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- PDB-8en8: Cross-reactive 3180 TCR recognition of HLA-B*35:01-NP4 epitope fr... -

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基本情報

登録情報
データベース: PDB / ID: 8en8
タイトルCross-reactive 3180 TCR recognition of HLA-B*35:01-NP4 epitope from 1972 influenza strain
要素
  • 3180 TCR alpha chain
  • 3180 TCR beta chain
  • Beta-2-microglobulin
  • MHC class I antigen
  • Nucleoprotein NP4 epitope
キーワードIMMUNE SYSTEM / HLA B*3501 / NP418 EPITOPE / T CELL IMMUNITY / GLYCOPROTEIN / HOST-VIRUS INTERACTION / IMMUNE RESPONSE
機能・相同性
機能・相同性情報


helical viral capsid / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib ...helical viral capsid / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / viral penetration into host nucleus / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / ribonucleoprotein complex / symbiont entry into host cell / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / signaling receptor binding / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
類似検索 - 分子機能
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / : / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / : / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
MHC class I antigen / Beta-2-microglobulin / Nucleoprotein
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Influenza A virus (A型インフルエンザウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.70001191123 Å
データ登録者Littler, D.R. / Rossjohn, J.
資金援助 オーストラリア, 1件
組織認可番号国
Australian Research Council (ARC) オーストラリア
引用ジャーナル: To Be Published
タイトル: Molecular determinants of cross-strain influenza A virus recognition by T-cell receptors
著者: Quinones-Parra, S.M. / Littler, D.R. / Rossjohn, J. / Kedzierska, K.
履歴
登録2022年9月29日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年3月27日Provider: repository / タイプ: Initial release

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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: MHC class I antigen
B: Beta-2-microglobulin
C: Nucleoprotein NP4 epitope
D: 3180 TCR alpha chain
E: 3180 TCR beta chain
F: MHC class I antigen
G: Beta-2-microglobulin
H: Nucleoprotein NP4 epitope
I: 3180 TCR alpha chain
J: 3180 TCR beta chain


分子量 (理論値)分子数
合計 (水以外)190,19310
ポリマ－190,19310
非ポリマー00
水8,449469
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Nucleoprotein NP4 epitope
D: 3180 TCR alpha chain
E: 3180 TCR beta chain


分子量 (理論値)分子数
合計 (水以外)95,0975
ポリマ－95,0975
非ポリマー00
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
F: MHC class I antigen
G: Beta-2-microglobulin
H: Nucleoprotein NP4 epitope
I: 3180 TCR alpha chain
J: 3180 TCR beta chain


分子量 (理論値)分子数
合計 (水以外)95,0975
ポリマ－95,0975
非ポリマー00
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)79.770, 116.686, 253.184
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

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要素

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タンパク質 , 4種, 8分子 AFBGDIEJ

#1: タンパク質 MHC class I antigen


分子量: 31940.246 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-B / プラスミド: PET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: F4NBT2
#2: タンパク質 Beta-2-microglobulin


分子量: 11879.356 Da / 分子数: 2 / Fragment: UNP residues 21-119 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M, CDABP0092, HDCMA22P / プラスミド: PET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P61769
#4: タンパク質 3180 TCR alpha chain


分子量: 22704.129 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TRAV / プラスミド: PET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#5: タンパク質 3180 TCR beta chain


分子量: 27520.750 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TRBV / プラスミド: PET30 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)

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タンパク質・ペプチド / 非ポリマー , 2種, 471分子 CH

#3: タンパク質・ペプチド Nucleoprotein NP4 epitope / Nucleocapsid protein / Protein N


分子量: 1052.265 Da / 分子数: 2 / 由来タイプ: 合成
由来: (合成) Influenza A virus (strain A/Memphis/101/1972 H3N2) (A型インフルエンザウイルス)
参照: UniProt: Q08041
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 469 / 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: 3.1 Å3/Da / 溶媒含有率: 60.29 %
結晶化温度: 297 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: PEG

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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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.9537 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2019年3月21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: 0.9537 Å / 相対比: 1
反射解像度: 2.7→27.2 Å / Num. obs: 65736 / % possible obs: 100 % / 冗長度: 2 % / Biso Wilson estimate: 46.2104378326 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.072 / Net I/σ(I): 13.9
反射 シェル解像度: 2.7→2.8 Å / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2 / Num. unique obs: 6466 / CC1/2: 0.702

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解析

ソフトウェア
名称バージョン分類
BUSTER精密化
PHENIX1.10.1_2155精密化
XDSデータ削減
XSCALE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: 3LKS

3lks


解像度: 2.70001191123→27.1962626061 Å / SU ML: 0.325826636756 / 交差検証法: FREE R-VALUE / σ(F): 1.34868867294 / 位相誤差: 24.4109587079
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.248523938852 3280 4.99185779293 %
Rwork0.207066336869 62427 -
obs0.209126284475 65707 99.9346007605 %
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: 83.2517618709 Å2
精密化ステップサイクル: LAST / 解像度: 2.70001191123→27.1962626061 Å
タンパク質核酸リガンド溶媒全体
原子数13374 0 0 469 13843
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.011788809200913752
X-RAY DIFFRACTIONf_angle_d1.6227003258618698
X-RAY DIFFRACTIONf_chiral_restr0.07370816171091982
X-RAY DIFFRACTIONf_plane_restr0.00702350363652458
X-RAY DIFFRACTIONf_dihedral_angle_d21.21998094895096
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.70002-2.74030.3405782013531400.2810492088822699X-RAY DIFFRACTION99.9647887324
2.7403-2.78310.3961642458611340.2654221530182677X-RAY DIFFRACTION99.9644381223
2.7831-2.82860.2875691376271490.2570621278932684X-RAY DIFFRACTION100
2.8286-2.87740.2895144366261550.249456700032634X-RAY DIFFRACTION100
2.8774-2.92960.2909974519091470.2481624242212682X-RAY DIFFRACTION100
2.9296-2.98590.3068807997351610.2337794283562660X-RAY DIFFRACTION100
2.9859-3.04680.270981489661110.2391617509392697X-RAY DIFFRACTION100
3.0468-3.11290.290470813541510.2269105184882673X-RAY DIFFRACTION99.9646017699
3.1129-3.18520.2892211771961390.2151525551522717X-RAY DIFFRACTION100
3.1852-3.26480.2525547853691370.2148409273162666X-RAY DIFFRACTION100
3.2648-3.35290.2481591842841490.2160514273982713X-RAY DIFFRACTION100
3.3529-3.45140.2587228612331300.2219767550872718X-RAY DIFFRACTION99.8247458815
3.4514-3.56250.2184177466151420.1999371291372666X-RAY DIFFRACTION100
3.5625-3.68960.2423806208061420.2087888254722689X-RAY DIFFRACTION99.6129486277
3.6896-3.83690.2367214353471510.2007747707762711X-RAY DIFFRACTION100
3.8369-4.0110.247136478881280.2023903592172714X-RAY DIFFRACTION99.3011879804
4.011-4.22170.2314137666781400.1777505103012721X-RAY DIFFRACTION100
4.2217-4.48510.1901739307411530.1709998618012707X-RAY DIFFRACTION100
4.4851-4.82970.1966805539791310.1643900286332757X-RAY DIFFRACTION100
4.8297-5.31240.2236074849921450.1751543610372763X-RAY DIFFRACTION100
5.3124-6.07370.2369238532131320.1916974481562766X-RAY DIFFRACTION100
6.0737-7.62420.2857635936341550.2261300946262790X-RAY DIFFRACTION100
7.6242-27.10.2463763959081580.2259411871312923X-RAY DIFFRACTION99.8703403566
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)
16.19683370343-1.26605018511-0.09124877186192.19609149278-0.4413923161370.9020690843850.252392655553-0.880637015412-0.09515981365510.185554150403-0.419378606233-0.692368106802-0.1445207877030.526165189767-0.01306255573580.2346528679210.0214722154529-0.02114239271470.7183857290890.3586183011130.70968759993845.7591733632-11.1418305954-81.1947578705
22.06119897698-0.0401423745584-0.3015235649241.319055548280.3309086408660.3973288381560.152793550492-0.8827197279060.273801761997-0.00218360334263-0.259421605565-0.459128095432-0.1194230364080.282583654409-0.03475874705410.197269655394-0.001845593821490.008603704717840.6220100493330.2434943870650.48395691016238.2218038719-2.64671530655-84.7570134465
34.72290244536-0.954477498868-0.8417459844222.26527638425-0.1382307496343.346674883480.228800406488-0.207023839176-0.3718863640020.224805155519-0.373446651205-0.2781325894490.0915975586442-0.3018082959010.07955494572530.21921142702-0.0892517399594-0.01577391792110.5129977438720.2813623007570.43492630217330.2099825606-11.8367819873-81.9187477009
45.75262798361-5.60330732279-2.889848520288.631157959885.978245632584.637949552150.3998644740.818497370603-0.368914057333-0.492748831179-0.176133528725-0.6327291418080.4946761087350.3926155578140.5476088395640.3598240621790.09600712501710.05222315144090.6198182816930.2566436923720.76226553774438.3785929153-20.8598871515-95.1928899191
54.30400450698-0.5458783913951.44859933474.05138796566-0.357212579796.191670353340.334543628744-0.534363885775-0.706620330283-0.208119993593-0.1500883015160.147969787440.634382094242-0.14015621553-0.1287317313360.2647126117190.0215998391811-0.02806557360240.415925847330.08948637685380.48632683820526.8924673564-16.9637661197-91.8296891206
62.24221130274-0.90372015823-0.4134675914740.8285192589920.08743394534451.149543245520.144561309648-0.121195712051-0.718257941202-0.238163486767-0.301315937046-0.5519715860410.3888626501120.281248676971-0.06662272930780.3298825608360.1436317145550.1154151127570.4569951510740.254604887050.81491590426142.0973490686-15.0828645815-94.7556571632
70.00521160281750.0652278255637-0.1041515201773.03435578687-1.943291296072.77243894224-0.0199984121084-0.476811841278-0.7117531734250.486558819510.1237392690740.3811676919730.168174973892-0.327977491441-0.4897713055410.861043718220.1633270685850.1112129769571.07711587511.174633767542.1919575563247.2855780552-44.390626387-72.6599434703
83.49622432507-3.55207339926-0.3326888764163.98411452373-0.7703703104883.37552531886-0.464377738521-0.533998549415-1.23971811667-0.03738945417570.1065205152840.8560942707830.502637857646-0.154595856369-0.2008145957560.6438086856180.124983189243-0.07303380449661.127276074380.8617033828561.6904454896243.6572552931-38.9272892624-76.3810281129
90.244626381023-0.5904753080750.3265532416181.67307276839-0.6659156137380.459122837725-0.0919594284639-0.152426084168-0.802957502915-0.584576780163-0.105473813021-0.09211542578711.232182272770.2675604224410.2203987092361.330754386290.2961980100450.3126443757091.067948884261.048457860532.353027699345.2718886463-49.7706476435-74.3589659378
102.2793153291-0.7492679864530.2339661960343.56330674656-4.022007945028.543221245280.110145182208-0.909293796398-0.964729477481-0.1462009779980.06177918478270.03776636883050.9222819463920.195816815279-0.06235577588361.399892443860.4655574300890.09579463801891.265521422450.6325700613472.1981296331953.6656327816-47.6804645958-80.53260753
115.6830831939-3.172147010393.0070960413.82631322484-1.084976940594.95828623735-0.297810421995-0.05153835431460.0366047762722-0.341638745309-0.1265356227230.00218015872713-0.388488935683-0.221510070448-0.5534906560840.673955484811-0.0724285501161-0.2057087427850.9750405060190.7263316381780.90697841348437.3197368503-26.6634297481-68.7172930762
123.226971306490.2538862108072.436615490930.468279326724-0.5760260998193.145417831170.0728416067321-0.172767625733-0.2380481852760.265739349397-0.0162959492513-0.3560798177120.1831243341790.447786735313-0.1169174039950.6456126619120.222995177884-0.169969418252.165338434180.5926745276561.5958082847360.1815847575-32.8862175701-65.1285413964
131.59448528717-1.03810582280.4408147010530.8096996660440.05016102749350.992240249608-0.201828341726-0.5249531980020.08470770038390.6478438765460.170163646505-0.6750755636230.2426740171520.4584359969560.09747058205220.4746057008560.0907345230606-0.3330066067431.308682741030.7186258495330.94104504962743.8096725856-22.1759121504-65.7779910114
142.00061028585-1.72412664706-2.567572306298.9542475641-2.946627238057.60393573267-0.598315616227-0.3706690331830.569336946080.7643333112680.2470575363570.0339397806916-0.815127465633-0.1801938525410.2432373643390.8698345946660.153036433661-0.2821027616332.12753026670.258561978181.2425227326249.3273851771-21.6034235573-52.9614828877
151.87192639188-1.16944683723-0.2406593776113.50391570826-4.065213255416.47255374813-0.137113828096-0.3289568228940.4685761493920.867424574832-0.213946718287-0.458489458275-0.5971570227760.5835891243240.3188907828790.884312407805-0.248845561575-0.136348473880.8041134214760.2898056468810.93514890978351.5133493577-15.3487094719-63.132321833
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 103 )
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 118 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 137 )
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 185 )
7X-RAY DIFFRACTION7chain 'A' and (resid 186 through 219 )
8X-RAY DIFFRACTION8chain 'A' and (resid 220 through 242 )
9X-RAY DIFFRACTION9chain 'A' and (resid 243 through 263 )
10X-RAY DIFFRACTION10chain 'A' and (resid 264 through 276 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 11 )
12X-RAY DIFFRACTION12chain 'B' and (resid 12 through 19 )
13X-RAY DIFFRACTION13chain 'B' and (resid 20 through 41 )
14X-RAY DIFFRACTION14chain 'B' and (resid 42 through 46 )
15X-RAY DIFFRACTION15chain 'B' and (resid 47 through 51 )
16X-RAY DIFFRACTION16chain 'B' and (resid 52 through 61 )
17X-RAY DIFFRACTION17chain 'B' and (resid 62 through 71 )
18X-RAY DIFFRACTION18chain 'B' and (resid 72 through 90 )
19X-RAY DIFFRACTION19chain 'B' and (resid 91 through 99 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1 through 9 )
21X-RAY DIFFRACTION21chain 'D' and (resid 0 through 18 )
22X-RAY DIFFRACTION22chain 'D' and (resid 19 through 37 )
23X-RAY DIFFRACTION23chain 'D' and (resid 38 through 57 )
24X-RAY DIFFRACTION24chain 'D' and (resid 58 through 91 )
25X-RAY DIFFRACTION25chain 'D' and (resid 92 through 120 )
26X-RAY DIFFRACTION26chain 'D' and (resid 121 through 134 )
27X-RAY DIFFRACTION27chain 'D' and (resid 135 through 147 )
28X-RAY DIFFRACTION28chain 'D' and (resid 148 through 168 )
29X-RAY DIFFRACTION29chain 'D' and (resid 169 through 193 )
30X-RAY DIFFRACTION30chain 'D' and (resid 194 through 207 )
31X-RAY DIFFRACTION31chain 'D' and (resid 208 through 218 )
32X-RAY DIFFRACTION32chain 'E' and (resid 3 through 136 )
33X-RAY DIFFRACTION33chain 'E' and (resid 137 through 257 )
34X-RAY DIFFRACTION34chain 'F' and (resid 1 through 37 )
35X-RAY DIFFRACTION35chain 'F' and (resid 38 through 56 )
36X-RAY DIFFRACTION36chain 'F' and (resid 57 through 84 )
37X-RAY DIFFRACTION37chain 'F' and (resid 85 through 103 )
38X-RAY DIFFRACTION38chain 'F' and (resid 104 through 118 )
39X-RAY DIFFRACTION39chain 'F' and (resid 119 through 137 )
40X-RAY DIFFRACTION40chain 'F' and (resid 138 through 162 )
41X-RAY DIFFRACTION41chain 'F' and (resid 163 through 185 )
42X-RAY DIFFRACTION42chain 'F' and (resid 186 through 206 )
43X-RAY DIFFRACTION43chain 'F' and (resid 207 through 219 )
44X-RAY DIFFRACTION44chain 'F' and (resid 220 through 242 )
45X-RAY DIFFRACTION45chain 'F' and (resid 243 through 262 )
46X-RAY DIFFRACTION46chain 'F' and (resid 263 through 276 )
47X-RAY DIFFRACTION47chain 'G' and (resid 1 through 11 )
48X-RAY DIFFRACTION48chain 'G' and (resid 12 through 19 )
49X-RAY DIFFRACTION49chain 'G' and (resid 20 through 41 )
50X-RAY DIFFRACTION50chain 'G' and (resid 42 through 46 )
51X-RAY DIFFRACTION51chain 'G' and (resid 47 through 51 )
52X-RAY DIFFRACTION52chain 'G' and (resid 52 through 77 )
53X-RAY DIFFRACTION53chain 'G' and (resid 78 through 83 )
54X-RAY DIFFRACTION54chain 'G' and (resid 84 through 90 )
55X-RAY DIFFRACTION55chain 'G' and (resid 91 through 99 )
56X-RAY DIFFRACTION56chain 'H' and (resid 1 through 9 )
57X-RAY DIFFRACTION57chain 'I' and (resid 0 through 134 )
58X-RAY DIFFRACTION58chain 'I' and (resid 135 through 165 )
59X-RAY DIFFRACTION59chain 'I' and (resid 166 through 191 )
60X-RAY DIFFRACTION60chain 'I' and (resid 192 through 218 )
61X-RAY DIFFRACTION61chain 'J' and (resid 3 through 132 )
62X-RAY DIFFRACTION62chain 'J' and (resid 133 through 257 )

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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://pdbjlc1.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