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- PDB-7uvq: Pfs230 domain 1 bound by RUPA-97 and 15C5 Fabs -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 7uvq
タイトルPfs230 domain 1 bound by RUPA-97 and 15C5 Fabs
要素
  • (Fab Heavy Chain) x 2
  • (Fab Kappa Light Chain) x 2
  • Gametocyte surface protein P230
キーワードCELL INVASION/IMMUNE SYSTEM / Antibody-fragment / malaria transmission / CELL INVASION / CELL INVASION-IMMUNE SYSTEM complex
機能・相同性6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain / cell surface / plasma membrane / Gametocyte surface protein P230
機能・相同性情報
生物種Plasmodium falciparum (マラリア病原虫)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.29 Å
データ登録者Ivanochko, D. / Julien, J.P.
資金援助 カナダ, 米国, 4件
組織認可番号国
Canadian Institutes of Health Research (CIHR)428410 カナダ
Ontario Early Researcher Awards カナダ
Bill & Melinda Gates FoundationOPP1170236 米国
Canada Research Chairs カナダ
引用ジャーナル: Immunity / 年: 2023
タイトル: Potent transmission-blocking monoclonal antibodies from naturally exposed individuals target a conserved epitope on Plasmodium falciparum Pfs230.
著者: Ivanochko, D. / Fabra-Garcia, A. / Teelen, K. / van de Vegte-Bolmer, M. / van Gemert, G.J. / Newton, J. / Semesi, A. / de Bruijni, M. / Bolscher, J. / Ramjith, J. / Szabat, M. / Vogt, S. / ...著者: Ivanochko, D. / Fabra-Garcia, A. / Teelen, K. / van de Vegte-Bolmer, M. / van Gemert, G.J. / Newton, J. / Semesi, A. / de Bruijni, M. / Bolscher, J. / Ramjith, J. / Szabat, M. / Vogt, S. / Kraft, L. / Duncan, S. / Lee, S.M. / Kamya, M.R. / Feeney, M.E. / Jagannathan, P. / Greenhouse, B. / Sauerwein, R.W. / Richter King, C. / MacGill, R.S. / Bousema, T. / Jore, M.M. / Julien, J.P.
履歴
登録2022年5月2日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年2月15日Provider: repository / タイプ: Initial release
改定 1.12023年8月30日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _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
改定 1.22023年10月25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: Gametocyte surface protein P230
B: Fab Kappa Light Chain
C: Fab Heavy Chain
D: Fab Heavy Chain
E: Fab Kappa Light Chain


分子量 (理論値)分子数
合計 (水以外)117,6325
ポリマ－117,6325
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)155.000, 155.000, 92.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22

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
111ALAALAGLNGLN(chain 'B' and (resid 111 through 125 or resid 127...BB111 - 124110 - 123
121SERSERTYRTYR(chain 'B' and (resid 111 through 125 or resid 127...BB127 - 140126 - 139
131ALAALATHRTHR(chain 'B' and (resid 111 through 125 or resid 127...BB144 - 164143 - 163
141ASPASPASPASP(chain 'B' and (resid 111 through 125 or resid 127...BB167166
151ASPASPTYRTYR(chain 'B' and (resid 111 through 125 or resid 127...BB170 - 186169 - 185
161VALVALARGARG(chain 'B' and (resid 111 through 125 or resid 127...BB191 - 211190 - 210
211ALAALAGLNGLN(chain 'E' and (resid 111 through 125 or resid 127...EE111 - 124112 - 125
221SERSERTYRTYR(chain 'E' and (resid 111 through 125 or resid 127...EE127 - 140128 - 141
231ALAALATHRTHR(chain 'E' and (resid 111 through 125 or resid 127...EE144 - 164145 - 165
241ASPASPASPASP(chain 'E' and (resid 111 through 125 or resid 127...EE167168
251ASPASPTYRTYR(chain 'E' and (resid 111 through 125 or resid 127...EE170 - 186171 - 187
261VALVALARGARG(chain 'E' and (resid 111 through 125 or resid 127...EE191 - 211192 - 212
112VALVALPROPRO(chain 'C' and (resid 109 through 127 or resid 134...CC109 - 126114 - 131
122GLYGLYSERSER(chain 'C' and (resid 109 through 127 or resid 134...CC134 - 161139 - 166
132HISHISSERSER(chain 'C' and (resid 109 through 127 or resid 134...CC164 - 188169 - 193
142TYRTYRASNASN(chain 'C' and (resid 109 through 127 or resid 134...CC194 - 199199 - 204
152PROPROASNASN(chain 'C' and (resid 109 through 127 or resid 134...CC202 - 204207 - 209
162VALVALLYSLYS(chain 'C' and (resid 109 through 127 or resid 134...CC207 - 214212 - 219
212VALVALPROPRO(chain 'D' and (resid 109 through 127 or resid 134...DD109 - 126120 - 137
222GLYGLYSERSER(chain 'D' and (resid 109 through 127 or resid 134...DD134 - 161145 - 172
232HISHISSERSER(chain 'D' and (resid 109 through 127 or resid 134...DD164 - 188175 - 199
242TYRTYRASNASN(chain 'D' and (resid 109 through 127 or resid 134...DD194 - 199205 - 210
252PROPROASNASN(chain 'D' and (resid 109 through 127 or resid 134...DD202 - 204213 - 215
262VALVALLYSLYS(chain 'D' and (resid 109 through 127 or resid 134...DD207 - 214218 - 225

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質 Gametocyte surface protein P230


分子量: 22694.705 Da / 分子数: 1 / 断片: domain 1 / 由来タイプ: 組換発現
由来: (組換発現) Plasmodium falciparum (マラリア病原虫)
遺伝子: PFS230, PF230, S230, PF3D7_0209000 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P68874
#2: 抗体 Fab Kappa Light Chain


分子量: 23192.758 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 Fab Heavy Chain


分子量: 24158.791 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#4: 抗体 Fab Heavy Chain


分子量: 24074.934 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#5: 抗体 Fab Kappa Light Chain


分子量: 23511.209 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)

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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: 2.74 Å3/Da / 溶媒含有率: 55.09 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.2 M di-ammonium hydrogen citrate, 17.5 %(w/v) polyethylene glycol 3350

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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-D / 波長: 1.03319 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2021年6月19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: 1.03319 Å / 相対比: 1
反射解像度: 3.29→29.76 Å / Num. obs: 19432 / % possible obs: 99.9 % / 冗長度: 16.7 % / Biso Wilson estimate: 128.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.037 / Rrim(I) all: 0.152 / Net I/σ(I): 14.5
反射 シェル解像度: 3.29→3.55 Å / Rmerge(I) obs: 1.565 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3974 / CC1/2: 0.778 / Rpim(I) all: 0.39 / Rrim(I) all: 1.613

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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
Aimless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: 6OHG

6ohg


解像度: 3.29→29.76 Å / SU ML: 0.5063 / 交差検証法: FREE R-VALUE / σ(F): 1.37 / 位相誤差: 30.9346
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2635 987 5.09 %
Rwork0.2154 18420 -
obs0.2178 19407 99.97 %
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: 150.73 Å2
精密化ステップサイクル: LAST / 解像度: 3.29→29.76 Å
タンパク質核酸リガンド溶媒全体
原子数8062 0 0 0 8062
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01358255
X-RAY DIFFRACTIONf_angle_d1.63111236
X-RAY DIFFRACTIONf_chiral_restr0.08291263
X-RAY DIFFRACTIONf_plane_restr0.01221433
X-RAY DIFFRACTIONf_dihedral_angle_d12.04841127
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.460.37661420.33032608X-RAY DIFFRACTION100
3.46-3.680.28641370.29752612X-RAY DIFFRACTION100
3.68-3.960.33931390.28642616X-RAY DIFFRACTION100
3.96-4.360.27751450.21642615X-RAY DIFFRACTION100
4.36-4.990.23871380.18842637X-RAY DIFFRACTION100
4.99-6.270.26461430.21342642X-RAY DIFFRACTION100
6.28-29.760.23591430.18642690X-RAY DIFFRACTION99.79
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)
16.595515205230.274623851799-0.7571142497291.627544348251.442144407332.954040158260.621161361106-0.0439948721606-1.747187807670.180719224744-0.4887330741780.1007952837910.9668650617160.2182319015520.06737480341181.246738611550.05659101119870.1515879776880.996610266856-0.01112258914521.3028455822270.205295773-72.17611876536.947579363
27.446703249622.178005429982.691949163511.95299486307-1.56027534376.73370711237-0.7146505813410.6464102954692.736494356780.136881284979-0.131784272433-0.957210041362-2.031100627780.9518423217880.7287121856561.0097243439-0.191917387375-0.2081019097630.706501976443-0.00184800743281.2048076665869.7532826869-50.350573360937.219665151
36.782129382211.23208460761-3.431893476046.156811941621.329445391727.59763975779-0.7578737774990.705817000223-0.7286180898480.2931281966580.1287211134570.283818370816-0.01105976773531.330069310790.5019773817210.97045261304-0.278654927620.05448713022611.27033321018-0.03681885885181.1379940339483.7181203583-64.797654449732.1846605816
49.71083584151-3.51717283463-3.234732002316.072369676321.760734336294.140194250950.2673319854070.347877430939-0.404089302139-0.473468177819-0.1573074643120.340303760705-0.4055839649880.616383094026-0.1718229680010.854081592196-0.1538202286710.01504921526040.874156162666-0.08801937836640.70467733774871.5420011146-58.261240895232.5707413186
53.82924753174-3.023342359260.4665696600214.722281318560.8007839409261.628733579160.0402357798921.24448489911-3.05281198343-1.07065777049-0.211664788839-0.4278629672620.0402878352138-0.622569374856-0.007755855310711.03879815721-0.2186615368080.01777626054651.17359923351-0.2959171812581.0922426437671.8139203712-68.180881526724.2749701822
68.60773030614-5.9092328028-1.347105162489.46804272678-0.7377260575854.035352473810.240536427710.47281092603-0.8422126623230.625560159744-1.035955204931.22583301875-0.2832645003860.471859893380.7910415584650.834896138335-0.356377999231-0.1379272810130.971644778561-0.05509444068960.99996212833657.932040252-65.304038915833.3772867883
77.3991975334-4.40408704071-0.7192119135597.489206937723.268890210277.16829000162-0.4241203948850.739514452155-0.28644426329-0.2238665159850.022753772741-0.1392688821170.4766187661940.1670095655720.2195932826630.682930444111-0.17258373240.05524426286170.684370976506-0.07756917519120.73863435970966.8143056048-61.661609010233.5029325112
84.579387672180.2170616576793.256650564471.385263504542.250256816177.65238474214-0.2496472190270.08665780367590.624028507868-0.4749614944171.07728775995-0.617632078969-1.613131915370.158167886643-1.183882576091.67982775941-0.187640721273-0.2519996022071.038026620980.2115416904182.2076565241942.2597613784-27.328905728430.0666000359
92.06134774451-0.998444425844-0.134573644436.33911462693-0.296212580774.672477612790.08157177738680.6767803348560.646876970301-0.2666518348680.175972685379-0.124091455271-0.460563747275-0.570780865416-0.5000712981520.948971529097-0.0818738482381-0.07322429125151.192411157230.4407435807891.5592368006243.7077944292-39.020385143328.1400652062
102.132590674440.540577822292-2.357786146893.74226431255-0.004254460778077.23934876071-0.1911277667040.7538479131341.91349269315-1.05305022249-0.102961939991.906112758610.0660900841318-0.9419101608360.3259336583471.27257400198-0.293882890676-0.4539808453561.114665761920.2233543593272.3017099932443.908276834-33.901207856426.0846912061
114.39600875159-2.18907071561-1.072427461183.42133560051-1.047061752063.089275468820.419250740483-0.2904508196790.20732364077-0.9508465288770.5756169846210.409455904988-0.641104042751-0.993743536876-0.5861167378121.48163767192-0.15215134646-0.2834721944480.849358367463-0.03767726827841.8193841730737.4673365821-31.007887998630.7135759445
123.993560467521.855919880171.132674585014.81109159968-0.303669240790.134674451871.4933250596-3.872453188731.1762168052-0.664180164708-0.1006998472611.581727452890.2764425162471.363047708390.1647876615391.31975723450.2475702309360.3435317104672.496643874220.7622233142082.748444551162.02105821656-20.444245811733.4129250792
132.273084014863.115608272841.151254916830.8506591326011.693443727175.620214696410.703942277422-0.9841613097340.5368026612740.4396206873161.282145586941.490118307240.862810375806-0.621504378547-1.390619911241.375294812760.5917921300610.2554116536371.841682750620.6540041921033.1051827552610.2038116564-19.786879142332.7707602051
145.37549555922-0.7844425726452.905967705093.275831804491.752430159726.67157380814-0.614421398511-0.5629116366580.6022561217270.4698733670441.062929979921.09610453128-1.41852668059-0.991455280463-0.7997911337781.388903647950.1385818152160.5178201494711.548551805190.11460131193.0399750452916.304255807-12.865364893337.1533340715
154.74958795317-2.482984076651.873862360912.536643838771.615821103262.294058473220.67243715065-0.354655701630.278842297635-1.431818348381.342217817251.207797890150.158736148809-0.854590307405-0.007246286959471.91022077342-0.05293904166160.1850507093671.409754902850.4353099401062.6640574851620.5365701467-24.081660028926.747208762
163.32732248506-2.99652827047-1.845969979212.382643489561.573361479230.7971737044490.232350622226-1.348139884660.7585862164220.7012664842270.7277067328883.69556557464-1.315374322430.534213256690.1001529926291.498057101730.2889883758260.5605968379343.202740154670.2045670948294.4702738593-0.0172857471858-13.443713209344.3707945195
170.1157073247740.588953254660.6139671253171.275583087092.689464625034.322392443081.22963652934-1.77898914550.117517825705-0.675396535382-1.734349880151.33180475008-0.0992302323555-1.4155239406-0.198363705791.640319057330.1399870117080.1964097284642.357469158420.4579078727513.711456214389.46463731477-9.0306605831630.3726817975
186.94834484940.2449006255650.6117049861927.845543971690.9552253283727.703793984150.16071677022-0.7084571768140.913433782634-0.0261865917843-0.1267317544610.690040905564-0.231151928872-0.2772795474330.06217657891460.687811156895-0.1326184939110.01407275264520.719253045961-0.1164253992751.2569135955733.0716628969-50.590491106741.6819192406
194.49868367053-5.703489568012.113008923541.13087376835-1.274527174994.952811973490.234610634694-0.620808487530.544955970917-0.6431466168761.249461048060.666028864758-0.184611805045-1.64898481151-1.46568555791.50625323713-0.34092707673-0.1656763361221.847324894250.2065382929482.645807669637.74122441087-30.603994360131.5677391201
209.95741267029-0.1361688187650.3843610959546.88685731720.4269411753057.91619428535-0.0702817515086-0.8976152760710.2610627976421.141361604570.211432671761-0.672478967090.5350539100650.0913056399306-0.1379778023730.8844289533640.0172156635093-0.09239720205070.711837541690.006138055901190.55602013432690.0463962913-50.664447903653.6306585407
213.58141007072.41519957426-0.2718565964458.975239175622.499803282386.160375057050.308754794856-0.515591883132-0.8544209374291.331656324950.01695284034770.06301167125940.9068341833840.424293705601-0.392383876610.964440660006-0.034515015799-0.06050111769860.8308823843140.08321633087890.58966676313791.2406435154-55.478825626255.1589858477
229.3347101562.056996125573.158150485744.794110699792.490615504544.25437104414-0.0273463182927-0.4281468245940.06454094947590.5177671282140.348307039853-1.359979739760.206758410940.691036190329-0.3882166096191.101787635110.15150921908-0.0222840987311.019735318360.005092762287460.913826518345106.392025437-44.94585920952.124866946
237.46675217385-0.176288222591.880497160186.01206673421-1.396979635833.9411210546-0.0977142139052-0.545504017575-0.1977617134690.8737799988820.925562995631-2.109298742320.003767118745180.540387156032-0.7881747895771.112109098470.157343048718-0.2789986987711.49728540644-0.5669877674391.82374707716122.125955666-38.680806482159.8016389581
244.925565282970.4457509454931.343224092383.052847223794.289055036175.709160064850.2270884614270.2678445279240.972947206223-0.1735734587820.724525658816-0.727318286927-1.067084714711.80653000365-0.8884571277790.967945539743-0.1570695618390.271007571181.79706228088-0.2336873877281.18604266517103.46369641-44.404211031930.4136624801
256.66185601601-0.357088483194-2.338443927935.390714013071.544736401128.70657195562-0.204273222290.9288679499680.483177281739-1.562020245030.302857776256-0.661981255491-1.278369212520.514598925852-0.08312832358461.26581770344-0.4231300819570.1698385157181.237420522230.1062790245530.81735454123793.41993322-42.365621055633.358209191
268.078054652962.69846320627-1.164353879373.35848382669-2.173702568842.024673822740.174340680832-0.3626941671860.3814902455190.0343202699559-0.0717759518642-0.496747792574-0.8835534283230.646631956219-0.2172620739871.30784443346-0.2295194109750.2178312690941.35274336272-0.1697983492640.688903472305102.088304288-42.577150012836.1854526037
276.61805375516-2.322557639022.265256241915.20687411109-1.405246665610.726344663880.565158085411-0.719815683480.9101006207242.101181170860.799670606189-0.502042361181-0.335246438131-1.41959824908-0.1841862978781.454526157890.0641040804772-0.597431758991.9861417221-0.2361737073931.97913077694133.534134046-44.329172273357.5853440269
287.60254649672-0.962971930799-0.398204146446.32071548166-1.118890664140.424058802224-0.610984131725-1.442728254041.300313724720.5031295535030.66166664715-2.19216794861-0.286316927946-1.32506146823-0.2688323023941.32760422806-0.1993715923420.2236858576911.92211120343-0.5261259536821.86663665708127.927002987-42.46250565348.4428823969
293.624092994333.13701444221-1.414374502063.10367928290.109678918464.53292300619-1.31848375951.08613330551-3.56191178414-1.843402377692.40682863651-0.8855095614910.9829923345191.41788152263-1.117062699291.79277151545-0.1436291044590.3128693996332.47284174977-0.9493155443131.68333208804127.177976133-45.966618116839.3775366807
303.388395751231.85243397256-1.85644918251.09318544194-0.8332043690582.39391884493-0.7776913644540.2545702512190.0364363547271.302191616651.63266370353-2.184507816380.6388582780690.556948802395-0.4963849877351.34209125230.0721608978985-0.3418777721281.94157737067-0.7879334909382.20256003123123.99072865-44.38337486544.0298425739
314.31495435808-2.97965697111-2.513920739252.51462059650.647302356390.8585300435651.948869274872.12135897242-1.25170066366-0.727062037341-0.856984478522-0.5070009462731.621971111.95845017456-0.8203914684051.317507518380.19612946346-0.3542134350571.82381356942-0.5177799636482.45696679629134.194832464-49.87748814350.0822247104
322.30930395765-4.503726413662.693729227199.49550078942-3.733669874247.05103261613-1.14877274443-0.178224630293-0.369813999720.0903861316276-0.144382688078-1.872391460040.7368533062791.451316858671.29899090221.400372063470.1350622462680.557058278482.37580604515-0.4010858319642.29290197008137.555523022-42.011344080543.3987394257
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 561 through 583 )
2X-RAY DIFFRACTION2chain 'A' and (resid 584 through 594 )
3X-RAY DIFFRACTION3chain 'A' and (resid 595 through 607 )
4X-RAY DIFFRACTION4chain 'A' and (resid 608 through 635 )
5X-RAY DIFFRACTION5chain 'A' and (resid 636 through 645 )
6X-RAY DIFFRACTION6chain 'A' and (resid 646 through 676 )
7X-RAY DIFFRACTION7chain 'A' and (resid 677 through 734 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 18 )
9X-RAY DIFFRACTION9chain 'B' and (resid 19 through 61 )
10X-RAY DIFFRACTION10chain 'B' and (resid 62 through 90 )
11X-RAY DIFFRACTION11chain 'B' and (resid 91 through 113 )
12X-RAY DIFFRACTION12chain 'B' and (resid 114 through 126 )
13X-RAY DIFFRACTION13chain 'B' and (resid 127 through 139 )
14X-RAY DIFFRACTION14chain 'B' and (resid 140 through 163 )
15X-RAY DIFFRACTION15chain 'B' and (resid 164 through 179 )
16X-RAY DIFFRACTION16chain 'B' and (resid 180 through 190 )
17X-RAY DIFFRACTION17chain 'B' and (resid 191 through 214 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 109 )
19X-RAY DIFFRACTION19chain 'C' and (resid 110 through 216 )
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 59 )
21X-RAY DIFFRACTION21chain 'D' and (resid 60 through 95 )
22X-RAY DIFFRACTION22chain 'D' and (resid 96 through 135 )
23X-RAY DIFFRACTION23chain 'D' and (resid 136 through 216 )
24X-RAY DIFFRACTION24chain 'E' and (resid 1 through 18 )
25X-RAY DIFFRACTION25chain 'E' and (resid 19 through 75 )
26X-RAY DIFFRACTION26chain 'E' and (resid 76 through 113 )
27X-RAY DIFFRACTION27chain 'E' and (resid 114 through 128 )
28X-RAY DIFFRACTION28chain 'E' and (resid 129 through 139 )
29X-RAY DIFFRACTION29chain 'E' and (resid 140 through 150 )
30X-RAY DIFFRACTION30chain 'E' and (resid 151 through 172 )
31X-RAY DIFFRACTION31chain 'E' and (resid 173 through 197 )
32X-RAY DIFFRACTION32chain 'E' and (resid 198 through 214 )

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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