984583742-0.2916909628630.1901771574470.327621472241-0.2367159795480.580492171767-0.143883059945-0.1750257539410.633029498690.01616935930180.76657440067929.956178430417.450943433248.1679630955
235.556258191180.894579715262.616284686494.493750600221.570368202726.71046298157-0.1381782105810.2806733757280.89732381275-0.5722582055020.125894496888-0.230419916368-1.203518191720.5723293905890.03918570752751.01286594784-0.1287408562420.07372421405020.920451884117-0.0471818486130.91791594541740.050608270319.74134945117.55549154
243.817529477660.532066787777-1.210592544433.59717026342-0.3196714765255.962241233690.08073963611560.107018392102-0.7395673464720.0881065228268-0.103545723313-0.4867878612510.493177696089-0.158247214156-0.005389142812120.553307209386-0.13080748355-0.1281533827340.559272311494-0.001220257525430.79393989671312.78705866374.9607995174641.5541753036
252.50937954081-0.572675662645-1.768727947630.3510990055870.3022651173583.534348473860.22744930050.201013921545-0.524241052971-0.103730415207-0.161346455494-0.196709779570.100936720849-0.00184650309057-0.1451922876330.669228208956-0.0705703924613-0.1002614727110.632359321401-0.05288430307550.76786742115322.70785313136.0789415363130.5238030938
263.82904785003-0.688488691814-0.01925549891753.630110167391.021145504934.509107535840.198663509535-0.07976120903540.0118957555304-0.0799014684986-0.0228943563376-0.2891930683450.2917203056920.772482424221-0.1935506898850.8412374969240.00936757985386-0.0548375486850.970472995653-0.02980467563460.60009552875738.62483831742.3937723192813.6604372686
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 327 through 375 )
2X-RAY DIFFRACTION2chain 'E' and (resid 376 through 393 )
3X-RAY DIFFRACTION3chain 'E' and (resid 394 through 459 )
4X-RAY DIFFRACTION4chain 'E' and (resid 460 through 494 )
5X-RAY DIFFRACTION5chain 'E' and (resid 495 through 529 )
6X-RAY DIFFRACTION6chain 'H' and (resid 0 through 52 )
7X-RAY DIFFRACTION7chain 'H' and (resid 53 through 138 )
8X-RAY DIFFRACTION8chain 'H' and (resid 139 through 161 )
9X-RAY DIFFRACTION9chain 'H' and (resid 162 through 219 )
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 81 )
11X-RAY DIFFRACTION11chain 'L' and (resid 82 through 134 )
12X-RAY DIFFRACTION12chain 'L' and (resid 135 through 156 )
13X-RAY DIFFRACTION13chain 'L' and (resid 157 through 180 )
14X-RAY DIFFRACTION14chain 'L' and (resid 181 through 219 )
15X-RAY DIFFRACTION15chain 'A' and (resid 332 through 342 )
16X-RAY DIFFRACTION16chain 'A' and (resid 343 through 364 )
17X-RAY DIFFRACTION17chain 'A' and (resid 365 through 375 )
18X-RAY DIFFRACTION18chain 'A' and (resid 376 through 393 )
19X-RAY DIFFRACTION19chain 'A' and (resid 394 through 451 )
20X-RAY DIFFRACTION20chain 'A' and (resid 452 through 516 )
21X-RAY DIFFRACTION21chain 'A' and (resid 517 through 532 )
22X-RAY DIFFRACTION22chain 'B' and (resid 0 through 138 )
23X-RAY DIFFRACTION23chain 'B' and (resid 139 through 220 )
24X-RAY DIFFRACTION24chain 'C' and (resid 1 through 67 )
25X-RAY DIFFRACTION25chain 'C' and (resid 68 through 134 )
26X-RAY DIFFRACTION26chain 'C' and (resid 135 through 219 )

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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