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- PDB-7dmu: Structure of SARS-CoV-2 spike receptor-binding domain complexed w... -

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基本情報

登録情報
データベース: PDB / ID: 7dmu
タイトルStructure of SARS-CoV-2 spike receptor-binding domain complexed with high affinity ACE2 mutant 3N39
要素
  • Angiotensin-converting enzyme 2
  • Spike protein S1
キーワードVIRAL PROTEIN / SARS-CoV-2 / COVID-19 / ACE2
機能・相同性
機能・相同性情報


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; 金属プロテアーゼ / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / negative regulation of signaling receptor activity / regulation of vasoconstriction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; 金属プロテアーゼ / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / negative regulation of signaling receptor activity / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / Attachment and Entry / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / regulation of transmembrane transporter activity / cilium / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / virus receptor activity / regulation of inflammatory response / regulation of cell population proliferation / endopeptidase activity / Potential therapeutics for SARS / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / apical plasma membrane / symbiont entry into host cell / membrane raft / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / 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. ...Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
類似検索 - ドメイン・相同性
Spike glycoprotein / Angiotensin-converting enzyme 2
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: 3.2 Å
データ登録者Arimori, T. / Takagi, J.
資金援助 日本, 1件
組織認可番号国
Japan Agency for Medical Research and Development (AMED)20am0101075 日本
引用ジャーナル: Nat Commun / 年: 2021
タイトル: Engineered ACE2 receptor therapy overcomes mutational escape of SARS-CoV-2.
著者: Higuchi, Y. / Suzuki, T. / Arimori, T. / Ikemura, N. / Mihara, E. / Kirita, Y. / Ohgitani, E. / Mazda, O. / Motooka, D. / Nakamura, S. / Sakai, Y. / Itoh, Y. / Sugihara, F. / Matsuura, Y. / ...著者: Higuchi, Y. / Suzuki, T. / Arimori, T. / Ikemura, N. / Mihara, E. / Kirita, Y. / Ohgitani, E. / Mazda, O. / Motooka, D. / Nakamura, S. / Sakai, Y. / Itoh, Y. / Sugihara, F. / Matsuura, Y. / Matoba, S. / Okamoto, T. / Takagi, J. / Hoshino, A.
履歴
登録2020年12月7日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02020年12月23日Provider: repository / タイプ: Initial release
改定 1.12021年3月10日Group: Structure summary / カテゴリ: entity / entity_name_com / Item: _entity.pdbx_description / _entity_name_com.name
改定 1.22021年6月30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_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 1.32023年11月29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

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Angiotensin-converting enzyme 2
B: Spike protein S1
C: Angiotensin-converting enzyme 2
D: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)196,42720
ポリマ－189,5134
非ポリマー6,91416
水362
1
A: Angiotensin-converting enzyme 2
B: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,39610
ポリマ－94,7562
非ポリマー3,6408
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-20 kcal/mol
Surface area36520 Å2
手法PISA
2
C: Angiotensin-converting enzyme 2
D: Spike protein S1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,03110
ポリマ－94,7562
非ポリマー3,2748
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-22 kcal/mol
Surface area36000 Å2
手法PISA
単位格子
Length a, b, c (Å)227.800, 227.800, 147.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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要素

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タンパク質 , 2種, 4分子 ACBD

#1: タンパク質 Angiotensin-converting enzyme 2 / Angiotensin-converting enzyme homolog / ACEH / Angiotensin-converting enzyme-related ...Angiotensin-converting enzyme homolog / ACEH / Angiotensin-converting enzyme-related carboxypeptidase / ACE-related carboxypeptidase / Metalloprotease MPROT15


分子量: 70354.938 Da / 分子数: 2 / 変異: A25V,K26E,K31N,E35K,N64I,L79F,N90H / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ACE2, UNQ868/PRO1885 / 発現宿主: Homo sapiens (ヒト)
参照: UniProt: Q9BYF1, angiotensin-converting enzyme 2, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; 金属プロテアーゼ
#2: タンパク質 Spike protein S1 / S glycoprotein / E2 / Peplomer protein / Spike glycoprotein


分子量: 24401.455 Da / 分子数: 2 / Fragment: receptor-binding domain / 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

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糖 , 5種, 12分子

#3: 多糖 alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 多糖
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 4 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 3 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: 多糖 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 586.542 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#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


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 , 3種, 6分子

#8: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#9: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 2 / 由来タイプ: 合成 / 式: SO4
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2 / 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

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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

結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 1.6 M ammonium sulfate, 0.25 M lithium sulfate, and 0.05 M CAPS pH 10.5

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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: SPring-8 / ビームライン: BL44XU / 波長: 0.9 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年11月11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: 0.9 Å / 相対比: 1
反射解像度: 3.2→48.13 Å / Num. obs: 123844 / % possible obs: 99.9 % / 冗長度: 32.5 % / Biso Wilson estimate: 130.87 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.38
反射 シェル解像度: 3.2→3.28 Å / Mean I/σ(I) obs: 0.56 / Num. unique obs: 9153 / CC1/2: 0.293

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解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3260精密化
XDSデータ削減
XDSデータスケーリング
PHASERv.2.8.1位相決定
精密化構造決定の手法: 分子置換
開始モデル: 6m0j

6m0j


解像度: 3.2→47.91 Å / SU ML: 0.5269 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 24.5872 / 立体化学のターゲット値: CDL v1.2
Rfactor反射数%反射
Rfree0.1979 6149 4.99 %
Rwork0.1788 117056 -
obs0.1797 123205 99.43 %
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: 135.47 Å2
精密化ステップサイクル: LAST / 解像度: 3.2→47.91 Å
タンパク質核酸リガンド溶媒全体
原子数12867 0 437 2 13306
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.007413714
X-RAY DIFFRACTIONf_angle_d0.960118711
X-RAY DIFFRACTIONf_chiral_restr0.05772049
X-RAY DIFFRACTIONf_plane_restr0.00582368
X-RAY DIFFRACTIONf_dihedral_angle_d9.69548007
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.240.40361820.40613579X-RAY DIFFRACTION90.15
3.24-3.270.42111940.39863738X-RAY DIFFRACTION96.42
3.27-3.310.40062030.38353870X-RAY DIFFRACTION99.2
3.31-3.360.37752040.37253930X-RAY DIFFRACTION99.42
3.36-3.40.3322040.36643880X-RAY DIFFRACTION99.66
3.4-3.450.3872040.35183875X-RAY DIFFRACTION99.8
3.45-3.50.35032050.34073887X-RAY DIFFRACTION99.88
3.5-3.550.34512060.3243914X-RAY DIFFRACTION99.93
3.55-3.60.33592060.30033917X-RAY DIFFRACTION99.93
3.6-3.660.30532060.27283903X-RAY DIFFRACTION99.93
3.66-3.730.30212040.25893891X-RAY DIFFRACTION99.95
3.73-3.790.27792060.23473912X-RAY DIFFRACTION99.93
3.79-3.870.24062070.21973921X-RAY DIFFRACTION99.95
3.87-3.950.22012040.2023882X-RAY DIFFRACTION99.93
3.95-4.030.2392060.19493914X-RAY DIFFRACTION100
4.03-4.130.22732060.18813914X-RAY DIFFRACTION100
4.13-4.230.19182080.17883951X-RAY DIFFRACTION99.98
4.23-4.340.16922020.14653847X-RAY DIFFRACTION100
4.34-4.470.1442090.13763964X-RAY DIFFRACTION100
4.47-4.610.18312060.1383908X-RAY DIFFRACTION99.98
4.61-4.780.16642060.14153918X-RAY DIFFRACTION100
4.78-4.970.16112060.14163925X-RAY DIFFRACTION100
4.97-5.20.16172080.14023947X-RAY DIFFRACTION100
5.2-5.470.15242060.14773907X-RAY DIFFRACTION100
5.47-5.810.17232070.15873945X-RAY DIFFRACTION100
5.81-6.260.20922060.17653903X-RAY DIFFRACTION100
6.26-6.890.19052090.16083983X-RAY DIFFRACTION100
6.89-7.880.17772080.15373942X-RAY DIFFRACTION100
7.88-9.910.14132100.12373982X-RAY DIFFRACTION100
9.91-47.910.16062110.1614007X-RAY DIFFRACTION99.08
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)
14.05356782588-2.26692541579-1.794925495353.789832546612.841177655434.64390495212-0.004763718702950.31798915588-0.03232674961520.03541948122740.1496942347820.04197075633250.05816641270990.23356453875-0.1446475990081.211434297960.00374082841929-0.008960600225731.09765102772-0.01267942161221.1743529778213.3500167302-35.124726835629.7661930402
24.99416840954-1.68142543553-3.960186179523.326644885060.576964836339.839144494130.189746009856-0.2415327782940.7908505756320.1484163485990.155993747786-0.154132666661-0.558775020928-0.28030414605-0.396292544410.904930302595-0.0763864476122-0.1513221533350.9086921041120.03556674640731.14866188464-9.16687648985-21.527562633346.6076361366
32.631850039-0.983063745649-2.244194437213.264862991062.679220033185.33339722389-0.06056712186410.332471928715-0.82117360769-0.32571491176-0.2349590713440.3095288412840.362697703997-0.3217865390090.2944496634181.21769694752-0.0918585682025-0.1539741971481.06454556663-0.1100967098331.26879386789-9.39723766685-47.08350246543.944272217
42.53648132428-0.31082428795-0.6641749829571.417839862150.03581999697841.092603355140.0271032113169-0.238635811145-0.3104284016240.05275167061410.01361163709520.06449846644520.2044747650710.100774696606-0.05530350287761.09846220095-0.00872014668596-0.06460538202980.9499176041870.03150551479251.08339116192-0.24641305522-38.400599563555.337654114
55.79109716173-0.831003002611-2.33224337441.48195600934-0.1991038481922.67295055187-0.160184840204-0.187890742349-1.14567114648-0.01748579025070.02516696173620.3500106101380.588564089003-0.2415223560620.1448908809381.25172678975-0.059784832459-0.1118714464670.915272555093-0.02842039091381.2528809955-10.599011466-49.152978100554.0972238565
65.02013582756-0.2181403201053.27486492052.41625200128-0.2908217340458.74479187433-0.213006677730.2613280970160.8726348507540.1325294044250.383802344035-1.24684733071-1.6841919583-0.2898545165990.0793970166911.307400564060.1629063274010.05513767283551.049465017610.004479020072891.54011359853.064070133-33.422130505141.4898327537
73.595251679852.134138715323.629589371572.401124680092.166237551073.669510862461.22460438894-2.499421043452.007392365061.13530187363-0.908152868347-0.619767698525-0.412822937711-0.2961592512180.4235391188631.39196436654-0.105340436401-0.1408355043151.6954702445-0.3507078703521.5984565554857.5202815316-37.708338169653.1989194902
82.9707430104-3.999643602290.4565920678946.47120135155-2.288785817532.62039718679-1.54880353289-1.08546073724-1.202032890170.6055313952990.9996174914530.5586738200980.0474275624406-0.1350543287550.5786972905631.291526857750.025433043452-0.06032262793411.596860597670.04650202934941.5228598211954.0160905963-45.514607873252.3918388816
95.6823807999-1.910176277442.130087509373.46098873889-0.3721909870474.609967706040.0115547490537-0.0901124444256-0.717091003025-0.3737586939650.4745301116190.098139079670.381259989790.188104527281-0.4687806454490.9569854319410.0662811551628-0.0190360182250.88392244858-0.1103116356661.1944792867140.6497789105-41.279289367638.7921153514
108.31216094649-1.774293099654.804078532592.4379233334-2.91346432724.638371070090.8100558810820.651053883733-1.47882650252-1.01375307197-0.454614900370.3563462387150.541682180191-0.0250972777869-0.4028531409131.433553908690.263772223585-0.06974065017991.18591306801-0.4078837563391.615175871939.970976444-45.370728050622.7815804428
114.00534913626-0.3241879056020.4414886114551.653867732960.4016875378852.53982199098-0.139421030240.157499477840.418393117235-0.325068449219-0.0262355916061-0.1782846064860.212272736387-0.1652356468140.158290866911.337157830450.08970399840110.002220379062960.973055994235-0.08400288654341.2511885012641.6459483568-39.17319373135.8902132891
124.84762689492-3.11563312612.464831423793.90740668352-5.650553616429.372632633530.6537468220190.4278232942470.304750141422-0.573365061686-0.4217432936360.5451997060050.0971234745356-0.286046951703-0.1373598442291.056677123330.209002563282-0.02161429219820.933303853207-0.03760784680211.18290222724101.270463018-71.755558315229.0212471362
133.32163057038-1.069773110321.086739710731.72770209125-0.06913727923222.484207123820.2236182012260.296326104467-0.20977381654-0.315348106276-0.04712243460660.2282769366120.1301869374530.196791360512-0.2101304026691.08509478392-0.01406355868060.09441637754870.98189572099-0.02934701766281.14225102913118.424894276-86.251409292334.3081705962
142.20700091588-0.2769863283551.429763652781.77846059036-1.357773375283.79092926233-0.1382077885960.05536318287920.573593720339-0.0495559211608-0.137419719408-0.43189675243-0.3988208319310.112180959050.2835872036851.05172204453-0.09635660623180.02674501854720.937193298367-0.02256370636151.30584771138133.236955688-75.357924108248.8048416293
152.492635436160.7344452278790.6928327994982.199524527040.7025148692063.045500064290.14991960007-0.51521684198-0.01260922212150.1525021596910.1695271497150.387807236838-0.123494842045-0.150065472196-0.2078992641681.103311730090.07367582496640.08677786815861.26838391102-0.03952795463941.15580224354107.594202689-80.470784988756.1816714015
163.02382854569-0.4614338250780.3716054180451.7954806281-0.3759829694681.769568594190.208860004589-0.2845118735790.276417619124-0.03076231549450.07930730547670.162056737274-0.09392927927930.0575091368833-0.1994757060511.133136582170.03701912425640.08118956862861.03186585876-0.03558922324081.29142931197113.660234483-72.221998320754.2917327052
172.924810967610.1531515795570.8485763193350.817990753702-0.6732904098942.77822151082-0.04796258758490.25130322406-0.0716315267315-0.0197219959147-0.221793757651-0.2975342269860.07090500178710.1355622525270.3125717438451.00405569927-0.1112088297950.02516119070810.999776974547-0.02701456288131.20252709205133.885874395-81.806743028143.5461834291
183.38264526859-0.9654647361820.6708449258621.07131381037-0.04376008422892.26081422354-0.179233674959-0.1731227703860.6430430901920.04972442287970.0988615401934-0.230765791335-0.6049180115910.1172167121410.0384884634541.29292758118-0.0220554978273-0.03018501786590.871871012261-0.01083287253531.28288671796127.52781423-64.99012130352.841480954
192.676798830881.687203386361.002075941671.39394311515-1.012124764738.13574797475-0.1695155217550.7490842557320.6987046520420.03943155102220.5066287154890.52839861481.22641930222-0.5113952876-0.3936234828771.212152689630.223059969406-0.1065690256241.118605545-0.0251130192891.4956185126969.1793980243-70.584159085538.1992598474
201.778937581362.55433627564-0.5499460962699.303350925663.693774950288.219569964360.706072493925-2.75135391196-1.947007550121.83112483349-0.8053160145690.5103631228281.14803403757-0.4442383892790.1636546480631.83935879435-0.04232992117310.4236033011511.823911452080.348197163281.2787233487165.0554619802-65.372622765650.4699935321
215.79482623899-4.20042892644-3.714394210527.211399761913.675495083874.35960599221-0.0379256182469-0.294708265611.370359620370.3023819665370.1756249939040.0210954660011-0.1726072073050.0880898202619-0.01643576076591.123589382190.13515562789-0.06655110320891.20041720313-0.01559308966141.5767829607774.2788431413-61.292562021444.8098033159
223.16538296174-1.70594266264-0.1777070118561.391831673741.166544045344.32100615570.0301207960601-0.02759168209630.333585592133-0.1845195751010.1027151899530.260541362029-0.218995442152-0.0299925848061-0.09949518096761.116021167120.01819524191340.03410280772371.06935775367-0.01451234212721.5095716484282.2522552181-64.58862303833.6924046552
234.599401976374.0858329882-0.865769597566.71087600069-4.669551985455.052819479850.9030275990770.3385465615551.30969519665-2.24613649317-1.06508169809-0.358883378289-0.1916058149620.27252254743-0.3530488113961.528316132830.1349597705380.3281360555641.274161460320.2628677872251.6896950573790.6232572891-63.425862513713.0698983126
248.977038800043.31704650359-6.527475384732.11480568068-2.368337120599.31158612961-0.166234255481.51642567236-0.254671704108-1.07170602180.385702257441-0.1025981516570.4353697191950.339552332997-0.2894973136641.33260704854-0.0989031952458-0.02934318501761.440080367520.02122770757691.4763865571792.2211850344-69.095971731816.6384837948
256.51696067826-1.66483269363-2.640317382174.109920776583.945753232275.14201266416-0.09183879245610.142907464814-0.279515793169-0.256177288936-0.16913694438-0.36811444465-0.07107932472020.5363896769650.2711084274951.042038362870.06774139598470.08576955887950.8725833586440.07117678541571.1749333611183.7836109505-70.455916725440.8381481294
266.72994730712-0.887419038365-0.4963971033623.025460237294.978630054518.550319669390.144636558868-0.390776197121-1.30931997426-0.1752238552020.638922426564-0.3006945063511.269210478020.562436910101-0.4418704331261.256832786730.179913880896-0.03710625319271.11828770333-0.07597895603641.7154636562156.9771406053-55.958701551641.8469651086
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 194 )
3X-RAY DIFFRACTION3chain 'A' and (resid 195 through 251 )
4X-RAY DIFFRACTION4chain 'A' and (resid 252 through 558 )
5X-RAY DIFFRACTION5chain 'A' and (resid 559 through 615 )
6X-RAY DIFFRACTION6chain 'B' and (resid 332 through 358 )
7X-RAY DIFFRACTION7chain 'B' and (resid 359 through 371 )
8X-RAY DIFFRACTION8chain 'B' and (resid 372 through 393 )
9X-RAY DIFFRACTION9chain 'B' and (resid 394 through 459 )
10X-RAY DIFFRACTION10chain 'B' and (resid 460 through 479 )
11X-RAY DIFFRACTION11chain 'B' and (resid 480 through 527 )
12X-RAY DIFFRACTION12chain 'C' and (resid 18 through 52 )
13X-RAY DIFFRACTION13chain 'C' and (resid 53 through 193 )
14X-RAY DIFFRACTION14chain 'C' and (resid 194 through 293 )
15X-RAY DIFFRACTION15chain 'C' and (resid 294 through 352 )
16X-RAY DIFFRACTION16chain 'C' and (resid 353 through 431 )
17X-RAY DIFFRACTION17chain 'C' and (resid 432 through 512 )
18X-RAY DIFFRACTION18chain 'C' and (resid 513 through 615 )
19X-RAY DIFFRACTION19chain 'D' and (resid 333 through 358 )
20X-RAY DIFFRACTION20chain 'D' and (resid 359 through 371 )
21X-RAY DIFFRACTION21chain 'D' and (resid 372 through 409 )
22X-RAY DIFFRACTION22chain 'D' and (resid 410 through 469 )
23X-RAY DIFFRACTION23chain 'D' and (resid 470 through 479 )
24X-RAY DIFFRACTION24chain 'D' and (resid 480 through 494 )
25X-RAY DIFFRACTION25chain 'D' and (resid 495 through 516 )
26X-RAY DIFFRACTION26chain 'D' and (resid 517 through 527 )

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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://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る