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- PDB-7rk7: The complex between TIL 1383i TCR and human Class I MHC HLA-A2 wi... -

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基本情報

登録情報
データベース: PDB / ID: 7rk7
タイトルThe complex between TIL 1383i TCR and human Class I MHC HLA-A2 with the bound Tyrosinase(369-377)(N371D) nonameric peptide
要素
  • (TIL1383i (h3T) T cell receptor ...) x 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • Tyrosinase peptide
キーワードIMMUNE SYSTEM / TCR / Class I Major Histocompatibility Complex / HLA-A*02
機能・相同性
機能・相同性情報


eye pigment biosynthetic process / melanin biosynthetic process from tyrosine / Melanin biosynthesis / tyrosinase / tyrosinase activity / response to blue light / melanin biosynthetic process / melanosome membrane / response to vitamin D / positive regulation of memory T cell activation ...eye pigment biosynthetic process / melanin biosynthetic process from tyrosine / Melanin biosynthesis / tyrosinase / tyrosinase activity / response to blue light / melanin biosynthetic process / melanosome membrane / response to vitamin D / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / Golgi-associated vesicle / pigmentation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / Regulation of MITF-M-dependent genes involved in pigmentation / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / response to cAMP / detection of bacterium / response to UV / T cell receptor binding / visual perception / negative regulation of receptor binding / early endosome lumen / thymus development / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / antibacterial humoral response / positive regulation of cellular senescence / E3 ubiquitin ligases ubiquitinate target proteins / melanosome / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / ER-Phagosome pathway / T cell receptor signaling pathway / negative regulation of neuron projection development / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / cell population proliferation / lysosome / defense response to Gram-positive bacterium / immune response
類似検索 - 分子機能
Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 ...Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
HLA class I histocompatibility antigen, A alpha chain / Tyrosinase / Beta-2-microglobulin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.54 Å
データ登録者Singh, N.K. / Davancaze, L.M. / Arbuiso, A. / Weiss, L.I. / Keller, G.L.J. / Baker, B.M.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118166 米国
引用ジャーナル: To Be Published
タイトル: The complex between TIL 1383i TCR and human Class I MHC HLA-A2 with the bound Tyrosinase(369-377)(N371D) nonameric peptide
著者: Singh, N.K. / Davancaze, L.M. / Arbuiso, A. / Weiss, L.I. / Keller, G.L.J. / Baker, B.M.
履歴
登録2021年7月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年11月2日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.22024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Tyrosinase peptide
D: TIL1383i (h3T) T cell receptor alpha chain
E: TIL1383i (h3T) T cell receptor beta chain


分子量 (理論値)分子数
合計 (水以外)97,0405
ポリマ－97,0405
非ポリマー00
水1,47782
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: surface plasmon resonance, Binding orientation typical of TCR/pMHC complexes. Steady-state affinity determined by SPR to be 13 +/- 5 uM.
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10670 Å2
ΔGint-51 kcal/mol
Surface area37550 Å2
手法PISA
単位格子
Length a, b, c (Å)114.738, 74.428, 131.058
Angle α, β, γ (deg.)90.000, 93.487, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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要素

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タンパク質 , 2種, 2分子 AB

#1: タンパク質 HLA class I histocompatibility antigen, A alpha chain / Human leukocyte antigen A / HLA-A


分子量: 31854.203 Da / 分子数: 1 / 断片: UNP residues 25-299 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-A, HLAA / プラスミド: pHN1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): XL1Blue / 参照: UniProt: P04439
#2: タンパク質 Beta-2-microglobulin


分子量: 11879.356 Da / 分子数: 1 / 断片: 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: pHN1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): XL1Blue / 参照: UniProt: P61769

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TIL1383i (h3T) T cell receptor ... , 2種, 2分子 DE

#4: タンパク質 TIL1383i (h3T) T cell receptor alpha chain


分子量: 23655.314 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pGMT7 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): pLysS
#5: タンパク質 TIL1383i (h3T) T cell receptor beta chain


分子量: 28619.744 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pGMT7 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): pLysS

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タンパク質・ペプチド / 非ポリマー , 2種, 83分子 C

#3: タンパク質・ペプチド Tyrosinase peptide / LB24-AB / Monophenol monooxygenase / SK29-AB / Tumor rejection antigen AB


分子量: 1031.161 Da / 分子数: 1 / 断片: UNP residues 369-377 / Mutation: N371D / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P14679, tyrosinase
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 82 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY

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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: 2.88 Å3/Da / 溶媒含有率: 57.26 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5 / 詳細: 16% PEG 3350, 2% tacsimate, 100mM Tris (pH 8.5)

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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 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2017年6月20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 Å / 相対比: 1
反射解像度: 2.54→37.31 Å / Num. obs: 36440 / % possible obs: 99.52 % / 冗長度: 1.1 % / Biso Wilson estimate: 56.46 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 8.27
反射 シェル解像度: 2.54→2.631 Å / Mean I/σ(I) obs: 2.07 / Num. unique obs: 3527 / CC1/2: 1 / CC star: 1

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
DIALS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: 3QDM

3qdm


解像度: 2.54→37.21 Å / SU ML: 0.3881 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 28.9272
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2549 2006 5.51 %
Rwork0.2111 34426 -
obs0.2135 36432 99.48 %
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: 89.53 Å2
精密化ステップサイクル: LAST / 解像度: 2.54→37.21 Å
タンパク質核酸リガンド溶媒全体
原子数6213 0 0 82 6295
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00526359
X-RAY DIFFRACTIONf_angle_d0.92318601
X-RAY DIFFRACTIONf_chiral_restr0.0545914
X-RAY DIFFRACTIONf_plane_restr0.00461105
X-RAY DIFFRACTIONf_dihedral_angle_d18.21312294
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.60.37831420.31792304X-RAY DIFFRACTION94.62
2.6-2.670.35061390.30252456X-RAY DIFFRACTION99.88
2.67-2.750.34171400.3032469X-RAY DIFFRACTION99.92
2.75-2.840.35671510.28262459X-RAY DIFFRACTION99.89
2.84-2.940.3381290.24962431X-RAY DIFFRACTION99.92
2.94-3.060.27761470.23562445X-RAY DIFFRACTION99.88
3.06-3.20.28211450.24552479X-RAY DIFFRACTION100
3.2-3.370.28041530.24932447X-RAY DIFFRACTION99.88
3.37-3.580.30671390.21532474X-RAY DIFFRACTION99.85
3.58-3.850.24661410.20412442X-RAY DIFFRACTION99.73
3.85-4.240.21191430.18952489X-RAY DIFFRACTION99.62
4.24-4.850.19481450.16062496X-RAY DIFFRACTION99.81
4.85-6.110.23541430.18192478X-RAY DIFFRACTION100
6.11-37.210.23521490.20012557X-RAY DIFFRACTION99.74
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)
14.061001471321.7757005752-1.784288482784.77156958035-0.7314146172315.501353857310.0406102270331.043483474490.793685725488-1.316504908180.3297488720430.283924360914-0.782434517355-0.397728292796-0.3972550457940.8883975558030.05143594683760.1514250075990.9326336644040.2843560597360.7886259442482.69798529445-33.7057359361-45.4295442295
25.600905518241.13005432918-1.211269881425.15222472679-1.218087639674.249466686670.2277054661010.1945412680630.206307606638-0.254585093966-0.00659551187379-0.451199249621-0.1714584302380.369311700585-0.2080631987960.491552953855-0.005035379355840.1550211434280.5818947574250.06013893733760.6574998200398.22721576186-38.1436108646-31.475418166
32.843095364580.891143723463-2.200408912443.120712959241.658367664779.51417409676-0.5912487700630.371889806098-0.454677159826-0.614083109906-0.135410665541-0.01655942933010.836587248258-0.6101997127420.5667847103750.631632124290.02532020549990.08171073211590.657679791464-0.03527730807630.7301835513813.19281503189-50.2821511526-39.4637036716
45.2561652163-2.98535386914-2.551814603242.716609324880.4235881866292.08836371001-0.3429533639150.4857932332330.999530425559-0.7688778447470.0328508973536-0.3291852782640.331847573102-0.9527368376270.3531325412491.457312189840.08647933663610.1889157047411.52787844868-0.1534773603180.7468016536918.2662637722-42.3764451098-61.4744858103
52.711363157020.3062561752112.947379440131.986378734391.184597108733.744158759240.413153982566-0.300356055077-1.35324644833-0.3031563266650.289792398741-0.6001361667951.07083389272-0.0162902229224-0.4909481619221.45111773236-0.01412378487110.3921018455451.399060037190.2553952817561.2206024978428.5783812341-37.317374375-55.6500025192
60.8942651940370.19071204459-1.231586609210.9581693079611.193462810972.63344952086-0.260277860374-0.000939048767511-0.9338422770210.1940582838330.564855181449-0.3490065708090.2765192222250.143534735053-0.3313047634461.25084459061-0.0433651369420.3177288028321.447277875220.01107762873531.3085106218829.9354314776-38.4523027097-60.0618185199
77.04443711709-1.388015226-6.141639336870.8658705326460.3400955951977.230167425211.01100172752-0.5561522264981.44942820867-0.144764837565-0.384197876792-0.3238567189780.967905576111-0.267897722545-0.662483226371.06313903973-0.1551925006260.5094376534971.270372838970.2483282728061.5648598055422.171507418-23.9659627204-45.5126687588
81.67477510386-1.62682408177-0.356605068612.08733821976-0.9847804505314.11292963195-0.200742997379-0.1330935054920.739968253415-0.104614977435-2.108900786850.0516463821584-0.1573411813930.61005451191.757091695881.39398423722-0.3299903360740.1131448493781.81787608380.1093886616111.7142965397317.6740904806-25.9948594261-68.7617416277
92.803884563120.220533435594-0.2712889848293.45216128826-2.888784223538.62853999916-0.4255608751670.3342424168120.291292680359-0.314310102088-0.6420114072850.446800476617-0.8204299357261.047861156610.9247286917761.2764594393-0.1879578146860.1388416472451.190089264690.3958598069231.243200053215.9528215214-19.3654160929-50.7234486648
100.1524495574950.873782715814-0.03216635421976.18483045065-0.404250135180.03950637345750.0355489093704-1.30944629386-0.159733026884-0.490075810484-0.608071220742-1.80611869038-0.01357550077360.09055294813320.1558402859751.681869732170.1838672199110.2467418970431.82390443440.01574186849951.429282480486.85961465978-18.6201085706-56.8057924816
112.122148945252.27181002902-1.213123886073.14642645173-0.9281984153464.962125548480.2218983997490.1809177511990.546411639661-0.07731730465160.5290972221120.72070387617-0.974396187635-0.258340762187-0.5527957447910.999341116993-0.006145761814530.2788163118371.033878196890.2810030839991.1183590025913.9051497122-29.2863491491-46.5371811332
120.4160197015730.5775744464210.3930144811380.8893758614480.4929973493440.414181554438-0.555590462864-0.445487771781-0.295295860858-1.137567692090.8502765342340.665459550742-0.164026370517-0.780006807581-0.363541078671.65338629245-0.3798631241240.1539925753662.907285816911.055638976370.67429514631118.5968729209-16.183414957-69.1805948698
133.83470593927-0.77542864188-1.523646763390.934383824467-0.8629775389132.52771954643-0.0106496166752-0.2992384158780.633654362772-1.313256554520.776188402515-0.488659852517-1.590571303670.0637916957356-0.4899888116111.47415380014-0.1988713657970.4441949671141.043432088430.5082655766251.646618308620.4183573121-14.1803521322-45.8624004462
143.76011692084-3.21083468560.00561819583435.391270218293.763671882425.398609910090.8030114997060.8126234974781.69970658054-1.410677321791.66528689919-0.02018759628631.29969769087-0.923546687858-1.308463383491.90275489555-0.07592641649190.7887043340431.306967673240.2666701248591.4895969061125.5431216397-18.5129564609-59.8130720246
156.42466091251-0.9499801568070.7713507682152.669508498880.03821046772.13945443144-0.2208407828570.6412241101351.2652605903-0.5055498567180.1636159746130.756216797632-0.8464445102211.13804900101-0.1584527336190.6634196887210.00786413242462-0.02061239753990.6357682813380.1510303425220.7761321914780.577675652138-40.5594883738-32.9828037276
163.56346399407-0.604993026545-3.64663837730.313585151394-0.2661774423244.39635644190.1201285594530.447659334597-0.20493600393-0.0873793365002-0.1215954312560.121186220711-0.123986307883-0.6371750340090.04819202032930.400933894380.00158885346637-0.1003912364330.354652820142-0.04792003572760.480557692065-15.3583490345-55.0088281074-13.8544282962
176.18768778217-0.469576640732-2.643050569422.293736986820.7612078840752.693069946650.2346751691330.1453928984850.1472970077150.124461535702-0.125653686634-0.4370939736040.0377392602845-0.000507316033639-0.1062924798710.328768249126-0.00280956804817-0.1024985134880.3180312479120.04264301642670.467061859244-9.53140462593-46.0680547173-12.8569655851
183.367745869480.165967116663-2.486897000480.824829083867-1.201216717433.301112335930.2667944110250.2516407064440.107752892188-0.0478308434792-0.00289806724606-0.0729775746234-0.327991805095-0.0882815469424-0.2515262548090.3857958084420.0321509356521-0.1236769009480.364776888682-0.009746988702210.534789248187-12.9568067127-48.6497327222-16.2824051909
195.04204066774-1.92758683302-4.525403614893.12789603159-0.04681039778498.57381193949-0.380687817336-0.418402963682-0.4331091225320.613640328170.2559279045450.298746925819-0.6597978728030.1115879679590.1309532069140.5214051387060.004041308813750.02800189758750.2787863812870.02049391140560.687260746794-24.5081320983-53.11362046386.9089784047
202.976986487193.294869984633.612387817716.510903805190.8264407373688.60009411171-0.602452308416-1.48260849084-0.5182084739121.14848776028-0.2195382306392.496078859610.187294315102-1.8886968467-0.6289863771310.857856019635-0.05021392453840.5642129702670.4923842487960.2601175467381.24672268822-44.7459564877-41.806244528613.3694169654
217.00266041071-1.151341236351.445132063923.03388015873-0.4162906694814.453180471310.07651476372070.512528030448-1.92832115844-0.251702288916-0.0868599726851.724989500720.630283664992-0.621022005310.0491883293490.6422879827080.0834407423218-0.1123615700930.702179865092-0.1376809971281.28839906731-39.0216401046-54.41797057143.84916163648
226.28988300688-1.445748606361.441285379975.19670095234-0.2037676727745.1339284233-0.109407401280.0996581744506-0.3330828290130.413213717555-0.05695350055670.8412885929320.4415147532190.009467916378050.2361883210950.5831141767740.00767764216547-0.007224281925330.3364506465280.1141083513780.824584881567-32.4225339251-45.34833744818.28298120962
233.52527709048-3.00068671516-2.709831159192.540030809732.283142570132.03618764246-0.2482050123770.728451160155-0.9135279574580.224217252431-0.6212668234591.224315481871.56367654388-1.780663278280.7317748669541.01318921004-0.2017381327760.1404075648820.8068384915160.1837986328311.84455821829-48.3356621382-51.47287034199.13687339797
245.09513910108-0.928984527522-0.5151887614954.439581160490.357380470783.003059711330.5259035123570.7715874037990.66163366354-1.21380663515-0.594817320433-0.16238317178-0.439706410138-0.274648205360.03818017981370.6805711159760.233905226936-0.07382531014360.56379027880.0677500901930.497572538342-25.1921833441-31.5201745952-25.0006019711
255.63233645421-3.79104565304-3.27772943442.982669183921.406406276862.210412628240.376257370562-0.01559053665320.41485904777-0.477215463368-0.179534505052-0.0663938926547-0.3736327722950.12321185362-0.1401031706250.429204402770.0533990723086-0.08571617376740.3883160290510.04226683330890.483982557531-24.6547489968-33.337766853-17.8537706202
263.11526201319-0.6354886380320.05204576278453.249984687410.805737251013.59173488693-0.353147834558-0.442890841798-0.06790744873390.606848445760.04246842639390.7125644403210.3980213865640.1437062730470.2525527040920.494797872520.06220982991340.09824448491750.392475988105-0.03315272014920.723881201275-37.803144695-36.61572447798.74082614662
273.86896608182-1.72637502081.835260625794.667327366810.2603386812044.031951217540.3700933760560.258358687552-0.792262609005-0.112007151633-0.1588374445240.7209417731060.813877741664-0.0145205704541-0.0651745670.4305291258450.0170324249148-0.05895847921990.381178934202-0.0292999239960.653460264587-37.5084300671-38.1687582511-1.54471313813
282.30495718252-1.376059938661.493271016561.88654954965-1.433990400843.73671196608-0.303034091225-0.181595873385-0.01394465633590.4236787303910.1540679687090.374206966722-0.591102061002-0.1551116451880.1508485890430.4910528175440.05304617616940.001344495760220.330693379958-0.02552258024550.617976222533-39.5667366822-28.56472553094.4445914887
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 57 )AA1 - 571 - 57
22chain 'A' and (resid 58 through 149 )AA58 - 14958 - 149
33chain 'A' and (resid 150 through 173 )AA150 - 173150 - 173
44chain 'A' and (resid 174 through 202 )AA174 - 202174 - 189
55chain 'A' and (resid 203 through 233 )AA203 - 233190 - 209
66chain 'A' and (resid 234 through 272 )AA234 - 272210 - 238
77chain 'B' and (resid 1 through 11 )BB1 - 111 - 11
88chain 'B' and (resid 12 through 23 )BB12 - 2312 - 20
99chain 'B' and (resid 24 through 47 )BB24 - 4721 - 41
1010chain 'B' and (resid 48 through 52 )BB48 - 5242 - 46
1111chain 'B' and (resid 53 through 69 )BB53 - 6947 - 63
1212chain 'B' and (resid 71 through 79 )BB71 - 7964 - 70
1313chain 'B' and (resid 80 through 91 )BB80 - 9171 - 82
1414chain 'B' and (resid 92 through 99 )BB92 - 9983 - 90
1515chain 'C' and (resid 1 through 9 )CC1 - 91 - 9
1616chain 'D' and (resid 8 through 37 )DD8 - 371 - 30
1717chain 'D' and (resid 38 through 71 )DD38 - 7131 - 64
1818chain 'D' and (resid 72 through 113 )DD72 - 11365 - 106
1919chain 'D' and (resid 114 through 127 )DD114 - 127107 - 120
2020chain 'D' and (resid 128 through 146 )DD128 - 146121 - 139
2121chain 'D' and (resid 147 through 161 )DD147 - 161140 - 154
2222chain 'D' and (resid 162 through 186 )DD162 - 186155 - 179
2323chain 'D' and (resid 187 through 198 )DD187 - 198180 - 189
2424chain 'E' and (resid 7 through 90 )EE7 - 901 - 84
2525chain 'E' and (resid 91 through 132 )EE91 - 13285 - 126
2626chain 'E' and (resid 133 through 170 )EE133 - 170127 - 164
2727chain 'E' and (resid 171 through 196 )EE171 - 196165 - 190
2828chain 'E' and (resid 197 through 253 )EE197 - 253191 - 247

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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