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- PDB-7k93: DENV2 NS1 in complex with neutralizing 2B7 single chain Fab varia... -

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基本情報

登録情報
データベース: PDB / ID: 7k93
タイトルDENV2 NS1 in complex with neutralizing 2B7 single chain Fab variable region (scFv)
要素
  • 2B7 single chain fab variable region
  • Non-structural protein 1
キーワードVIRAL PROTEIN (ウイルスタンパク質) / Flavivirus NS1 / Antibody (抗体) / Fab fragment
機能・相同性
機能・相同性情報


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / フラビビリン / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / : / カプシド / nucleoside-triphosphate phosphatase / double-stranded RNA binding ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / フラビビリン / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / : / カプシド / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / ヘリカーゼ / induction by virus of host autophagy / RNA依存性RNAポリメラーゼ / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / エンベロープ (ウイルス) / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / タンパク質分解 / extracellular region / ATP binding / 生体膜 / metal ion binding
類似検索 - 分子機能
: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
Genome polyprotein / Genome polyprotein
類似検索 - 構成要素
生物種Dengue virus 2 (デング熱ウイルス)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.89 Å
データ登録者Akey, D.L. / Smith, J.L.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 米国
引用ジャーナル: Science / 年: 2021
タイトル: Structural basis for antibody inhibition of flavivirus NS1-triggered endothelial dysfunction.
著者: Biering, S.B. / Akey, D.L. / Wong, M.P. / Brown, W.C. / Lo, N.T.N. / Puerta-Guardo, H. / Tramontini Gomes de Sousa, F. / Wang, C. / Konwerski, J.R. / Espinosa, D.A. / Bockhaus, N.J. / ...著者: Biering, S.B. / Akey, D.L. / Wong, M.P. / Brown, W.C. / Lo, N.T.N. / Puerta-Guardo, H. / Tramontini Gomes de Sousa, F. / Wang, C. / Konwerski, J.R. / Espinosa, D.A. / Bockhaus, N.J. / Glasner, D.R. / Li, J. / Blanc, S.F. / Juan, E.Y. / Elledge, S.J. / Mina, M.J. / Beatty, P.R. / Smith, J.L. / Harris, E.
履歴
登録2020年9月28日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年12月23日Provider: repository / タイプ: Initial release
改定 1.12021年1月20日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
改定 1.22023年10月18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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Non-structural protein 1
B: Non-structural protein 1
C: Non-structural protein 1
D: Non-structural protein 1
E: 2B7 single chain fab variable region
G: 2B7 single chain fab variable region
I: 2B7 single chain fab variable region
K: 2B7 single chain fab variable region
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)278,46012
ポリマ－277,5758
非ポリマー8854
水0
1
A: Non-structural protein 1
B: Non-structural protein 1
E: 2B7 single chain fab variable region
G: 2B7 single chain fab variable region
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)139,2306
ポリマ－138,7884
非ポリマー4422
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Non-structural protein 1
D: Non-structural protein 1
I: 2B7 single chain fab variable region
K: 2B7 single chain fab variable region
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)139,2306
ポリマ－138,7884
非ポリマー4422
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)69.627, 165.593, 258.589
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
12
22
32
42

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAASNASN(chain 'A' and (resid 0 through 82 or resid 84...AA0 - 8224 - 106
121VALVALPROPRO(chain 'A' and (resid 0 through 82 or resid 84...AA84 - 106108 - 130
131THRTHRTYRTYR(chain 'A' and (resid 0 through 82 or resid 84...AA132 - 158156 - 182
141ASNASNLYSLYS(chain 'A' and (resid 0 through 82 or resid 84...AA166 - 172190 - 196
151LYSLYSASNASN(chain 'A' and (resid 0 through 82 or resid 84...AA174 - 255198 - 279
161ARGARGLEULEU(chain 'A' and (resid 0 through 82 or resid 84...AA257 - 349281 - 373
271ALAALAASNASN(chain 'B' and (resid 0 through 82 or resid 84...BB0 - 8224 - 106
281VALVALPROPRO(chain 'B' and (resid 0 through 82 or resid 84...BB84 - 106108 - 130
291THRTHRTYRTYR(chain 'B' and (resid 0 through 82 or resid 84...BB132 - 158156 - 182
2101ASNASNLYSLYS(chain 'B' and (resid 0 through 82 or resid 84...BB166 - 172190 - 196
2111LYSLYSASNASN(chain 'B' and (resid 0 through 82 or resid 84...BB174 - 255198 - 279
2121ARGARGLEULEU(chain 'B' and (resid 0 through 82 or resid 84...BB257 - 349281 - 373
3131ALAALAASNASN(chain 'C' and (resid 0 through 82 or resid 84...CC0 - 8224 - 106
3141VALVALPROPRO(chain 'C' and (resid 0 through 82 or resid 84...CC84 - 106108 - 130
3151THRTHRTYRTYR(chain 'C' and (resid 0 through 82 or resid 84...CC132 - 158156 - 182
3161ASNASNLYSLYS(chain 'C' and (resid 0 through 82 or resid 84...CC166 - 172190 - 196
3171LYSLYSASNASN(chain 'C' and (resid 0 through 82 or resid 84...CC174 - 255198 - 279
3181ARGARGLEULEU(chain 'C' and (resid 0 through 82 or resid 84...CC257 - 349281 - 373
4191ALAALAASNASN(chain 'D' and (resid 0 through 82 or resid 84...DD0 - 8224 - 106
4201VALVALPROPRO(chain 'D' and (resid 0 through 82 or resid 84...DD84 - 106108 - 130
4211THRTHRTYRTYR(chain 'D' and (resid 0 through 82 or resid 84...DD132 - 158156 - 182
4221ASNASNLYSLYS(chain 'D' and (resid 0 through 82 or resid 84...DD166 - 172190 - 196
4231LYSLYSASNASN(chain 'D' and (resid 0 through 82 or resid 84...DD174 - 255198 - 279
4241ARGARGLEULEU(chain 'D' and (resid 0 through 82 or resid 84...DD257 - 349281 - 373
1252GLUGLUVALVAL(chain 'E' and (resid 1 through 12 or resid 14 through 120 or resid 138 through 247))EE1 - 124 - 15
1262PROPROSERSER(chain 'E' and (resid 1 through 12 or resid 14 through 120 or resid 138 through 247))EE14 - 12017 - 123
1272ASNASNLEULEU(chain 'E' and (resid 1 through 12 or resid 14 through 120 or resid 138 through 247))EE138 - 247141 - 250
2282GLUGLUVALVAL(chain 'G' and (resid 1 through 12 or resid 14 through 120 or resid 138 through 247))GF1 - 124 - 15
2292PROPROSERSER(chain 'G' and (resid 1 through 12 or resid 14 through 120 or resid 138 through 247))GF14 - 12017 - 123
2302ASNASNLEULEU(chain 'G' and (resid 1 through 12 or resid 14 through 120 or resid 138 through 247))GF138 - 247141 - 250
3312GLUGLUVALVAL(chain 'I' and (resid 1 through 12 or resid 14 through 120 or resid 138 through 248))IG1 - 124 - 15
3322PROPROSERSER(chain 'I' and (resid 1 through 12 or resid 14 through 120 or resid 138 through 248))IG14 - 12017 - 123
3332ASNASNILEILE(chain 'I' and (resid 1 through 12 or resid 14 through 120 or resid 138 through 248))IG138 - 189141 - 192
3342TYRTYRLEULEU(chain 'I' and (resid 1 through 12 or resid 14 through 120 or resid 138 through 248))IG191 - 248193 - 250
4352GLUGLUVALVAL(chain 'K' and (resid 1 through 12 or resid 14 through 120 or resid 138 through 247))KH1 - 124 - 15
4362PROPROSERSER(chain 'K' and (resid 1 through 12 or resid 14 through 120 or resid 138 through 247))KH14 - 12017 - 123
4372ASNASNLEULEU(chain 'K' and (resid 1 through 12 or resid 14 through 120 or resid 138 through 247))KH138 - 247141 - 250

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
Non-structural protein 1


分子量: 42674.211 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Dengue virus 2 (デング熱ウイルス)
発現宿主: unidentified baculovirus (ウイルス)
参照: UniProt: D0EPS0, UniProt: P29990*PLUS, フラビビリン, nucleoside-triphosphate phosphatase, ヘリカーゼ
#2: 抗体
2B7 single chain fab variable region / scFv


分子量: 26719.617 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Escherichia coli (大腸菌)
#3: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン / N-アセチルグルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.68 Å3/Da / 溶媒含有率: 54.06 %
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 / pH: 8.5
詳細: 50 mM Tris pH 8.5, 50 mM (NH4)2SO4, 10% (v/v) glycerol

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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: APS / ビームライン: 23-ID-B / 波長: 1.0332 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年12月14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: 1.0332 Å / 相対比: 1
反射解像度: 2.89→47.38 Å / Num. obs: 67710 / % possible obs: 99.34 % / 冗長度: 13.2 % / Biso Wilson estimate: 79.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1982 / Rpim(I) all: 0.05668 / Rrim(I) all: 0.2063 / Net I/σ(I): 11.4
反射 シェル解像度: 2.89→2.994 Å / Rmerge(I) obs: 2.319 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 6307 / CC1/2: 0.532 / Rpim(I) all: 0.6531 / Rrim(I) all: 2.411

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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
XDSデータ削減
XDS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: 6EWQ

6ewq


解像度: 2.89→47.38 Å / SU ML: 0.4469 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 29.9881
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2686 2412 3.57 %
Rwork0.2227 65131 -
obs0.2244 67543 99.01 %
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: 84.73 Å2
精密化ステップサイクル: LAST / 解像度: 2.89→47.38 Å
タンパク質核酸リガンド溶媒全体
原子数17525 0 56 0 17581
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.009917986
X-RAY DIFFRACTIONf_angle_d1.199324378
X-RAY DIFFRACTIONf_chiral_restr0.06172664
X-RAY DIFFRACTIONf_plane_restr0.00733117
X-RAY DIFFRACTIONf_dihedral_angle_d21.83976569
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.950.50021190.38243201X-RAY DIFFRACTION84.18
2.95-3.010.2891420.3313821X-RAY DIFFRACTION99.97
3.01-3.080.30861400.30923786X-RAY DIFFRACTION99.92
3.08-3.160.37951440.29833848X-RAY DIFFRACTION99.95
3.16-3.240.31971400.29893785X-RAY DIFFRACTION99.87
3.24-3.340.32941430.28313857X-RAY DIFFRACTION99.93
3.34-3.450.30741360.2673809X-RAY DIFFRACTION99.9
3.45-3.570.32721450.25333816X-RAY DIFFRACTION99.9
3.57-3.710.28231430.24973841X-RAY DIFFRACTION99.92
3.71-3.880.28921400.22873871X-RAY DIFFRACTION99.93
3.88-4.080.2821440.22253861X-RAY DIFFRACTION99.95
4.08-4.340.25221430.19033850X-RAY DIFFRACTION99.97
4.34-4.670.22121430.17613866X-RAY DIFFRACTION99.9
4.68-5.150.22661430.17993892X-RAY DIFFRACTION99.98
5.15-5.890.25471460.20213923X-RAY DIFFRACTION99.95
5.89-7.410.27681460.21753953X-RAY DIFFRACTION99.95
7.41-47.380.22021550.19674151X-RAY DIFFRACTION99.81
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)
11.225019092140.7443563833550.8483392694641.98244437766-0.4226711509641.55852236151-0.63453592185-0.590549677478-0.03655041365860.3370765476730.1871020787040.0438981225630.5494826053420.998185921421-0.002991093158921.183972008210.1022339977670.1225257399270.8671901687690.1809848937811.0158246987115.181561587315.789877765118.5933285667
21.329382971540.5623111605150.5552110452191.54498911703-0.8206310893320.796868486798-0.0950847495194-0.8241183080690.2960553092420.8324217967210.0900188550957-0.698820786311-0.02502454807611.523822196730.03082970625650.9095995170870.370742330073-0.3511294957622.44030136611-0.1723594345011.0670782324834.702929282331.615136749940.7476828442
33.06088943725-1.13743257654-2.260923387830.7342733205371.129493537814.385601899550.00220008206415-0.242831841980.308655389432-0.01964365410930.158178572865-0.0858107982293-0.1054363317670.38378547491-0.0002217721145030.714026456938-0.0561127593328-0.0485382021780.664032983165-0.0116277381990.8422596369539.1611027022340.658029498728.0184529314
41.21219608459-0.09656670534660.1519947679871.962596475091.64390956922.34934205748-0.05011699498510.422651863718-0.146812802344-0.00325798173428-0.273704142170.319197447434-0.02092033198-0.3776988765490.0006800709304420.7685635330180.0984574973598-0.01939702847771.076202982930.01439526437280.9565845062245.9403862768621.9290239497-7.40736963081
52.39133150367-0.71245467689-1.645859064260.463255602050.9652079329712.36767791743-0.08010754724-0.06296284054540.1372838475780.114620813961-0.0733218620919-0.02663694887-0.08180222576930.2620956223910.0004409507557280.651725654670.05978814716420.03835277071740.8152066957290.1164627129750.87501429847827.841769992625.9009115053-2.36852485809
63.84888013318-2.942616462813.896973587652.9942973705-3.781296999714.80867847876-0.12338484526-0.00599192689623-0.19448054212-0.128630735446-0.516895377092-0.07281815025720.08555955216310.0962236403307-0.2076316887761.930294087760.737354423949-0.09552127765540.9274090660980.2349858976250.93949527944124.480228542926.1151448407-20.4456429421
70.2159376876510.145210816989-0.1180695734540.5668019530960.2527467622080.808381921871-0.261208577425-0.3910062458210.4559946287650.0211320107066-0.0991223491260.236831865217-0.514127888731-0.204128213095-0.001166989553091.0373920986-0.04994081430230.1209605574510.684427878210.01226728110281.026625149317.89817214492-7.6878752594219.2809400291
82.29106202406-0.410559692243-0.1441562791643.73242358735-0.2926615041293.81728343450.09226770858940.2754137132460.0338512198186-0.161407498067-0.201981076125-0.3513985643390.311404263190.01204172342350.0001456944992150.622792810457-0.00570324154121-0.005880949365180.6253294700710.03672678425140.71361588627717.9904357266-33.6937690334-2.90027627178
90.379597678147-0.122701796047-0.4354800121990.2834759029540.1898296063830.4194134770260.324203348886-0.6441854174370.702220594930.634372415738-0.405074746287-0.1212354504340.1090546794020.791331410542-0.001718819690040.845591135779-0.0644327483994-0.05766179550240.844695883198-0.002399233422690.8793495162317.2918604515-27.945139987811.4127123413
102.74258318772-0.3152067195841.016189554371.28423218424-0.1852794591963.959092845750.0573330271504-0.04935531346760.1597862234370.0185276676025-0.06519844351190.1590640188120.0966994468252-0.277190212185-6.07286877088E-50.626445078261-0.0327544192017-0.009494516006040.5286186616380.002670851137970.698598727473-10.9743171955-23.59339190926.62149553204
110.01929832444430.156264738592-0.02139518404931.03077601012-0.2001283447620.3644037443180.203743725220.2482149632670.356202408084-1.22399105897-0.3277417746540.082489862426-0.0597252370168-0.1081043529210.01536630269930.911032133289-0.0712863330430.09178200848180.5052061376170.0314063097770.99901546673712.4036402842-8.1399526015317.3881989549
120.2234866889630.2534118163860.08709924952131.80702917233-0.2659815087431.345221923510.46104743540.3297289574540.592049399712-0.027214562526-0.3315073872250.0203290646948-1.73688444212-0.7163348722220.03142385306460.9674493685460.03505044126-0.0975399388470.853242317658-0.1720170865820.848000399369-6.70741379233-4.2424657042138.7717859302
133.24593608380.289687311657-0.4191733187681.034886317870.8490255918410.7222082494060.2912553879-0.5218001421310.7360223187670.27265678472-0.1653048059480.319982225286-0.102740933417-0.2688018340050.0001733030663790.978360725082-0.005675117973410.09483968951040.943304339165-0.2295355393571.03919182844-11.18388741-8.1212172405445.3331533022
141.600935628770.1073903608311.306370781111.161121086530.9453145228692.66155025070.149269908992-0.239152611247-0.1841196191650.2460672298180.0884454563539-0.2290997226390.4497684447490.2598031761770.002186689566490.8238685340120.0309000290743-0.05520212110680.76671686863-0.05078159379470.72902688113611.7898905859-25.818532730842.6046336582
151.443853719380.595836031791-0.7558816412330.76284930235-0.2149696524260.7701106371-0.109597344212-0.410891850204-0.323201280620.378588285761-0.05143086355810.4262693040231.01248303307-0.7489045241470.0005196129531981.19477243018-0.00259668232838-0.2291866895040.8609678063720.1011904565540.98056403867-4.6417778053821.922180300857.0070390236
160.4589527680390.815860265339-0.5243437647611.72161706117-0.3030554435511.563017920660.170076639975-0.122511423888-0.812340262196-0.2037721563010.2925352620070.2541331515610.9735735609190.102542695698-0.0006559481833171.164338869060.0245901638098-0.2098317654090.774933636136-0.01532519426841.07196250377-0.080473307448623.558185722252.9314269047
170.2754594529360.363349761588-0.1084751003950.502150014479-0.1266466334320.0123615720744-0.222049410671-0.4692966947680.37902945680.1073524448720.6985869460780.3369515918441.167237948130.0225976258606-0.001633309986411.393152325010.255707761774-0.1198060046290.9005817272720.1165880691350.9923499475746.123031197219.274318150962.3715238427
181.64300211485-0.4493226289070.7292191148761.351766075771.134290946292.36305286426-0.107201818727-0.3369917882120.1462049568910.232538376941-0.054566535208-0.1962195126190.0673870705130.7677781515530.0004286803715250.9098032629130.007047352816-0.08339322272420.7853292548640.01897592600230.811717136874.7385895512141.743836295165.7867619736
191.280896670481.044933606781.018772126311.123084106220.6331535533330.8475504934290.0923979939892-0.0689995525589-0.145840757070.594715104799-0.0735158635201-0.1517624210330.4797884697370.0738625690960.0003770965209221.009020889050.0462079729162-0.1274782836170.8958800589520.01278172315210.8600620791054.0197908486936.696308106468.8756896389
200.761306823004-0.278108628937-1.053371043923.64074935381-0.730241275321.689121582680.114811539575-0.47259795238-0.2246945969450.2078972924630.0787057531908-0.288982758680.4934997628010.07390523225270.0001508036138140.7777270993030.1254646841540.002964383229950.9442870770630.2918112341510.92840535960628.2947147906-6.34319148291-12.5974870778
210.2834781997370.651104039847-0.1596232533740.794411314244-0.05451164104311.16289064722-0.0506902205329-0.245470417476-0.01659739989060.00279833559633-0.204386017765-0.5031614211250.03922481659090.1978041751090.0005863179306860.8260369697610.1466634631380.02745470560010.6312757092070.1827235946170.90210644247328.3639092397-3.10345027192-19.5940043335
222.71640572334-0.4642074193260.8929799757281.314773089930.2509797021822.3155208898-0.007529609459760.0940227532502-0.0490765674356-0.2126719814210.00944047627589-0.116395116110.1338647723310.266483180023-0.0002944583018270.7629574175190.08712195752950.0826931337170.6890948016350.1536752619120.82098664444528.38576582053.26946743208-33.8704509917
230.522857692293-0.291237029875-0.06960627535970.5573679871410.4929391494220.480310412644-0.1032444636780.8399647183620.307845071530.2399714484670.5356582245940.623982442897-0.33200817239-0.7136088433610.0001253823564210.7436285915130.08796992174810.02837799789170.9003642348860.2874295417871.12636766918-7.63898774422-1.04040013554-22.6715119854
241.772769493561.68067111092-1.066171780933.71739375283-0.1262533187851.328494492250.1260382687060.292119325660.401638013585-0.1006065898870.1488374186780.2733911303620.0461451508762-0.158796681822-0.000591245505560.6960200185630.129608563123-0.02998066888910.7718334159940.1846861403080.785465940684-3.56212132312-5.72933054127-20.1759902423
250.443308838342-0.234863008762-0.3374602633912.95881280107-0.03098007774790.278959288756-0.7858334691870.749160371319-0.138159645505-1.78438945820.685486964394-0.070051092570.2603949692370.05817307736610.05409090373820.823788884657-0.08121062570250.08294770757251.04757660250.1359987626060.8015955347151.86478013749-13.1396330584-33.7148598898
263.223413184481.10277801549-1.067130294030.8039923106080.01939455588050.90524324513-0.4315882399040.714652386563-0.490778051751-0.8750808441630.407163339240.2459409365970.966077623005-0.529330874427-0.0002131275616381.25358897452-0.157060183906-0.02466782767370.9629203749530.004979662335240.788519356266-9.73135886397-24.5110761105-30.0964376912
270.1115908140760.0133677416456-0.1327843574740.06860461398840.1487009804320.510357685461-0.9649258457430.912635653133-0.580635415948-1.821479532641.13101821310.1657629940830.0326370204971-1.797954027490.02457214181151.90050847121-0.40465448276-0.1266009577931.647784107220.01988635304070.917794203186-9.85137050087-20.430040375-37.8010386056
280.8063685666360.301851778965-0.2171751401890.521155507130.1195949278670.1510504453180.1575160278471.284770597260.0226772160718-1.052122921730.430267757334-0.6970796492090.6586274383080.5875498612010.01166830008641.343246357350.01324459366160.08220433949621.075241466070.07312016472240.671299724758-2.47766380305-19.5159700907-31.004350994
290.694047432359-0.0345496911399-0.7103419112090.102912802732-0.00399088627520.616538709527-0.2939424572110.7752770416920.6197430454710.1371001050480.367337411168-0.857608947746-0.9572437604191.157125626180.00145981334551.15973933555-0.2078754217830.05164303444941.24035772133-0.02365090703521.074064985731.96174625287.3208267713154.6594721379
300.09307873574310.0624752886934-0.08998515862150.2455217235010.04265426830820.1267358267820.5663533937860.421613635797-0.3676596753790.487081837006-0.205469678099-0.661666728087-0.4336111764550.358773341622-0.002933754134490.9873500234330.0224356503068-0.02285051559160.936946539712-0.2135193072171.1037727759226.6411074453-5.215091914355.4899491154
310.4131415224180.2175934269750.09107531117680.308862274808-0.230626884620.365997858670.5828600123860.560823996343-0.439001850360.378972337346-0.630717876443-0.016000196923-0.412672732425-0.297017185978-0.001170909046110.952310482361-0.00514466949626-0.04411166192740.894999766655-0.05326398188580.82899711574519.83304470663.1054186548859.3688191274
32-0.004804512180720.1093089661030.01128092350220.651254789861-0.01919355224170.1101434341280.1375135189950.6454503513-0.001946091018150.143011891802-0.2956275878010.1031574296240.231138976405-0.04893778641570.001716235805281.03773609682-0.0933050161282-0.09911567225341.320462333960.004329499486420.89855161711821.4247738576-0.072393567103348.249240377
330.4521834484830.260040729363-0.3338398817370.3703281779250.1969840414890.7390107014530.5280597656970.7069583395970.432278050651-0.357112640211-0.00991331443914-0.0581552561865-0.8553107217530.3398935036130.0006293889058961.07940717649-0.1925307561070.08043172795320.973835850586-0.07490028688121.0793204383226.23575209185.9872472106553.7903302632
340.2623117848410.109644856240.3382800094510.263353388021-0.1641106212080.6819002606870.392031323478-0.479875427906-0.169550860010.5193697195470.417659026742-0.8791800767560.9332880957730.6428690089180.003920344641620.697970028775-0.00189237718995-0.08632377548380.988032661728-0.1339801988740.85106053811224.3356924648-7.6447283370861.1156005707
350.3048949148170.345378772124-0.3015684696950.219120262555-0.2759919874950.2601771290930.3998282540590.225803467126-0.08338455435260.176102478854-0.0636695516747-0.276572960381-0.3912951098690.4698409430.0008335993554490.894676835323-0.00992887104581-0.03228737211690.788458977286-0.1338060883011.0418685788516.92303629316.3665840098968.8727597762
361.3352859330.494684454404-0.8226641214950.141983072491-0.2918083089110.514826117734-0.2040103328990.225559394438-0.170474376502-0.08325531006710.3202971355480.1903460213860.3978857216370.3819378939420.0004079941679610.9102248971170.0833043988287-0.1023087735290.716966339645-0.1108327280540.74632310590812.84649002-9.2811201586573.7965810118
370.54024964131-0.704586315368-0.2231948777051.333664304660.5902602244071.273935415740.0610767388283-0.00112171092442-0.1556496088860.3043185920480.288597204679-0.08402128763070.124282561580.5931002747280.0001880716569290.799330420396-0.00666351951578-0.09964895509030.762085521039-0.09808725480910.79802482667421.1906437947-8.3206348688173.8793620496
380.056148478791-0.0422897303075-0.1541149630870.5028338618820.1285809813220.277718110599-0.02893743430560.628484582450.3392523903690.567208288410.2286060077180.0829520157322-0.277970396081.534705570520.0003029511454590.98835331401-0.153159893794-0.05809661971791.03747135229-0.1785218936540.95356255404322.9180373083-2.560635797577.9367036276
390.8305617439140.0654053618751-0.517236750740.664496384398-0.4195198452330.5319207444330.222221074202-0.257458276190.329158424716-0.215566603481-0.172545610086-0.104246105523-0.775059484456-0.872941153958-0.001569235783840.963503449198-0.0723791507827-0.1094597305540.807739060563-0.1207990187080.84146834203316.5087968031-0.58120498346970.5871039022
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -7 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 171 )
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 349 )
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 155 )
5X-RAY DIFFRACTION5chain 'B' and (resid 156 through 349 )
6X-RAY DIFFRACTION6chain 'B' and (resid 350 through 352 )
7X-RAY DIFFRACTION7chain 'C' and (resid -9 through 32 )
8X-RAY DIFFRACTION8chain 'C' and (resid 33 through 150 )
9X-RAY DIFFRACTION9chain 'C' and (resid 151 through 180 )
10X-RAY DIFFRACTION10chain 'C' and (resid 181 through 352)
11X-RAY DIFFRACTION11chain 'D' and (resid -1 through 18 )
12X-RAY DIFFRACTION12chain 'D' and (resid 19 through 51 )
13X-RAY DIFFRACTION13chain 'D' and (resid 52 through 189 )
14X-RAY DIFFRACTION14chain 'D' and (resid 190 through 349 )
15X-RAY DIFFRACTION15chain 'E' and (resid 1 through 44 )
16X-RAY DIFFRACTION16chain 'E' and (resid 45 through 113 )
17X-RAY DIFFRACTION17chain 'E' and (resid 114 through 140 )
18X-RAY DIFFRACTION18chain 'E' and (resid 141 through 216 )
19X-RAY DIFFRACTION19chain 'E' and (resid 217 through 248 )
20X-RAY DIFFRACTION20chain 'G' and (resid 1 through 99 )
21X-RAY DIFFRACTION21chain 'G' and (resid 100 through 140 )
22X-RAY DIFFRACTION22chain 'G' and (resid 141 through 248 )
23X-RAY DIFFRACTION23chain 'I' and (resid 1 through 39 )
24X-RAY DIFFRACTION24chain 'I' and (resid 40 through 113 )
25X-RAY DIFFRACTION25chain 'I' and (resid 114 through 150 )
26X-RAY DIFFRACTION26chain 'I' and (resid 151 through 217 )
27X-RAY DIFFRACTION27chain 'I' and (resid 218 through 232 )
28X-RAY DIFFRACTION28chain 'I' and (resid 233 through 249 )
29X-RAY DIFFRACTION29chain 'K' and (resid 1 through 25 )
30X-RAY DIFFRACTION30chain 'K' and (resid 26 through 39 )
31X-RAY DIFFRACTION31chain 'K' and (resid 40 through 52 )
32X-RAY DIFFRACTION32chain 'K' and (resid 53 through 73 )
33X-RAY DIFFRACTION33chain 'K' and (resid 74 through 99 )
34X-RAY DIFFRACTION34chain 'K' and (resid 100 through 113 )
35X-RAY DIFFRACTION35chain 'K' and (resid 114 through 150 )
36X-RAY DIFFRACTION36chain 'K' and (resid 151 through 173 )
37X-RAY DIFFRACTION37chain 'K' and (resid 174 through 216 )
38X-RAY DIFFRACTION38chain 'K' and (resid 217 through 231 )
39X-RAY DIFFRACTION39chain 'K' and (resid 232 through 248 )

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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