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- PDB-6vso: DengueV-2 Capsid Structure -

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基本情報

登録情報
データベース: PDB / ID: 6vso
タイトルDengueV-2 Capsid Structure
要素Capsid premembrane protein
キーワードVIRAL PROTEIN / Capsid / Inhibitor
機能・相同性
機能・相同性情報


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
類似検索 - 分子機能
Arc Repressor Mutant, subunit A - #930 / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B ...Arc Repressor Mutant, subunit A - #930 / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / 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 / Arc Repressor Mutant, subunit A / 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 / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
NITRATE ION / Capsid premembrane protein / Genome polyprotein
類似検索 - 構成要素
生物種Dengue virus 2 (デング熱ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.001 Å
データ登録者White, M. / Xia, H. / Shi, P.
資金援助 米国, 4件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI142759 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127744 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI136126 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI145617 米国
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2020
タイトル: A cocrystal structure of dengue capsid protein in complex of inhibitor.
著者: Xia, H. / Xie, X. / Zou, J. / Noble, C.G. / Russell, W.K. / Holthauzen, L.M.F. / Choi, K.H. / White, M.A. / Shi, P.Y.
履歴
登録2020年2月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年7月15日Provider: repository / タイプ: Initial release
改定 1.12020年7月29日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.22020年8月12日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32023年10月11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: Capsid premembrane protein
B: Capsid premembrane protein
C: Capsid premembrane protein
D: Capsid premembrane protein
E: Capsid premembrane protein
F: Capsid premembrane protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)57,91929
ポリマ－56,4036
非ポリマー1,51623
水19811
1
A: Capsid premembrane protein
B: Capsid premembrane protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,2359
ポリマ－18,8012
非ポリマー4347
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-36 kcal/mol
Surface area8560 Å2
手法PISA
2
C: Capsid premembrane protein
D: Capsid premembrane protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,1117
ポリマ－18,8012
非ポリマー3105
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-44 kcal/mol
Surface area8370 Å2
手法PISA
3
E: Capsid premembrane protein
F: Capsid premembrane protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,57313
ポリマ－18,8012
非ポリマー77211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-37 kcal/mol
Surface area8480 Å2
手法PISA
単位格子
Length a, b, c (Å)142.000, 142.000, 67.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 24 through 27 or (resid 28...
21(chain C and (resid 24 through 40 or (resid 41...
31(chain E and (resid 24 through 27 or (resid 28...
12(chain C and (resid 23 through 26 or (resid 27...
22(chain D and (resid 23 through 27 or (resid 28...
32(chain F and (resid 23 through 26 or (resid 27...

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
111SERSERGLNGLN(chain A and (resid 24 through 27 or (resid 28...AA24 - 275 - 8
121GLNGLNGLNGLN(chain A and (resid 24 through 27 or (resid 28...AA289
131VALVALARGARG(chain A and (resid 24 through 27 or (resid 28...AA23 - 994 - 80
141VALVALARGARG(chain A and (resid 24 through 27 or (resid 28...AA23 - 994 - 80
151VALVALARGARG(chain A and (resid 24 through 27 or (resid 28...AA23 - 994 - 80
161VALVALARGARG(chain A and (resid 24 through 27 or (resid 28...AA23 - 994 - 80
211SERSERGLYGLY(chain C and (resid 24 through 40 or (resid 41...CC24 - 405 - 21
221ARGARGARGARG(chain C and (resid 24 through 40 or (resid 41...CC4122
231VALVALARGARG(chain C and (resid 24 through 40 or (resid 41...CC23 - 984 - 79
241VALVALARGARG(chain C and (resid 24 through 40 or (resid 41...CC23 - 984 - 79
251VALVALARGARG(chain C and (resid 24 through 40 or (resid 41...CC23 - 984 - 79
261VALVALARGARG(chain C and (resid 24 through 40 or (resid 41...CC23 - 984 - 79
271VALVALARGARG(chain C and (resid 24 through 40 or (resid 41...CC23 - 984 - 79
311SERSERGLNGLN(chain E and (resid 24 through 27 or (resid 28...EE24 - 275 - 8
321GLNGLNGLNGLN(chain E and (resid 24 through 27 or (resid 28...EE289
331VALVALARGARG(chain E and (resid 24 through 27 or (resid 28...EE23 - 984 - 79
341VALVALARGARG(chain E and (resid 24 through 27 or (resid 28...EE23 - 984 - 79
351VALVALARGARG(chain E and (resid 24 through 27 or (resid 28...EE23 - 984 - 79
361VALVALARGARG(chain E and (resid 24 through 27 or (resid 28...EE23 - 984 - 79
112VALVALVALVAL(chain C and (resid 23 through 26 or (resid 27...CC23 - 264 - 7
122GLNGLNGLNGLN(chain C and (resid 23 through 26 or (resid 27...CC27 - 288 - 9
132VALVALARGARG(chain C and (resid 23 through 26 or (resid 27...CC23 - 984 - 79
142VALVALARGARG(chain C and (resid 23 through 26 or (resid 27...CC23 - 984 - 79
152VALVALARGARG(chain C and (resid 23 through 26 or (resid 27...CC23 - 984 - 79
162VALVALARGARG(chain C and (resid 23 through 26 or (resid 27...CC23 - 984 - 79
212VALVALGLNGLN(chain D and (resid 23 through 27 or (resid 28...DD23 - 274 - 8
222GLNGLNGLNGLN(chain D and (resid 23 through 27 or (resid 28...DD289
232ARGARGARGARG(chain D and (resid 23 through 27 or (resid 28...DD22 - 993 - 80
242ARGARGARGARG(chain D and (resid 23 through 27 or (resid 28...DD22 - 993 - 80
252ARGARGARGARG(chain D and (resid 23 through 27 or (resid 28...DD22 - 993 - 80
262ARGARGARGARG(chain D and (resid 23 through 27 or (resid 28...DD22 - 993 - 80
312VALVALVALVAL(chain F and (resid 23 through 26 or (resid 27...FF23 - 264 - 7
322GLNGLNGLNGLN(chain F and (resid 23 through 26 or (resid 27...FF27 - 288 - 9
332ASNASNARGARG(chain F and (resid 23 through 26 or (resid 27...FF21 - 992 - 80
342ASNASNARGARG(chain F and (resid 23 through 26 or (resid 27...FF21 - 992 - 80
352ASNASNARGARG(chain F and (resid 23 through 26 or (resid 27...FF21 - 992 - 80
362ASNASNARGARG(chain F and (resid 23 through 26 or (resid 27...FF21 - 992 - 80

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
Capsid premembrane protein


分子量: 9400.506 Da / 分子数: 6 / 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: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: A0A2D2BF61, UniProt: P07564*PLUS
#2: 化合物
ChemComp-NO3 / NITRATE ION


分子量: 62.005 Da / 分子数: 20 / 由来タイプ: 合成 / 式: NO3
#3: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C3H8O3
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 11 / 由来タイプ: 天然 / 式: H2O
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: 3.49 Å3/Da / 溶媒含有率: 64.8 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.2 / 詳細: 3.0 M NaNO3, 100 mM HEPES pH 7.2, 5% 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: 21-ID-G / 波長: 0.97857 Å
検出器タイプ: RAYONIX MX300-HS / 検出器: CCD / 日付: 2018年6月13日 / 詳細: Be lenses
放射モノクロメーター: C(111) / 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: 0.97857 Å / 相対比: 1
反射解像度: 3→50 Å / Num. obs: 15870 / % possible obs: 100 % / 冗長度: 11.1 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.042 / Rrim(I) all: 0.139 / Χ2: 0.937 / Net I/av σ(I): 19.722 / Net I/σ(I): 5 / Num. measured all: 176644
反射 シェル

Diffraction-ID: 1 / % possible all: 100

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
3-3.0511.10.9262.837850.9390.9840.290.970.871
3.05-3.1111.20.8672.957830.9290.9810.270.9080.838
3.11-3.1711.20.8483.147750.9130.9770.2650.8890.888
3.17-3.2311.30.7143.797770.9470.9860.2220.7480.881
3.23-3.311.20.5065.367920.9680.9920.1580.530.942
3.3-3.3811.20.4575.917860.9750.9940.1420.4790.962
3.38-3.4611.30.3777.067760.9780.9940.1170.3950.923
3.46-3.5611.30.3527.97940.9870.9940.1090.3690.956
3.56-3.6611.30.2859.917830.9820.9960.0880.2981.003
3.66-3.7811.20.23112.17810.9880.9970.0720.2421.009
3.78-3.9111.30.20313.168040.9920.9980.0630.2130.959
3.91-4.0711.30.15716.987800.9940.9990.0490.1650.975
4.07-4.2611.20.13419.347990.9960.9990.0420.1410.985
4.26-4.4811.20.12621.737910.9950.9990.0390.1321.042
4.48-4.7611.20.12423.447990.9950.9990.0390.131.172
4.76-5.1311.10.10825.417960.9950.9990.0340.1141.136
5.13-5.6411.10.10124.687860.9960.9990.0320.1060.952
5.64-6.46110.09125.888090.9970.9990.0290.0960.877
6.46-8.1310.90.04840.378170.99810.0150.0510.734
8.13-50100.03347.658570.9970.9990.0110.0350.61

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位相決定

位相決定手法: 分子置換
Phasing MR
最高解像度最低解像度
Rotation4.11 Å48.73 Å
Translation4.11 Å48.73 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX1.16_3549精密化
HKL-20002.3.12データスケーリング
PHASER2.8.1位相決定
PDB_EXTRACT3.22データ抽出
HKL-20002.3.12データ削減
精密化構造決定の手法: 分子置換
開始モデル: 6VG5

6vg5


解像度: 3.001→45.302 Å / SU ML: 0.35 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 21.37 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2246 1442 10.05 %Random
Rwork0.1858 12906 --
obs0.1896 14348 90.78 %-
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 max: 121.83 Å2 / Biso mean: 55.3994 Å2 / Biso min: 18.42 Å2
精密化ステップサイクル: final / 解像度: 3.001→45.302 Å
タンパク質核酸リガンド溶媒全体
原子数3592 0 98 11 3701
Biso mean--73.67 37.27 -
残基数----464
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A903X-RAY DIFFRACTION7.633TORSIONAL
12C903X-RAY DIFFRACTION7.633TORSIONAL
13E903X-RAY DIFFRACTION7.633TORSIONAL
21C891X-RAY DIFFRACTION7.633TORSIONAL
22D891X-RAY DIFFRACTION7.633TORSIONAL
23F891X-RAY DIFFRACTION7.633TORSIONAL
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0012-3.10840.2744740.2324656X-RAY DIFFRACTION47
3.1084-3.23290.32941000.2362895X-RAY DIFFRACTION64
3.2329-3.37990.26041520.21991352X-RAY DIFFRACTION95
3.3799-3.55810.28741570.22511400X-RAY DIFFRACTION100
3.5581-3.78090.22171600.18451407X-RAY DIFFRACTION100
3.7809-4.07260.20871590.17911415X-RAY DIFFRACTION100
4.0726-4.48220.20311620.15951434X-RAY DIFFRACTION100
4.4822-5.130.18411560.15831414X-RAY DIFFRACTION100
5.13-6.46020.22841620.20151441X-RAY DIFFRACTION100
6.4602-45.3020.211600.17461492X-RAY DIFFRACTION100
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)
10.14430.24430.04450.42860.08740.0246-0.00350.00620.00480.0048-0.0109-0.0129-0.02550.0006-0.00060.76260.0934-0.12910.8634-0.00510.940620.31275.5662.732
20.00010.0002-0.00040.0035-0.00090.0006-0.00740.01120.0136-0.0111-0.00950.0189-0.00560.0055-0.00010.4390.1603-0.0560.65150.03260.506517.90980.8631.763
30.0002-0.00190.00370.0106-0.01190.01420.0150.04310.010.0027-0.005-0.0011-0.0254-0.00320.00880.42790.3196-0.20260.3211-0.08090.545813.28589.384.311
40.023-0.0211-0.01170.02780.01230.02570.0287-0.0157-0.0207-0.0286-0.01130.00880.02330.0101-0.01340.41970.48990.06210.13330.14330.190715.8690.95713.339
50.01030.0079-0.0130.0279-0.02030.02040.00630.01310.0134-0.0148-0.0104-0.0613-0.04860.0301-0.01840.45820.25790.00720.0751-0.05770.233920.79299.15511.987
60.00590.00860.00910.0175-0.00940.0243-0.0185-0.1055-0.06570.0019-0.0423-0.0034-0.0030.05960.00040.45670.27530.05360.44060.10790.348316.02290.1822.26
70.00440.00880.00970.0320.03360.03940.034-0.0149-0.0642-0.0030.0118-0.0555-0.0325-0.0360.01320.22910.16250.01860.45090.12750.470135.21278.9421.125
80.0015-0.0004-0.00560.0020.00630.0224-0.0262-0.00520.0428-0.0002-0.0109-0.03260.0008-0.0027-0.00470.37870.16810.13950.3580.00910.460919.238104.3565.817
90.020.00540.01880.00430.01270.0294-0.03430.01190.02730.0151-0.00520.0151-0.05150.03840.00340.41930.22920.00960.15360.23460.380424.4595.2750.082
100.0301-0.0003-0.00760.00090.00010.0024-0.0182-0.03310.02390.0159-0.0032-0.0109-0.01460.04330.00460.43210.33780.05120.60530.21710.451233.07988.0763.974
110.0294-0.01420.01020.0185-0.00160.00540.01730.0146-0.0312-0.0572-0.0307-0.04730.01780.04120.01570.37390.37580.09860.01290.16090.161726.28182.97610.471
120.02510.02270.02710.0210.02270.02560.01850.0058-0.01410.01120.0192-0.0619-0.02530.0398-0.01430.36860.42760.03280.4815-0.12110.34437.98282.18310.574
13-0.00010.001400.00570.0030.0019-0.0111-0.02360.05890.0413-0.01330.0054-0.06430.030800.48440.165-0.03250.60220.04280.456731.75291.10621.745
140.00210.0018-0.00160.00460.00150.00290.0226-0.03190.02090.02480.0154-0.0511-0.0346-0.0112-00.53790.26880.00050.487-0.05430.262817.98597.72326.719
150.00460.00260.00160.0022-0.00080.0021-0.01690.0054-0.00740.00530.01640.00110.0064-0.00590.00010.87140.0466-0.0250.53870.08760.496619.579.341-6.834
160.0049-0.01230.00010.0351-0.01010.0051-0.0394-0.0099-0.03660.0113-0.0527-0.03390.00160.0176-0.06420.4810.39930.05530.3056-0.04970.40231.45781.109-9.845
170.00320.00220.00070.00110.00230.00280.08220.0024-0.00190.06410.0017-0.0463-0.04670.01670.00010.4530.1635-0.03660.5005-0.0830.277832.65583.558-18.703
180.00080.0018-0.00020.0025-0.00060.00380.05480.0038-0.0030.02480.0562-0.025-0.04270.045200.52140.02510.01510.56690.04680.522335.51192.654-18.215
190.00320.002-00.00170.00110.00090.02770.0136-0.01670.0203-0.036-0.0029-0.01970.0017-00.77060.09830.01621.0745-0.17190.924841.24682.975-23.399
200.00150.0025-0.00360.0068-0.00690.0014-0.01670.07510.0163-0.02230.01820.08430.00590.0366-0.00170.60530.2461-0.09150.5958-0.07590.311626.89282.955-30.148
210.0009-0.0001-0.00010.0003-0.00010.00220.0306-0.0307-0.00550.0182-0.0186-0.0112-0.01260.022100.48970.3037-0.00780.7874-0.02360.385510.85590.072-27.847
22-0.00020.00280.0005-0.0010.00130.0008-0.0076-0.00090.00780.03610.00330.0296-0.04960.0775-00.40870.07250.03480.3239-0.11470.454432.89892.725-8.154
230.0017-0.0025-0.0030.00180.0030.0033-0.0185-0.00760.0156-0.0142-0.0225-0.0292-0.01530.01400.7820.144-0.05690.75650.11110.419219.04395.535-10.552
240.0005-0.0004-0.00070.0021-0.00220.0047-0.0178-0.0387-0.0441-0.02-0.04780.0183-0.04390.0407-00.56070.28510.03370.58170.01550.459620.24289.766-17.264
250.00560.00220.00130.0034-0.00260.0048-0.0019-0.041-0.01620.0168-0.00510.0171-0.0253-0.0353-00.4784-0.10140.11680.6354-0.07850.48417.72483.63-14.702
260.00610.0059-0.0060.0082-0.00550.0276-0.0508-0.01810.0099-0.0024-0.01640.0458-0.00070.0058-0.00080.88060.3575-0.01670.67260.05470.617710.85995.932-17.721
270.0016-0.00060.0009-0.0005-0.00030.0058-0.0120.03860.02120.05170.0247-0.0256-0.0380.0105-00.54240.17-0.01330.4391-0.05070.365422.18395.699-27.967
280.004-0.00030.0025-0.0002-0.00050.0034-0.02920.0188-0.0001-0.0146-0.0233-0.01580.0098-0.0068-00.68580.23970.07770.8145-0.09110.452436.47388.865-33.05
290.03510.0303-0.05070.0262-0.04370.07450.0352-0.0190.0001-0.01510.04970.0064-0.0127-0.02920.0210.26920.24620.12540.55060.1530.455143.54962.2766.127
300.00190.00190.00030.00690.00160.0001-0.01790.0120.0142-0.0133-0.0173-0.01270.0021-0.0005-0.0150.23390.13860.17570.45440.00410.583846.42555.2627.8
310.02360.0220.00820.02870.00770.00080.0056-0.0098-0.01160.0490.05920.0311-0.01810.06650.06790.10940.4374-0.08660.2059-0.160.219243.16655.96416.205
32-0.0009-0.0113-0.00270.0243-0.00550.00190.0256-0.00270.00110.02370.0432-0.06650.11320.05610.03640.2350.427-0.04850.233-0.15860.380641.36448.73817.219
330.01160.0009-0.0160.00140.00080.0285-0.0058-0.05120.0313-0.0225-0.0740.1034-0.07390.0399-0.0430.15630.2428-0.00730.2736-0.02070.237140.09760.17927.469
340.0557-0.0322-0.03070.02840.01230.02010.02740.00080.0416-0.0255-0.011-0.0489-0.0229-0.02770.00080.36280.33640.11580.2362-0.02010.237924.73369.70324.459
350.00480.0007-0.00190.0054-0.00280.0017-0.0029-0.02560.0074-0.0235-0.0137-0.00080-0.0043-0.00790.38410.27250.0080.15360.0760.47539.24143.7648.312
360.0134-0.00740.00830.015-0.00250.0077-0.0043-0.0168-0.0398-0.0119-0.01040.01610.0168-0.04690.00530.16510.1435-0.00670.49560.02160.576134.10553.4673.337
370.00540.0051-0.00240.0215-0.00150.0099-0.0275-0.0118-0.0352-0.0164-0.03060.0572-0.0006-0.0015-0.02360.37960.35690.0070.4615-0.18130.154826.00360.9146.943
380.0109-0.0157-0.01660.02060.0210.02890.05340.027-0.00780.009-0.0506-0.0028-0.02750.02250.01270.36330.2797-0.05790.35750.07280.40432.94465.14913.381
390.00390.00110.00130.00180.00030.0002-0.0208-0.002-0.0019-0.0273-0.03130.0759-0.0245-0.0521-0.02590.19560.30410.04570.40620.05820.313420.5866.50714.061
400.02920.0181-0.01210.0114-0.01090.0108-0.0459-0.0343-0.0211-0.032-0.12390.0388-0.0901-0.078-0.0370.21380.16090.06160.26170.07090.211527.05357.18224.791
410.00880.005-0.00580.0067-0.0020.01490.0003-0.0087-0.0290.0163-0.0254-0.01430.03590.0179-0.00260.28730.34220.00110.29590.03230.401140.50348.88630.16
420.01410.0095-0.00210.02730.01270.0107-0.01720.01530.0025-0.008-0.0321-0.0129-0.0075-0.0219-0.02230.41230.11590.25040.4910.00240.388340.69569.185.201
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 23:25 )A23 - 25
2X-RAY DIFFRACTION2( CHAIN A AND RESID 26:30 )A26 - 30
3X-RAY DIFFRACTION3( CHAIN A AND RESID 31:39 )A31 - 39
4X-RAY DIFFRACTION4( CHAIN A AND RESID 40:54 )A40 - 54
5X-RAY DIFFRACTION5( CHAIN A AND RESID 55:66 )A55 - 66
6X-RAY DIFFRACTION6( CHAIN A AND RESID 67:89 )A67 - 89
7X-RAY DIFFRACTION7( CHAIN A AND RESID 90:99 )A90 - 99
8X-RAY DIFFRACTION8( CHAIN B AND RESID 21:27 )B21 - 27
9X-RAY DIFFRACTION9( CHAIN B AND RESID 28:36 )B28 - 36
10X-RAY DIFFRACTION10( CHAIN B AND RESID 37:45 )B37 - 45
11X-RAY DIFFRACTION11( CHAIN B AND RESID 46:64 )B46 - 64
12X-RAY DIFFRACTION12( CHAIN B AND RESID 65:76 )B65 - 76
13X-RAY DIFFRACTION13( CHAIN B AND RESID 77:89 )B77 - 89
14X-RAY DIFFRACTION14( CHAIN B AND RESID 90:98 )B90 - 98
15X-RAY DIFFRACTION15( CHAIN C AND RESID 23:28 )C23 - 28
16X-RAY DIFFRACTION16( CHAIN C AND RESID 29:39 )C29 - 39
17X-RAY DIFFRACTION17( CHAIN C AND RESID 40:54 )C40 - 54
18X-RAY DIFFRACTION18( CHAIN C AND RESID 55:66 )C55 - 66
19X-RAY DIFFRACTION19( CHAIN C AND RESID 67:73 )C67 - 73
20X-RAY DIFFRACTION20( CHAIN C AND RESID 74:89 )C74 - 89
21X-RAY DIFFRACTION21( CHAIN C AND RESID 90:98 )C90 - 98
22X-RAY DIFFRACTION22( CHAIN D AND RESID 22:36 )D22 - 36
23X-RAY DIFFRACTION23( CHAIN D AND RESID 37:45 )D37 - 45
24X-RAY DIFFRACTION24( CHAIN D AND RESID 46:55 )D46 - 55
25X-RAY DIFFRACTION25( CHAIN D AND RESID 56:65 )D56 - 65
26X-RAY DIFFRACTION26( CHAIN D AND RESID 66:76 )D66 - 76
27X-RAY DIFFRACTION27( CHAIN D AND RESID 77:89 )D77 - 89
28X-RAY DIFFRACTION28( CHAIN D AND RESID 90:99 )D90 - 99
29X-RAY DIFFRACTION29( CHAIN E AND RESID 29:33 )E29 - 33
30X-RAY DIFFRACTION30( CHAIN E AND RESID 34:39 )E34 - 39
31X-RAY DIFFRACTION31( CHAIN E AND RESID 40:54 )E40 - 54
32X-RAY DIFFRACTION32( CHAIN E AND RESID 55:73 )E55 - 73
33X-RAY DIFFRACTION33( CHAIN E AND RESID 74:89 )E74 - 89
34X-RAY DIFFRACTION34( CHAIN E AND RESID 90:98 )E90 - 98
35X-RAY DIFFRACTION35( CHAIN F AND RESID 21:27 )F21 - 27
36X-RAY DIFFRACTION36( CHAIN F AND RESID 28:36 )F28 - 36
37X-RAY DIFFRACTION37( CHAIN F AND RESID 37:45 )F37 - 45
38X-RAY DIFFRACTION38( CHAIN F AND RESID 46:65 )F46 - 65
39X-RAY DIFFRACTION39( CHAIN F AND RESID 66:76 )F66 - 76
40X-RAY DIFFRACTION40( CHAIN F AND RESID 77:89 )F77 - 89
41X-RAY DIFFRACTION41( CHAIN F AND RESID 90:99 )F90 - 99
42X-RAY DIFFRACTION42( CHAIN E AND RESID 23:28 )E23 - 28

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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る