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- PDB-7sts: Crystal Structure of Human Fab S24-1379 in the Complex with the N... -

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基本情報

登録情報
データベース: PDB / ID: 7sts
タイトルCrystal Structure of Human Fab S24-1379 in the Complex with the N-teminal Domain of Nucleocapsid Protein from SARS CoV-2
要素
  • Fab S24-1379, heavy chain
  • Fab S24-1379, light chain
  • Nucleoprotein
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / SARS Coronavirus 2 / Nucleocapsid protein / Human antibody Fab / COVID-19 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


cytoplasmic capsid assembly / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways ...cytoplasmic capsid assembly / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / VEGFR2 mediated vascular permeability / molecular condensate scaffold activity / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / MHC class I protein complex / Interleukin-1 signaling / RNA stem-loop binding / Interferon alpha/beta signaling / PIP3 activates AKT signaling / viral capsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell Golgi apparatus / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / Induction of Cell-Cell Fusion / Attachment and Entry / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / RNA binding / extracellular region / identical protein binding / cytoplasm
類似検索 - 分子機能
Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile.
類似検索 - ドメイン・相同性
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: 2.16 Å
データ登録者Kim, Y. / Maltseva, N. / Tesar, C. / Jedrzejczak, R. / Dugan, H. / Stamper, C. / Wilson, P. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
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: Iscience / 年: 2024
タイトル: Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies.
著者: Kim, Y. / Maltseva, N. / Tesar, C. / Jedrzejczak, R. / Endres, M. / Ma, H. / Dugan, H.L. / Stamper, C.T. / Chang, C. / Li, L. / Changrob, S. / Zheng, N.Y. / Huang, M. / Ramanathan, A. / ...著者: Kim, Y. / Maltseva, N. / Tesar, C. / Jedrzejczak, R. / Endres, M. / Ma, H. / Dugan, H.L. / Stamper, C.T. / Chang, C. / Li, L. / Changrob, S. / Zheng, N.Y. / Huang, M. / Ramanathan, A. / Wilson, P. / Michalska, K. / Joachimiak, A.
履歴
登録2021年11月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年8月10日Provider: repository / タイプ: Initial release
改定 2.02022年8月17日Group: Advisory / Atomic model / カテゴリ: atom_site / pdbx_unobs_or_zero_occ_residues / Item: _atom_site.occupancy
改定 2.12024年2月28日Group: Data collection / Database references
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 2.22024年4月3日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model

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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: Fab S24-1379, heavy chain
B: Fab S24-1379, light chain
C: Nucleoprotein
D: Nucleoprotein
H: Fab S24-1379, heavy chain
L: Fab S24-1379, light chain


分子量 (理論値)分子数
合計 (水以外)120,0926
ポリマ－120,0926
非ポリマー00
水1,62190
1
A: Fab S24-1379, heavy chain
B: Fab S24-1379, light chain
D: Nucleoprotein


分子量 (理論値)分子数
合計 (水以外)60,0463
ポリマ－60,0463
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Nucleoprotein
H: Fab S24-1379, heavy chain
L: Fab S24-1379, light chain


分子量 (理論値)分子数
合計 (水以外)60,0463
ポリマ－60,0463
非ポリマー00
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)99.084, 99.084, 221.890
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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要素

#1: 抗体 Fab S24-1379, heavy chain


分子量: 23269.016 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト)
#2: 抗体 Fab S24-1379, light chain


分子量: 22472.822 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト)
#3: タンパク質 Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


分子量: 14303.961 Da / 分子数: 2 / Fragment: N-terminal RNA binding domain, residues 47-173 / 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)
発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): Gold / 参照: UniProt: P0DTC9
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 90 / 由来タイプ: 天然 / 式: H2O

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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: 2.62 Å3/Da / 溶媒含有率: 53.02 %
結晶化温度: 289 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8
詳細: 0.2 M Calcium chloride, 0.1 M Tris pH 8.0, 20 % (w/v) PEG 6000

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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: 19-ID / 波長: 0.97918 Å
検出器タイプ: DECTRIS PILATUS3 X 6M / 検出器: PIXEL / 日付: 2021年4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: 0.97918 Å / 相対比: 1
反射解像度: 2.16→55.46 Å / Num. obs: 68533 / % possible obs: 100 % / 冗長度: 14.6 % / Biso Wilson estimate: 48.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 17.5
反射 シェル解像度: 2.16→2.2 Å / 冗長度: 8.3 % / Rmerge(I) obs: 2.21 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3330 / CC1/2: 0.334 / % possible all: 98.3

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19_4092精密化
HKL-3000データ削減
HKL-3000データスケーリング
xia2データ削減
HKL-3000位相決定
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: swisss model

解像度: 2.16→49.54 Å / 交差検証法: FREE R-VALUE / σ(F): 2.63 / 位相誤差: 23.4689
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2086 3543 5.18 %
Rwork0.1898 64814 -
obs0.1996 68357 99.76 %
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: 58.32 Å2
精密化ステップサイクル: LAST / 解像度: 2.16→49.54 Å
タンパク質核酸リガンド溶媒全体
原子数8133 0 0 90 8223
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00228373
X-RAY DIFFRACTIONf_angle_d0.526811436
X-RAY DIFFRACTIONf_chiral_restr0.04181269
X-RAY DIFFRACTIONf_plane_restr0.00481468
X-RAY DIFFRACTIONf_dihedral_angle_d14.00582994
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.20.26061850.27143149X-RAY DIFFRACTION93.22
2.2-2.240.3161660.26843167X-RAY DIFFRACTION94.2
2.24-2.280.3041810.28673196X-RAY DIFFRACTION94.28
2.28-2.330.31441910.27333164X-RAY DIFFRACTION94.22
2.33-2.380.28641570.28663246X-RAY DIFFRACTION95.3
2.38-2.430.2671720.27993195X-RAY DIFFRACTION94.47
2.43-2.490.32551830.27173186X-RAY DIFFRACTION94.18
2.49-2.560.28661740.26743208X-RAY DIFFRACTION94.58
2.56-2.640.34061460.25873229X-RAY DIFFRACTION95.56
2.64-2.720.22781490.25933248X-RAY DIFFRACTION95.53
2.72-2.820.29921870.24763248X-RAY DIFFRACTION94.34
2.82-2.930.24181750.23713198X-RAY DIFFRACTION94.73
2.93-3.060.22781870.23083248X-RAY DIFFRACTION94.47
3.06-3.230.26671610.21623250X-RAY DIFFRACTION95.25
3.23-3.430.20111810.21863250X-RAY DIFFRACTION94.7
3.43-3.690.2271790.21733285X-RAY DIFFRACTION94.83
3.69-4.060.24061880.18653234X-RAY DIFFRACTION94.51
4.06-4.650.18571710.15443311X-RAY DIFFRACTION94.98
4.65-5.860.14042040.13143321X-RAY DIFFRACTION94.21
5.86-49.540.20922000.17633487X-RAY DIFFRACTION94.47
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)
13.31990301704-1.84037121164-0.7887155964492.335925929010.05366873660481.450141909830.05278915477290.2546596193280.309993447914-0.3672337965220.10070883097-0.586662048023-0.504931469032-0.0712330261217-0.2829656256520.493494920280.08007106547680.132694074640.4822387502480.006222845356810.48986039933152.4804419705-42.793627039-26.984421194
23.87848409129-2.41013898904-0.006387312594122.93091532896-0.09132407389432.247895918410.3160808017630.740198140390.485345926412-0.4365015980580.0408147070938-0.357798954401-0.10621134294-0.0195979953565-0.3120638849960.394119990116-0.005016841774910.07975946352780.5011869923810.09725869530920.49438799020542.2021235419-39.1487022795-25.2380738746
34.33399107276-2.16534058178-0.5770705732235.03825536056-0.02999433088352.510595917260.1333895074-0.1298632141980.6855763110340.0006571719814980.0880541517071-0.559380476728-0.4351398184220.127225452788-0.3075141218370.272754104193-0.06403860316630.07078177599890.36670912644-0.02399905210980.5654653668744.4126227009-35.5839406241-17.3264269554
42.91944361957-1.52940676704-0.9644946673152.407761338350.1248512472940.4591962212160.181977269602-0.1581753859381.36346344204-0.1901820752550.173635181345-1.41449560254-0.5318893524910.48062688196-0.3298905623730.42340678920.04881392739120.08405752717170.530581208001-0.07513696926811.0338144195150.0606331236-31.2121266522-18.8610286234
53.26629904947-1.7857123088-1.864807783193.794431665390.1928775705631.308930637410.4770436696770.8307389821280.912971669947-0.62708215693-0.400565143732-0.0863604237636-0.1200049409830.0570205357092-0.2550595878010.5119910536320.1073142905820.2795681417480.4970096850250.2041736817570.79969137254945.6931161328-35.096928074-30.1384143771
62.61885737552-1.1746151614-0.2962420000483.297513706650.1772748962091.786436847250.2389965106980.6102250971730.405938503805-0.179161852822-0.0393628758146-0.4216347243550.007844548965090.144625784348-0.2676256446320.323996129415-0.0325331648140.06562762644310.3151884210330.06340608761010.42682587439943.7889054627-42.3207583863-19.7511349188
72.68384574761-1.94795660466-0.8766924634231.971879593350.1129930514280.9200615878710.1727766777690.01411787903370.3920975650250.0588768167338-0.144034634889-0.244827718151-0.309797601260.795139289317-0.3688787055390.333620030450.0752617554930.03424311691820.622756550919-0.04040494463390.58995185787163.513082477-48.7152731766-25.4290031252
83.67379961661-0.691876338137-1.212688725313.14187589815-0.4211605342551.094231090370.01795447841660.522217070921-0.383872101783-0.4750581044750.0427186537714-0.4152366725240.4806674866510.267790892036-0.1513771790730.5532133178160.0245030733377-0.2226658656670.5037413459580.08559226794050.6479441915661.9691409554-70.0143941299-28.4987141745
92.73091972388-1.316625901890.5231196396280.735133288549-0.7358764518424.675582876840.157934086634-0.1856542286520.146478480509-0.600277780514-0.09687369250420.817382175240.87403563557-0.219731213703-0.2454962949740.471658846492-0.0691735625666-0.2236403953560.5201110401520.1187943496640.9332743490753.1390077281-63.6593323356-28.9152195278
101.965119634190.6069457091580.25624288331.11387789683-0.6793267994762.65682974634-0.0739651985999-0.5759280431230.475355767699-0.2584726006390.07160798622130.108191404364-0.008829553958380.130231781535-0.1913741578230.280356737706-0.00482616091975-0.02056226174570.584087486816-0.0679205335450.88532681318965.2934177887-59.7935443016-19.3250011853
112.75449518232-1.61633367404-1.930167398153.42104991788-1.808361369864.839814907960.3318126317540.0798428291801-0.350365103844-0.6855933010860.1601798921130.371753227231.51850185945-0.759653945983-0.4331487952160.774049723087-0.167279820148-0.386745920550.5731913747980.1817013339210.74281134560456.4232835593-67.7251037261-30.0085352319
124.81062282024-0.9519515202921.100065768410.795298052235-1.980399355635.586347732910.2162348993880.542911068107-0.0412383898476-1.63869487874-0.04871668622211.335097007190.652946443924-0.321008912003-0.5978219503990.603105301822-0.132734896346-0.09355552657930.6905793409750.1637369917260.58558262334960.7953719367-64.874325097-36.1622882715
132.22961954123-2.968139798060.3106290458715.251595165460.1998951817644.26768706105-0.451081359623-0.1791746226210.08124384541510.5781867653820.716621931943-0.293821526370.4772572955740.471700232667-0.2085806139820.3913714107480.1205946115230.01461571307360.5703708969450.01936262669030.3723260280339.0236818463-52.48013443140.211554689754
143.01018835847-1.23963702265-0.4260204800350.8085031401380.6959833419321.14320153819-0.191171999766-0.183834143653-0.2979934266020.1220320353780.2474992224840.1494944166830.1287118737790.0874305357492-0.05585656305290.301159007611-0.0120480381753-0.02023036201990.3582331169360.04054010151390.41400947344137.6232589145-51.3317880905-8.23709992717
152.450909131570.349570340033-1.760545078952.41686960613-0.8066069563984.628213067-0.202545030225-0.0851554150832-0.1230585309170.33735938805-0.137418643223-0.300572851054-0.313739257628-0.2507034896490.3034318610950.5228212249740.124066255909-0.1544747465260.548629042932-0.06039509109940.68133868636765.4197589667-73.8746645989-16.3925602437
164.69991230769-6.17450933575-1.064834562079.200820438861.705040848433.6751631267-0.624437098114-0.169449164260.9740047858110.1072204494730.124501687412-0.417127075751-0.575560150635-0.0319413955290.4109764601310.34130329619-0.0671469381846-0.09903204132360.382142740313-0.09312442409550.80660385490126.7977438828-14.732335579212.4763026682
170.05660786520310.2792339137180.2037453280782.702856191113.37860702325.06989117771-0.304396843486-0.6955377701520.628870919880.666123462765-0.3835164134820.8356359800060.122654546671-0.949764286220.6475127221450.5349626049390.234846453017-0.1724666699440.663115478162-0.2578327876430.8811969475712.3569983573-13.491473657515.3612500998
184.032589533290.443043163837-1.89071616372.426063925360.4091501715131.44348485212-0.246978267651-0.3245065817570.0996461366281-0.0288104725027-0.1803494168650.133413490635-0.1424316108050.01434245422040.296092433790.3394269764660.0445768203023-0.07525670285750.389210393459-0.04694601062870.68120694318623.4730990992-21.109561457212.2224337547
193.59352569443-2.718798875843.286602524412.57276072295-3.717337980495.922613781170.0687865593062-0.48506163421-0.2262849287980.6095196968980.150992006380.459519643957-0.177712973432-0.590300279306-0.07712417432480.463596631247-0.04605342666170.07425067159130.490329168823-0.01350490966280.67369101205318.3877100589-24.78198957220.8815768721
201.964107250581.548870686821.163254013265.32617261333-0.8210829410535.61720049919-0.289055996834-0.209893556411-0.7248751268550.08686432141520.9123446286410.5609664978450.189224799952-0.696227919662-0.5528707881940.5044785562950.00826951495594-0.08357390086740.361414615360.08760589846510.79592433337821.4303579137-32.643304254310.6074340264
213.189456096021.048292632430.4985196576941.74120984927-1.147065933741.28810950024-0.144250888270.2455057245060.01855115896590.1132396450060.0188217463450.524593251971-0.218398098851-0.07561850901490.006778468859660.3489717599120.01701106997580.002746348084480.312643920599-0.1216670079760.76990899152424.9627928678-15.90851648248.32404511642
223.10320021469-0.3536507750570.1902512621052.577568313150.4740563585833.888727098160.3733300608740.01255472694450.824834755612-0.235960653885-0.292431443791-0.393036369455-0.130556307995-0.1676033360430.02847905059110.429840108862-0.00250654375420.183013226380.3375127359720.02052353710650.75254076022122.0813640778-16.4108379902-13.3116854766
230.05344171612890.08721368352970.1320907547080.2903983755730.5621827645391.1196780744-0.050672764930.42275944657-0.606882176233-0.7871367269010.09757956261640.4655823616940.1190518248970.229444659729-0.4369041643321.040919913860.202426786676-0.140737936860.846149423237-0.01101856390720.7147195880548.04885924489-31.800472029-27.0031549337
240.583671461933-0.562065243596-0.2548821048411.2124760078-0.3588264979840.7197789827870.360222121299-0.05152527560950.822217237991-0.316541618003-0.0925004293415-0.875670481984-0.325130771953-0.0272033617658-0.2580671230470.510475393388-0.03256716553520.2232441567830.3927900625460.06730333011820.89122901412425.1670326567-17.135821019-15.0619341904
252.623264730510.554056034082-1.119905776065.41794314582.459117624763.649131407390.241789543724-0.3245557000790.006932521577841.35789748531-0.101838798451-1.562563217630.5120201808290.0454211986887-0.1039149990510.357538635202-0.0179140671185-0.1026984205810.3700226675660.05875147639950.44381044685158.6075833624-32.459908710125.8642679809
261.352521552650.180007864653-0.4320747292152.59981367310.1459221327562.068198928190.0559232960635-0.128141750794-0.2187381602310.08843233749140.0009868027635990.5422210913140.00342799243371-0.0346278335779-0.06518633628480.360681948166-0.00717578113546-0.05049116820680.2848714650290.07036906851480.52287513488449.4402509337-27.032109067120.2343168331
272.25542161886-0.4936009772810.09083443969592.23828544954-0.3466503826521.134125828880.01407371764280.0103987834681-0.1232616234130.1683234061380.07470760718210.184708270961-0.01167136665820.029370874773-0.1008891961880.322382450028-0.024932582492-0.02775452477810.2987832743840.05990644059790.51856217827351.3336650465-29.066672916820.2467175464
282.962669700420.4012565225210.2468503013280.306328499227-0.2279333438110.6114384131370.024079908213-0.1468278737960.167859914043-0.08737494086770.0496066056796-0.09215636567190.07414388681160.0843878969047-0.07889414899850.38979130230.0459875611847-0.003973498345150.364474061945-0.01546355864170.47963346073279.0162773039-28.741919108825.8459478064
290.772832733291-1.14228366402-0.5558804543862.045058261240.54788935363.63213281120.215831105687-0.6585157403620.631108826717-0.0398367682414-0.269937382152-0.588807891043-0.6039214485160.07167873390990.01655495138630.443569536455-0.009309033399270.001926778009080.439112896014-0.1537931845150.7158738295485.2485972457-19.975940582130.9777935935
305.527725588792.593773858360.0248428009483.16631065653-0.1018244526591.90203833016-0.242546179361-0.627904949293-0.07958517855920.1601238453550.446344546161-0.622234935102-0.169364813453-0.169562783181-0.2881458903090.4873579454750.0371898904930.03058032188670.560453227584-0.06202739821160.73314267213581.7085482709-27.655532635735.3328108483
313.22347257846-0.849471587515-0.9154586138823.13457223654-0.3653165309413.76712637974-0.02120860694530.192598160831-0.0834235494651-0.657497854815-0.1551763518560.4200617541620.1224395384860.168865535860.09233897110060.4246355668070.04585315590790.02577696327450.323702003376-0.01398755891190.42374842998360.9283367176-14.6888350416-0.436509889299
322.22518900371-0.213349887554-0.2186489318991.088771403820.5350307233391.253939097050.111388238025-0.0144648516154-0.0774567881729-0.105112425629-0.02849149973810.0201135832969-0.03125323848120.0863198379959-0.09437771708650.334466601735-0.009680365210940.0002538819763670.2799064493650.0224134547280.43558520986753.8452744164-14.1859957177.60629110776
332.04201333551-0.135010186655-0.1493772641540.907510283791-0.377517804780.3605716219140.07102665413330.1279584058470.13946580706-0.0372932887138-0.0849019420859-0.0253362866296-0.02696274349790.3459699487060.03804942421570.3513733152210.014422962477-0.01857426525420.388948445485-0.1320447011320.56135220421486.9770611049-22.921377019115.4471845383
341.368022013190.791394381485-0.5602709021090.7132111787310.1080366640141.806995594470.05629245402590.128929302578-0.339593445186-0.182115314597-0.11158234966-0.00669099584010.3263887614530.1282631464760.002965521050640.3627814081440.005538888124250.0004275453356610.342140591985-0.0647260324170.53821652194689.8572678475-28.798818446415.750980212
351.283719300371.145770814130.2624655447891.49473920788-1.230216929174.61145268592-0.2474253447831.080264027370.00298539619789-0.202503659407-0.318090951121-0.8209205645020.1356910268741.103156400660.4781401551320.415509973214-0.04376586017910.07761020538430.607490198019-0.1682698498410.81124183997498.3258184968-24.615764311812.8215578859
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 17 )AA1 - 171 - 17
22chain 'A' and (resid 18 through 39 )AA18 - 3918 - 39
33chain 'A' and (resid 40 through 59 )AA40 - 5940 - 59
44chain 'A' and (resid 60 through 72 )AA60 - 7260 - 72
55chain 'A' and (resid 73 through 82 )AA73 - 8273 - 82
66chain 'A' and (resid 83 through 110 )AA83 - 11083 - 110
77chain 'A' and (resid 111 through 123 )AA111 - 123111 - 123
88chain 'A' and (resid 124 through 149 )AA124 - 149124 - 142
99chain 'A' and (resid 150 through 169 )AA150 - 169143 - 162
1010chain 'A' and (resid 170 through 179 )AA170 - 179163 - 172
1111chain 'A' and (resid 180 through 204 )AA180 - 204173 - 190
1212chain 'A' and (resid 205 through 218 )AA205 - 218191 - 204
1313chain 'B' and (resid 1 through 23 )BB1 - 231 - 23
1414chain 'B' and (resid 24 through 122 )BB24 - 12224 - 122
1515chain 'B' and (resid 123 through 212 )BB123 - 212123 - 212
1616chain 'C' and (resid 4 through 13 )CC4 - 131 - 10
1717chain 'C' and (resid 14 through 23 )CC14 - 2311 - 20
1818chain 'C' and (resid 24 through 72 )CC24 - 7221 - 55
1919chain 'C' and (resid 73 through 89 )CC73 - 8956 - 72
2020chain 'C' and (resid 90 through 99 )CC90 - 9973 - 82
2121chain 'C' and (resid 100 through 128 )CC100 - 12883 - 111
2222chain 'D' and (resid 4 through 45 )DD4 - 451 - 42
2323chain 'D' and (resid 46 through 61 )DD46 - 6143 - 58
2424chain 'D' and (resid 62 through 128 )DD62 - 12859 - 125
2525chain 'H' and (resid 1 through 17 )HE1 - 171 - 17
2626chain 'H' and (resid 18 through 59 )HE18 - 5918 - 59
2727chain 'H' and (resid 60 through 110 )HE60 - 11060 - 110
2828chain 'H' and (resid 111 through 179 )HE111 - 179111 - 171
2929chain 'H' and (resid 180 through 204 )HE180 - 204172 - 196
3030chain 'H' and (resid 205 through 218 )HE205 - 218197 - 210
3131chain 'L' and (resid 1 through 23 )LF1 - 231 - 23
3232chain 'L' and (resid 24 through 101 )LF24 - 10124 - 101
3333chain 'L' and (resid 102 through 154 )LF102 - 154102 - 154
3434chain 'L' and (resid 155 through 191 )LF155 - 191155 - 191
3535chain 'L' and (resid 192 through 212 )LF192 - 212192 - 212

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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