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- PDB-7o3b: Crystal structure of the TTBK2-CEP164 complex bound to a camelid ... -

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基本情報

登録情報
データベース: PDB / ID: 7o3b
タイトルCrystal structure of the TTBK2-CEP164 complex bound to a camelid nanobody
要素
  • Nanobody 36Z
  • Tau-tubulin kinase 2,Centrosomal protein of 164 kDa
キーワードSTRUCTURAL PROTEIN / Centriole / Centrosome / Basal body / Ciliogenesis
機能・相同性
機能・相同性情報


ciliary transition fiber / negative regulation of microtubule binding / negative regulation of protein localization to microtubule / cerebellar granular layer development / cerebellar granule cell precursor tangential migration / ciliary transition zone / negative regulation of microtubule depolymerization / microtubule plus-end binding / smoothened signaling pathway / tau-protein kinase activity ...ciliary transition fiber / negative regulation of microtubule binding / negative regulation of protein localization to microtubule / cerebellar granular layer development / cerebellar granule cell precursor tangential migration / ciliary transition zone / negative regulation of microtubule depolymerization / microtubule plus-end binding / smoothened signaling pathway / tau-protein kinase activity / kinesin binding / cilium assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / regulation of cell migration / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / cerebellum development / ciliary basal body / tau protein binding / microtubule cytoskeleton organization / Regulation of PLK1 Activity at G2/M Transition / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cell cycle / cell division / intracellular membrane-bounded organelle / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / signal transduction / extracellular space / nucleoplasm / ATP binding / nucleus / cytosol
類似検索 - 分子機能
: / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...: / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
Tau-tubulin kinase 2 / Centrosomal protein of 164 kDa
類似検索 - 構成要素
生物種Camelidae mixed library (哺乳類)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.4 Å
データ登録者e Silva, I.R. / van Breugel, M.
資金援助 英国, 1件
組織認可番号国
Medical Research Council (MRC, United Kingdom)MC_UP_1201/3 英国
引用ジャーナル: Structure / 年: 2022
タイトル: Molecular mechanisms underlying the role of the centriolar CEP164-TTBK2 complex in ciliopathies.
著者: Rosa E Silva, I. / Bino, L. / Johnson, C.M. / Rutherford, T.J. / Neuhaus, D. / Andreeva, A. / Cajanek, L. / van Breugel, M.
履歴
登録2021年4月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年9月15日Provider: repository / タイプ: Initial release
改定 1.12021年9月22日Group: Data collection / Database references
カテゴリ: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site
改定 1.22022年1月19日Group: Data collection / Database references / カテゴリ: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.year / _diffrn_source.pdbx_synchrotron_site
改定 1.32022年12月21日Group: Database references / カテゴリ: citation / Item: _citation.page_last
改定 1.42024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Nanobody 36Z
B: Nanobody 36Z
C: Nanobody 36Z
G: Tau-tubulin kinase 2,Centrosomal protein of 164 kDa
H: Tau-tubulin kinase 2,Centrosomal protein of 164 kDa
I: Tau-tubulin kinase 2,Centrosomal protein of 164 kDa


分子量 (理論値)分子数
合計 (水以外)84,4516
ポリマ－84,4516
非ポリマー00
水1,874104
1
A: Nanobody 36Z
G: Tau-tubulin kinase 2,Centrosomal protein of 164 kDa


  • 登録者が定義した集合体
  • 根拠: isothermal titration calorimetry, CEP164 (1-104) interaction with the proline-rich TTBK2 peptide (1074-1087) (chain G) through its WW domain was confirmed by ITC. CEP164(1-104) interaction ...根拠: isothermal titration calorimetry, CEP164 (1-104) interaction with the proline-rich TTBK2 peptide (1074-1087) (chain G) through its WW domain was confirmed by ITC. CEP164(1-104) interaction with the nanobody 36Z was not confirmed experimentally. However, the nanobody interacts with CEP164 N-terminal region through its CDR3 loop, as expected.
  • 28.2 kDa, 2 ポリマー
  • Omokage検索でこの集合体の類似形状データを探す (詳細)
分子量 (理論値)分子数
合計 (水以外)28,1502
ポリマ－28,1502
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Nanobody 36Z
H: Tau-tubulin kinase 2,Centrosomal protein of 164 kDa


  • 登録者が定義した集合体
  • 根拠: isothermal titration calorimetry, CEP164 (1-104) interaction with the proline-rich TTBK2 peptide (1074-1087) (chain G) through its WW domain was confirmed by ITC. CEP164(1-104) interaction ...根拠: isothermal titration calorimetry, CEP164 (1-104) interaction with the proline-rich TTBK2 peptide (1074-1087) (chain G) through its WW domain was confirmed by ITC. CEP164(1-104) interaction with the nanobody 36Z was not confirmed experimentally. However, the nanobody interacts with CEP164 N-terminal region through its CDR3 loop, as expected.
  • 28.2 kDa, 2 ポリマー
  • Omokage検索でこの集合体の類似形状データを探す (詳細)
分子量 (理論値)分子数
合計 (水以外)28,1502
ポリマ－28,1502
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Nanobody 36Z
I: Tau-tubulin kinase 2,Centrosomal protein of 164 kDa


  • 登録者が定義した集合体
  • 根拠: isothermal titration calorimetry, CEP164 (1-104) interaction with the proline-rich TTBK2 peptide (1074-1087) (chain G) through its WW domain was confirmed by ITC. CEP164(1-104) interaction ...根拠: isothermal titration calorimetry, CEP164 (1-104) interaction with the proline-rich TTBK2 peptide (1074-1087) (chain G) through its WW domain was confirmed by ITC. CEP164(1-104) interaction with the nanobody 36Z was not confirmed experimentally. However, the nanobody interacts with CEP164 N-terminal region through its CDR3 loop, as expected.
  • 28.2 kDa, 2 ポリマー
  • Omokage検索でこの集合体の類似形状データを探す (詳細)
分子量 (理論値)分子数
合計 (水以外)28,1502
ポリマ－28,1502
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)70.615, 127.741, 218.881
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 0 through 3 or resid 5...
d_2ens_1(chain "B" and (resid 0 through 3 or resid 5...
d_3ens_1(chain "C" and (resid 0 through 3 or resid 5...
d_1ens_2(chain "G" and (resid 2 through 45 or (resid 46...
d_2ens_2(chain "H" and (resid 2 through 45 or (resid 46...
d_3ens_2(chain "I" and (resid 2 through 66 or resid 68 through 80 or resid 82 through 104))
d_1ens_3(chain "G" and (resid 1074 through 1084))'
d_2ens_3(chain "H" and (resid 1074 through 1084))'
d_3ens_3(chain "I" and (resid 1074 through 1084))'

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERGLNA1 - 4
d_12ens_1GLNSERA8 - 56
d_13ens_1ASPTHRA59 - 62
d_14ens_1TYRLYSA66 - 82
d_15ens_1ALAALAA86 - 128
d_21ens_1SERGLNB3 - 6
d_22ens_1GLNSERB8 - 56
d_23ens_1ASPTHRB59 - 62
d_24ens_1TYRLYSB66 - 82
d_25ens_1ALAALAB86 - 128
d_31ens_1SERGLNC1 - 4
d_32ens_1GLNSERC6 - 54
d_33ens_1ASPTHRC57 - 60
d_34ens_1TYRLYSC62 - 78
d_35ens_1ALAALAC81 - 123
d_11ens_2ALAGLNG2 - 66
d_12ens_2ILEGLYG68 - 80
d_13ens_2SERSERG82 - 104
d_21ens_2ALAGLNH2 - 66
d_22ens_2ILEGLYH68 - 80
d_23ens_2SERSERH82 - 104
d_31ens_2ALAGLNI2 - 66
d_32ens_2ILEGLYI68 - 80
d_33ens_2SERSERI82 - 104
d_11ens_3PHETHRG1074 - 1084
d_21ens_3PHETHRH1074 - 1084
d_31ens_3PHETHRI1074 - 1084

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(-0.53505751493, -0.844809469601, -0.00322735031356), (-0.844783029105, 0.534999397979, 0.0108294920308), (-0.00742222694378, 0.00852081186784, -0.999936151118)70.377217448, -3.40223486082, 73.13931336
2given(0.517361221498, -0.855647986883, 0.0142789717183), (-0.855766364312, -0.51726654136, 0.00996267541416), (-0.00113850884718, -0.0173737656352, -0.999848416544)-2.621841461, -1.989952456, 36.7708935881
3given(-0.555295836345, -0.831648243185, -0.00278096117176), (-0.831573408443, 0.5552858906, -0.0119685450657), (0.0114978479783, -0.00433350988173, -0.999924507242)70.9223002843, -3.0578644084, 72.7543489571
4given(0.469423256725, -0.882536380266, 0.0277730724416), (-0.882632583644, -0.469883639013, -0.0130033871991), (0.0245260746153, -0.0184093263174, -0.999529673581)-1.74724933246, -0.816683377964, 36.3336506354
5given(-0.562224618324, -0.826983266246, -0.00146829851714), (-0.826931178627, 0.562207609203, -0.0103648429464), (0.00939704027287, -0.00461318804618, -0.999945205564)71.0917402715, -3.44471982497, 72.8075986121
6given(0.496109323389, -0.867146223851, 0.0439655058814), (-0.867131838438, -0.497409602962, -0.0258081701904), (0.0442483221496, -0.0253202160917, -0.998699640855)-3.33167975696, -0.736197557752, 35.7865319568

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要素

#1: 抗体 Nanobody 36Z


分子量: 13226.526 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Camelidae mixed library (哺乳類) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#2: タンパク質 Tau-tubulin kinase 2,Centrosomal protein of 164 kDa / Cep164


分子量: 14923.734 Da / 分子数: 3 / 由来タイプ: 組換発現
詳細: Chimera composed of TTBK2 (1074-1087, UNIPROT Q6IQ55) and CEP164 (1-109, UNIPROT Q9UPV0). GPLGS = expression tag amino acid residues left after protease cleavage.
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TTBK2, KIAA0847, CEP164, KIAA1052, NPHP15 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: Q6IQ55, UniProt: Q9UPV0, non-specific serine/threonine protein kinase
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 104 / 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: 2.92 Å3/Da / 溶媒含有率: 57.88 %
結晶化温度: 292 K / 手法: 蒸気拡散法 / 詳細: 100 mM Acetate, pH 4.5, 100 mM NaCl, 30% PEG-200

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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: Diamond / ビームライン: I03 / 波長: 0.97625 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2020年4月5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: 0.97625 Å / 相対比: 1
反射解像度: 2.4→61.8 Å / Num. obs: 38541 / % possible obs: 98.7 % / 冗長度: 3.8 % / Biso Wilson estimate: 43.41 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.052 / Net I/σ(I): 8.6
反射 シェル解像度: 2.4→2.49 Å / 冗長度: 3.8 % / Rmerge(I) obs: 0.705 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4025 / CC1/2: 0.498 / Rpim(I) all: 0.436 / % possible all: 99.4

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解析

ソフトウェア
名称バージョン分類
REFMAC5.7.0009精密化
PHENIX1.18_3845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: 7O0S

7o0s


解像度: 2.4→36.11 Å / SU ML: 0.2716 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.6969
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2395 1947 5.06 %
Rwork0.1894 36559 -
obs0.1919 38506 98.33 %
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: 55 Å2
精密化ステップサイクル: LAST / 解像度: 2.4→36.11 Å
タンパク質核酸リガンド溶媒全体
原子数5497 0 0 104 5601
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00445719
X-RAY DIFFRACTIONf_angle_d0.62337795
X-RAY DIFFRACTIONf_chiral_restr0.043815
X-RAY DIFFRACTIONf_plane_restr0.00441053
X-RAY DIFFRACTIONf_dihedral_angle_d15.0862792
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS0.515975563888
ens_1d_3CX-RAY DIFFRACTIONTorsion NCS0.6734654733
ens_2d_2HX-RAY DIFFRACTIONTorsion NCS0.62644196305
ens_2d_3IX-RAY DIFFRACTIONTorsion NCS0.838719332283
ens_3d_2HX-RAY DIFFRACTIONTorsion NCS1.07864973231
ens_3d_3IX-RAY DIFFRACTIONTorsion NCS0.906259256605
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.30481470.25122597X-RAY DIFFRACTION99.1
2.46-2.530.32071360.25342615X-RAY DIFFRACTION98.81
2.53-2.60.3011530.24442569X-RAY DIFFRACTION98.95
2.6-2.680.3151430.24762574X-RAY DIFFRACTION98.8
2.68-2.780.28561560.23152556X-RAY DIFFRACTION98.55
2.78-2.890.31691380.22372585X-RAY DIFFRACTION98.34
2.89-3.020.28121310.21832628X-RAY DIFFRACTION99.1
3.02-3.180.29061140.2192672X-RAY DIFFRACTION99.43
3.18-3.380.27271290.2122590X-RAY DIFFRACTION98.62
3.38-3.640.23451160.18682655X-RAY DIFFRACTION98.82
3.64-4.010.21311530.1722587X-RAY DIFFRACTION97.96
4.01-4.590.18151490.14292625X-RAY DIFFRACTION98.13
4.59-5.780.18941450.15282590X-RAY DIFFRACTION96.44
5.78-36.110.22191370.17912716X-RAY DIFFRACTION95.93
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)
17.515649147426.964129170241.21932419948.876688753922.21255752474.430045879280.16890161381-0.2900548787870.7572641683860.197317297463-0.3404122162511.420469617280.405704756693-0.4217831570290.2230447751760.342148795610.0413397142957-0.06051881025380.38410640287-0.1021138880470.46761661031721.360120004221.669309147.6755520483
25.882365865221.62568323016-0.6291239010280.366864485187-0.626941705963.377929948850.1481633710030.0922208563428-0.516273719840.417967065886-0.0631792176135-0.2439107084320.528108175018-0.273904299392-0.04691796419370.3195723603210.0811819597348-0.07672782888590.2673578860980.0198015777480.39870237347428.073022103418.404511492749.6548002874
34.50819191285-1.692635345580.4527746308186.87960289647-1.249208074595.271903184770.02549610599260.206045533312-0.0992085324451-0.4431871074580.08711037126230.08521424792730.357590468473-0.0761357708745-0.08086389670990.274509781662-0.0270999163434-0.04175865951430.281043034078-0.05792905412480.36251222183233.69658136318.969879680840.3306223662
46.941764633073.41729891487-3.820189446748.69487953177-5.492295535082.45077004724-0.1076196025940.0249759826597-0.4312842021480.07445549017-0.0418270476975-0.7802024097170.261157139080.4321352035750.2371951044120.353700238973-0.0342149397415-0.07244600238850.321308588223-0.04807290519690.44807841744335.517583050520.051364148248.9613858135
50.9211837533212.331885523340.373618168247.921727572791.167280096832.09518343908-0.2115896756660.07707791291490.0415611903881-0.0769762981670.100252624355-0.400407246106-0.07472833416590.1609023610630.1404517926940.2244315864560.0424154399214-0.07130734976830.2424238043220.010380838260.35572679140229.018660284520.497592946840.7631667419
69.144031183347.32156035033-0.3914762058086.01946033617-1.012098473892.95332944768-0.0419832909689-0.07423394179560.9382341093850.752726182529-0.1215520831090.382737072103-0.219108175916-0.01238698826690.1368789861290.386863641470.0495975397553-0.08627959435460.278810418089-0.01365701107970.58984747429629.30950805334.605112641744.7035280842
76.204557328250.01981292596941.140618318212.75861304729-0.8257029392143.33221667099-0.1105341019320.343872600922-0.1130862141820.0294837970346-0.0983588978656-0.269427930004-0.0953511268380.3069334246640.180769595720.2977544442120.00724228671073-0.03818725235430.254672022353-0.06452286100170.26551758062538.8911397173-13.89593036128.0539393443
81.71861922873-0.294239060911.863646986939.227673803171.559659618812.35260667597-0.130976931747-0.129724494007-0.554873765798-0.248227772335-0.178828309120.003946449104270.5501074376220.2143111075310.1793773534480.2726500988520.00490379460569-0.008834889482320.258639334349-0.00877754901090.38309256408139.6177327169-25.986133086329.4046298214
94.26380440987-0.31544906820.9137740623791.601998518070.3451639672071.42794935759-0.1322153621110.28564910121-0.243375292044-0.09892375140330.008336091422590.184593548120.0930625687423-0.1704410492860.1190474617860.28545404494-0.0110362256383-0.0187142872330.293318887309-0.06384432186890.30977267800434.1826414772-18.23322588828.5661210237
103.218875847811.476450926240.901274783174.561513379440.06437635359963.631989516090.069086719007-0.3230049488890.3957600874630.214220286647-0.02602477946310.0925910727533-0.597339984267-0.274633557434-0.003388445386410.4493142303450.12305336133-0.003090014667730.613745141825-0.20842277570.423843636974-6.50115783051-35.2141897894-9.02431711836
114.643099263161.04541182634-0.08973898685933.67355444864-0.8474359012952.103163992040.0972993442678-0.630158287055-0.07250179283660.516822965301-0.0225959317101-0.459050681146-0.2571409274030.153044593611-0.02163532653160.3651680320960.0154510513293-0.0225734590670.501978722308-0.1391813171210.3318221612441.05410557949-41.3428830914-10.0813150812
123.180305260463.891200534811.681225840466.343781447792.088925725582.690211956180.0547461448146-0.6578455744440.1552052685760.169529709613-0.3231284840510.2248609393940.114113278919-0.1855879852660.3168148411120.4056711751030.02403602699830.03128458463250.605764368566-0.1217979628070.348419770213-7.51444134909-38.7182506053-5.33664283163
134.93847422779-2.01491978242.702300919265.321836783054.006080288637.85746937406-0.0246577666413-0.5120112710780.1690621228740.275129408818-0.0715239870137-1.46141609275-0.3103398717110.46549886095-0.006156347385160.3389014388120.00473944784313-0.01118807612760.429838619039-0.03331165526030.69625376055737.39997213768.35537618935.5743695095
142.0132510507-1.33945974838-6.117598073223.183614911730.3393569495084.339091440590.141353991272-1.13118440322-0.9994841693370.437421623114-0.215433310719-0.324652754140.3547010804620.9173075577790.106525588640.681299596947-0.0819309013196-0.115599637120.5542148526540.03431152012380.54766097661725.5329424395-0.025683682122342.8250399163
159.19001100437-1.361816222834.549811415958.571602130617.023397662572.02793704589-0.32963296696-0.0701587731751.14212506359-0.2570119676090.167030485430.079933229685-1.389648031510.6846972710140.06836976300650.338499583008-0.0482350369265-0.04178095656220.3305533568970.001570418356510.44005314817210.35696819626.6633503206734.5507166198
166.974495553941.13067446219-1.056666050222.37833020190.8822539455092.268657029240.0854378284733-0.05575168091940.211342752609-0.0528837490406-0.0616569734580.184288418147-0.159034640869-0.278853079707-0.02551253496340.351684488304-0.000107863477151-0.02558692793780.3031969393530.005872967203570.2530823824746.22235278602-0.25259352086232.3794062453
174.322651798622.371623263310.7768743877172.078821779271.444187479314.74965167989-0.0783232239710.1648990415220.222578914972-0.405849863819-0.00636355243239-0.00434529587217-0.01655390119860.344452011771-0.00697660460640.2676540030880.003512518213630.01359626741590.3025542424630.006413827904490.29707015606529.62591992636.6382772371429.1602435306
187.82102474466-7.26577861497-6.108319285047.137982077435.583411111284.779753454580.5356201275740.735187956196-0.562495950865-1.57906883326-0.207557257566-0.0924126202026-0.5947920262130.168527911051-0.2623493738230.574925295708-0.0182893503640.07169077451780.460438203967-0.08341787371550.35938412409331.85599628323.7825400779921.647877262
199.732590358218.59007788249-7.281566855838.38023026816-7.373179277366.541975856950.07073435279360.1985915309780.0625734197482-0.09773279426960.08915589469790.7654089858740.372104265595-0.1667412621310.01564340512540.4533967700530.03491187380010.0002772972221440.362247412453-0.07315942030770.31478535198522.42888876235.7252700539525.8913338445
202.06899414333-1.267176641143.796218305247.014195401031.752347361998.416638008730.05562426292990.05719139134730.0236661120258-0.577102444685-0.2541990445740.3820550828660.290237447238-0.5977528254170.2210349785090.475521576599-0.0250305335848-0.03915205874120.381329613694-0.04560773708810.2932706083988.34334695563-3.3626239661823.7484257872
216.019870885963.238634023345.496090904045.832566225380.3970136116746.62014752926-0.1310141990470.553822583313-1.56699704562-0.8312160314860.01649725611860.5354888582210.480935095835-0.2782958092430.06805662976690.429839956496-0.0253469590518-0.005324826438520.318990729568-0.03747447050590.65071758659243.1457628695-29.97733172937.5155759749
227.584529203370.14177065477-1.424826430992.01119668744-0.9972192367057.64381793792-0.4701572602460.68946199207-0.945227609057-0.342497044510.03667244237520.3842249701341.232314031040.6446178745350.3354782154810.5706835036340.0001500203131440.02462341718460.570668190563-0.1357239936020.59506730335156.6325606811-24.683458133730.2259143251
237.99570838731.799840104248.587518406472.02076693729-1.707902799542.02526064768-0.556372841261-0.02565925085221.11747131009-0.0586637494990.08504296104130.526477504235-0.891408647497-0.9548630080030.269846885460.4507826938030.0274108850959-0.02822280789430.285648885243-0.0143829291230.42466563017559.2453312163-8.1239900619137.5739718813
244.617231054381.05755246168-1.383442342885.25968251994-3.734725553183.429902114110.0236355188116-0.1262944100270.1810877870030.304536523821-0.075057125629-0.301867997746-0.5525163063960.04702976824070.02120009068720.418360334525-0.0101041131863-0.07208022569020.339074847297-0.02020117418340.28301035585467.6939040077-8.4232061374740.7580724571
254.39358858954-0.1804162573131.337872343622.4922066853-0.373167674473.936358912080.052436605941-0.235166356401-0.4342306181850.1704386984460.0006409487021130.2451784848020.5468893377-0.245331046055-0.06559041040450.284259665305-0.0132407443259-0.01220806726880.198265859794-0.02217381519890.32930046790149.5743604581-24.264908578942.8319332647
266.569465183880.3148293665570.858975458390.868506121925-0.2075703638926.27380083242-0.195763737695-0.897228543722-0.3547090391270.644712811374-0.148200444208-0.414552467744-0.154488794376-0.001513499675180.2972928300390.3887591955620.0360221388868-0.0530591300850.3963164425530.06298493853420.34066509906850.5761560911-23.926241678348.62212439
277.685688336592.947696566610.8485944668632.125942802091.157892419917.636533219560.112651330351-0.4202691414390.1572654065170.157881561558-0.184996500047-0.350731797219-0.4331992630110.9871466309980.1017371756990.43738260925-0.0548507751289-0.1034270688170.4607911936510.03729544409050.37553878214269.0149194145-12.106782276149.2084620949
286.04107679697-3.755192632474.273423931982.031335081613.477439342266.639518293280.1389913742980.411683866924-0.837746217852-1.000353668490.672562391106-0.9332701735980.6120660117230.585703423449-0.9472018229020.6529361411760.0616132653695-0.002220768250990.687697260302-0.2422309119640.6961852521489.53692278195-38.25826832341.48450042023
295.02898813023-0.719690846870.9634823539766.55399541484-4.293627893637.41990943303-0.137627379430.213353399942-0.246854095285-1.92608813036-0.421341403174-0.765196554984-0.2260941953551.572099566960.4979391989811.08066442373-0.07603545735630.2157310388180.876024939505-0.1743737620450.64421420112711.2474236355-23.7712265848-5.9253891241
309.164089365022.689774747337.528080544457.30382582166.926249970229.58846138022-1.23812943164-0.9875072008570.7138641551410.6350250448010.8063346067650.5444911382580.34444219947-0.4854368442570.4822632424841.291419120080.283882848717-0.1820717567050.887338707354-0.2339972076620.612810472739-1.83386738988-13.56154264321.90255825919
313.1301496444-0.1669885872191.067801258233.48310530144-0.0359481559813.58337008714-0.3831730546160.1436374577130.1021735927580.04466725711760.151279454866-0.138278229277-1.31390652111-0.1899786330390.2203416662110.8193575091030.0174957141959-0.09777336923710.768109169407-0.1310528304750.3317998626655.51603068743-21.49712482277.75892614885
322.42560047995-1.12138336804-0.7224451253728.075737667443.002291288291.978857319070.339168145391-0.03382917290790.306498730086-1.15296722504-1.117086260920.434741660387-1.08343237968-0.08239404112090.745657752031.28921651420.210020341375-0.203416490520.788781643947-0.08251951423310.4428652832176.12869567854-6.7520266062912.7876761672
337.71134545088-3.356824693790.06178131698642.07533046262-1.695988916342.082780772560.6776472497421.234749627640.105193171331-0.834009818612-0.5542906923530.366280918672-0.509026388886-0.205882052398-0.001645636664110.650466651263-0.0143300602484-0.0293395682160.505976772218-0.03886041668460.46853772880329.299628269114.257561700324.0878154672
348.423735891210.784860746348-0.1096514212427.2092725071.50435447568.805420581780.0485557439834-0.853116280430.2523426849231.09095320531-0.2217007605930.448547749314-0.691634380342-0.5098474793330.1507447446340.3434354222910.112112389241-0.04683431742120.6176016388830.008702222749670.34940461624742.7655033919-19.896951842348.9406426568
354.15420398163-0.703704602804-1.45099378034.60402594870.09861155130344.121759112560.117526073218-0.71770256114-0.5032963923920.4148869154820.174669808942-0.00190768300190.3385848238340.295133383617-0.4033164229770.735895991952-0.0669366668064-0.1784887915270.87075168151-0.04671717615980.573391302991-0.101790862479-33.873489492312.807687064
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 0 through 15 )AA0 - 151 - 18
22chain 'A' and (resid 16 through 33 )AA16 - 3319 - 36
33chain 'A' and (resid 34 through 60 )AA34 - 6037 - 66
44chain 'A' and (resid 61 through 83 )AA61 - 8367 - 91
55chain 'A' and (resid 84 through 109 )AA84 - 10992 - 117
66chain 'A' and (resid 110 through 121 )AA110 - 121118 - 129
77chain 'B' and (resid -2 through 46 )BB-2 - 461 - 49
88chain 'B' and (resid 47 through 57 )BB47 - 5750 - 61
99chain 'B' and (resid 58 through 121 )BB58 - 12162 - 129
1010chain 'C' and (resid 0 through 45 )CC0 - 451 - 46
1111chain 'C' and (resid 46 through 83 )CC46 - 8347 - 86
1212chain 'C' and (resid 84 through 120 )CC84 - 12087 - 123
1313chain 'G' and (resid 2 through 14 )GD2 - 141 - 13
1414chain 'G' and (resid 15 through 25 )GD15 - 2514 - 24
1515chain 'G' and (resid 26 through 36 )GD26 - 3625 - 35
1616chain 'G' and (resid 37 through 55 )GD37 - 5536 - 54
1717chain 'G' and (resid 56 through 76 )GD56 - 7655 - 77
1818chain 'G' and (resid 77 through 83 )GD77 - 8378 - 84
1919chain 'G' and (resid 84 through 88 )GD84 - 8885 - 89
2020chain 'G' and (resid 89 through 104 )GD89 - 10490 - 105
2121chain 'H' and (resid 2 through 14 )HE2 - 141 - 13
2222chain 'H' and (resid 15 through 25 )HE15 - 2514 - 24
2323chain 'H' and (resid 26 through 35 )HE26 - 3525 - 34
2424chain 'H' and (resid 36 through 54 )HE36 - 5435 - 53
2525chain 'H' and (resid 55 through 71 )HE55 - 7154 - 72
2626chain 'H' and (resid 72 through 88 )HE72 - 8873 - 91
2727chain 'H' and (resid 89 through 104 )HE89 - 10492 - 107
2828chain 'I' and (resid 2 through 14 )IF2 - 141 - 13
2929chain 'I' and (resid 15 through 25 )IF15 - 2514 - 24
3030chain 'I' and (resid 26 through 36 )IF26 - 3625 - 35
3131chain 'I' and (resid 37 through 88 )IF37 - 8836 - 89
3232chain 'I' and (resid 89 through 104 )IF89 - 10490 - 105
3333chain 'G' and (resid 1074 through 1084 )GG1074 - 10841 - 11
3434chain 'H' and (resid 1074 through 1084 )HH1074 - 10841 - 11
3535chain 'I' and (resid 1074 through 1084 )II1074 - 10841 - 11

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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