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- PDB-8s7c: Ternary Complex of Cachd1, FZD5 and LRP6 -

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基本情報

登録情報
データベース: PDB / ID: 8s7c
タイトルTernary Complex of Cachd1, FZD5 and LRP6
要素
  • Frizzled-5
  • Low-density lipoprotein receptor-related protein 6
  • VWFA and cache domain-containing protein 1
キーワードSIGNALING PROTEIN / Cachd1 Frizzled-5 LRP6
機能・相同性
機能・相同性情報


regulation of chorionic trophoblast cell proliferation / Spemann organizer formation / intestinal epithelial cell maturation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Wnt-Frizzled-LRP5/6 complex / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / Regulation of FZD by ubiquitination / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Asymmetric localization of PCP proteins / chorionic trophoblast cell differentiation ...regulation of chorionic trophoblast cell proliferation / Spemann organizer formation / intestinal epithelial cell maturation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Wnt-Frizzled-LRP5/6 complex / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / Regulation of FZD by ubiquitination / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Asymmetric localization of PCP proteins / chorionic trophoblast cell differentiation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / embryonic camera-type eye morphogenesis / neural crest formation / glandular epithelial cell maturation / Signaling by RNF43 mutants / post-embryonic camera-type eye development / embryonic camera-type eye development / anterior/posterior axis specification, embryo / apoptotic process involved in morphogenesis / Ca2+ pathway / kinase inhibitor activity / toxin transmembrane transporter activity / cellular response to molecule of bacterial origin / Wnt receptor activity / non-canonical Wnt signaling pathway / low-density lipoprotein particle receptor activity / Wnt-protein binding / branching involved in labyrinthine layer morphogenesis / eye development / cellular response to cholesterol / midbrain dopaminergic neuron differentiation / dopaminergic neuron differentiation / frizzled binding / vasculature development / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / neural crest cell differentiation / labyrinthine layer blood vessel development / regulation of bicellular tight junction assembly / negative regulation of smooth muscle cell apoptotic process / protein serine/threonine kinase inhibitor activity / bicellular tight junction / canonical Wnt signaling pathway / coreceptor activity / positive regulation of cell cycle / Regulation of FZD by ubiquitination / positive regulation of interleukin-1 beta production / TCF dependent signaling in response to WNT / protein localization to plasma membrane / cell-cell adhesion / G protein-coupled receptor activity / response to peptide hormone / positive regulation of T cell cytokine production / Wnt signaling pathway / positive regulation of type II interferon production / endocytosis / positive regulation of tumor necrosis factor production / calcium ion transport / nervous system development / T cell differentiation in thymus / amyloid-beta binding / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / early endosome membrane / angiogenesis / perikaryon / chemical synaptic transmission / membrane raft / signaling receptor binding / Golgi membrane / negative regulation of cell population proliferation / axon / neuronal cell body / synapse / dendrite / ubiquitin protein ligase binding / lipid binding / protein kinase binding / positive regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular region / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Frizzled-5, CRD domain / Low density lipoprotein receptor-related protein 5/6 / : / Periplasmic sensor-like domain superfamily / : / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled ...Frizzled-5, CRD domain / Low density lipoprotein receptor-related protein 5/6 / : / Periplasmic sensor-like domain superfamily / : / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Coagulation Factor Xa inhibitory site / VWFA domain profile. / von Willebrand factor, type A / Epidermal growth factor-like domain. / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain
類似検索 - ドメイン・相同性
Low-density lipoprotein receptor-related protein 6 / VWFA and cache domain-containing protein 1 / Frizzled-5
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 4.7 Å
データ登録者Zhao, Y. / Ren, J. / Jones, E.Y.
資金援助 英国, 2件
組織認可番号国
Cancer Research UKC375/A17721 英国
Wellcome Trust223133/Z/21/Z 英国
引用ジャーナル: Science / 年: 2024
タイトル: Cachd1 interacts with Wnt receptors and regulates neuronal asymmetry in the zebrafish brain.
著者: Powell, G.T. / Faro, A. / Zhao, Y. / Stickney, H. / Novellasdemunt, L. / Henriques, P. / Gestri, G. / Redhouse White, E. / Ren, J. / Lu, W. / Young, R.M. / Hawkins, T.A. / Cavodeassi, F. / ...著者: Powell, G.T. / Faro, A. / Zhao, Y. / Stickney, H. / Novellasdemunt, L. / Henriques, P. / Gestri, G. / Redhouse White, E. / Ren, J. / Lu, W. / Young, R.M. / Hawkins, T.A. / Cavodeassi, F. / Schwarz, Q. / Dreosti, E. / Raible, D.W. / Li, V.S.W. / Wright, G.J. / Jones, E.Y. / Wilson, S.W.
履歴
登録2024年2月29日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年4月24日Provider: repository / タイプ: Initial release
改定 1.12024年5月15日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: VWFA and cache domain-containing protein 1
B: Frizzled-5
C: Low-density lipoprotein receptor-related protein 6
D: VWFA and cache domain-containing protein 1
E: Frizzled-5
F: Low-density lipoprotein receptor-related protein 6
G: VWFA and cache domain-containing protein 1
H: Frizzled-5
I: Low-density lipoprotein receptor-related protein 6
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)637,94241
ポリマ－630,4579
非ポリマー7,48532
水00
1
A: VWFA and cache domain-containing protein 1
B: Frizzled-5
C: Low-density lipoprotein receptor-related protein 6
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)212,56813
ポリマ－210,1523
非ポリマー2,41510
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: VWFA and cache domain-containing protein 1
E: Frizzled-5
F: Low-density lipoprotein receptor-related protein 6
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)212,58614
ポリマ－210,1523
非ポリマー2,43311
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
G: VWFA and cache domain-containing protein 1
H: Frizzled-5
I: Low-density lipoprotein receptor-related protein 6
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)212,78914
ポリマ－210,1523
非ポリマー2,63611
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)283.697, 198.236, 218.824
Angle α, β, γ (deg.)90.00, 128.07, 90.00
Int Tables number5
Space group name H-MC121

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要素

#1: タンパク質 VWFA and cache domain-containing protein 1 / Cache domain-containing protein 1


分子量: 123058.031 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Cachd1, Kiaa1573, Vwcd1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q6PDJ1
#2: タンパク質 Frizzled-5 / Fz-5 / mFz5


分子量: 15924.286 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Fzd5 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9EQD0
#3: タンパク質 Low-density lipoprotein receptor-related protein 6 / LRP-6


分子量: 71170.094 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: LRP6 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O75581
#4: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 糖...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 30 / 由来タイプ: 合成 / 式: C8H15NO6 / タイプ: SUBJECT OF INVESTIGATION
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
研究の焦点であるリガンドがあるかY
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: 3.84 Å3/Da / 溶媒含有率: 68 %
結晶化温度: 296 K / 手法: 蒸発脱水法 / pH: 4.5
詳細: 0.1 M Calcium Acetate 0.1 M Sodium Acetate 10% PEG 4000 pH 4.5

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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: Diamond / ビームライン: I03 / 波長: 0.9762 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2018年7月2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: 0.9762 Å / 相対比: 1
反射解像度: 4.7→172.259 Å / Num. obs: 23514 / % possible obs: 88.8 % / 冗長度: 6.8 % / CC1/2: 0.99 / Net I/σ(I): 6.3
反射 シェル解像度: 4.7→5.4 Å / Num. unique obs: 1177 / CC1/2: 0.437

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.18.2_3874: ???)精密化
xia2データスケーリング
xia2データ削減
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 4.7→86.13 Å / SU ML: 0.78 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 36.65 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2608 1186 5.05 %
Rwork0.2063 --
obs0.2092 23464 47.21 %
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
精密化ステップサイクル: LAST / 解像度: 4.7→86.13 Å
タンパク質核酸リガンド溶媒全体
原子数41238 0 476 0 41714
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00242599
X-RAY DIFFRACTIONf_angle_d0.57757838
X-RAY DIFFRACTIONf_dihedral_angle_d9.69715777
X-RAY DIFFRACTIONf_chiral_restr0.0496591
X-RAY DIFFRACTIONf_plane_restr0.0047456
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.7-4.910.5734120.3167203X-RAY DIFFRACTION3
4.92-5.170.3495190.3085505X-RAY DIFFRACTION9
5.17-5.50.4165610.3072899X-RAY DIFFRACTION15
5.5-5.920.3808780.30861529X-RAY DIFFRACTION26
5.92-6.520.36821660.29332903X-RAY DIFFRACTION50
6.52-7.460.30382240.24844498X-RAY DIFFRACTION76
7.46-9.40.26652940.18995810X-RAY DIFFRACTION98
9.4-86.130.20933320.17395931X-RAY DIFFRACTION99
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)
10.0279-0.8538-0.85831.31081.97892.3675-0.98671.6628-0.1886-0.79750.0106-0.09820.3964-0.7427-0.15990.6673-0.6103-0.72872.0004-0.1941.7951-60.6769-82.842115.6162
25.888-2.0135-2.61414.3685-3.77437.0873-0.89020.54391.101-0.5333-0.0624-1.06940.206-1.00110.26750.54650.0141-0.33991.80890.34272.061-24.6874-105.263219.7284
31.76411.37340.39241.08150.88052.855-0.5761-0.0870.9136-1.2768-0.1508-0.7357-0.34940.3212-0.26960.92590.29530.04151.65930.16181.3259-30.9645-101.95525.9867
41.8016-1.7122-0.43081.6588-0.4496.85510.55021.16020.72480.77910.0361-0.9514-2.3150.9479-0.24672.2393-0.5126-0.2471.5543-0.25241.6007-26.927-83.184350.5281
50.7136-0.34650.35871.97950.7674.0847-1.32430.04010.98450.440.1841-0.8207-0.37290.76870.20331.37470.085-0.17942.0915-0.10731.9629-22.4799-95.076861.6537
63.9160.26321.69912.9190.66290.6615-0.40650.3165-0.26020.42090.28940.34660.2370.23840.25421.2791-0.18670.29661.1659-0.13561.3504-51.4344-87.830424.9867
70.8596-0.1244-1.13011.88490.28121.7295-0.26580.04150.02180.7271-0.17630.5032-0.64340.5683-0.0681.4876-0.0183-0.18772.02780.29281.1217-56.7928-78.13062.9613
81.4853-0.88570.77776.093-0.70670.34651.10061.23060.36892.0467-0.64010.8632-0.51950.81540.19832.92090.15270.19291.6815-0.25571.2496-56.6479-56.436611.2695
96.7071.44954.58920.59290.53715.79511.7922-0.35770.77581.3647-0.81390.5017-1.9948-1.4958-1.05482.724-0.0240.62931.6730.19981.8572-53.8305-51.936726.6764
100.6778-2.15680.1155.2163-0.30131.1079-0.0789-0.40390.0648-0.83740.1849-1.9258-1.7058-0.73740.08053.0008-0.46030.49541.1682-0.44021.8364-49.5697-59.348232.0564
114.4358-3.1621-0.01092.31611.1598.1897-1.5029-2.63281.7931-1.39810.9782-1.5860.20060.53270.81481.7957-0.6209-0.03972.0652-0.12732.2677-37.7412-55.67350.7245
126.08261.83380.5955.50182.10996.7754-2.817-0.6911.5602-0.3839-1.44480.8243-1.0416-1.64333.84182.14220.86650.34563.0272-0.75182.5642-51.3554-30.871452.3781
133.51032.67863.4792.33932.64833.444-2.34990.9026-0.8091-0.9645-1.34830.5356-0.4849-1.35993.1092.37740.66130.86192.4709-0.02271.4421-45.9505-39.267852.028
143.00612.51070.27745.53832.43633.98970.14081.44650.6873-6.6020.49641.38121.0433-0.5983-0.38155.05840.9212-0.31881.05170.69612.9335-47.4047-28.692343.8707
157.45632.6938-0.81051.9991-8.94289.61321.76532.06481.3454-5.94261.52590.2325-3.2653-0.679-1.08835.03360.13340.57572.212-0.60062.1728-44.5674-43.769542.4656
163.37213.0121-4.30282.6982-3.88965.8308-0.15313.37731.662-1.14971.8132-2.3166-1.3581-0.33120.01174.7324-0.2478-0.35863.59780.09912.9858-39.6269-38.197945.6117
174.6776-1.2562-0.95076.2607-0.97882.48243.65330.06772.8196-2.4654-0.597-1.9794-2.7798-0.7999-1.46213.95760.12360.28271.6991-1.12832.1223-38.9005-25.020752.668
181.9969-5.3073-7.82055.55163.43615.7158-2.3717-1.743-3.3812.9141-1.1679-0.52630.34921.23120.452.53090.1171-0.65393.14-0.55452.0647-30.3998-44.260840.169
199.69614.37750.45795.5546-5.33819.1153-2.19511.0831-1.77361.39671.1163-0.0505-0.70540.94671.61632.5145-0.56011.06042.74520.05412.2314-37.4384-45.091233.4525
207.45181.27733.6293.70710.19442.6073-0.04541.4257-0.41170.249-0.5291.79420.4105-1.19380.6141.5337-0.29251.28723.3715-1.04242.7787-32.3599-32.726836.7477
210.74370.24860.88078.4578-1.33361.41760.15991.31840.48812.00110.10240.6024-1.3263-0.598-0.03210.89070.93011.12152.61090.67971.7978-41.5722-135.961827.3146
223.66010.39950.67072.5461-1.51752.7777-1.38770.06160.1156-0.26070.36431.3951.1302-0.3392-0.00870.8403-0.15160.66162.0306-0.30891.2225-28.1911-138.908232.2304
231.392-0.89621.29815.4132-1.27956.7285-1.2870.23041.4436-1.14050.68690.79881.03750.4482-0.12381.0791-0.0639-0.28761.5622-0.03251.6202-19.2781-137.022424.1006
240.6027-0.3311.68372.410.45735.5399-0.33630.3061-0.69780.1749-0.9815-1.2339-1.0424-0.0182-0.52730.3665-0.46810.03971.49690.10771.5866-23.005-133.226913.0002
251.72070.3824-1.77631.67460.81932.9228-0.0020.51431.2703-0.50010.1577-0.6149-1.4202-0.5347-0.01871.27770.14250.0321.88490.22861.0891-36.3399-128.080511.0414
261.8972-0.35510.09191.91780.79390.1739-1.06370.6695-0.4596-0.46950.49260.0412-0.266-0.99220.22911.7512-0.3132-0.24781.63140.15921.1483-19.9242-148.683432.4728
271.2986-0.8929-2.65349.96911.23516.3099-1.1017-0.04880.76462.64830.88390.63392.0453-0.1575-1.15251.06250.5225-0.60781.65730.35871.3493-18.4454-139.657453.2244
283.9659-0.6784-2.14872.7296-1.7844.36010.0766-0.3459-0.67881.15031.4243-1.265-1.38040.5237-0.78962.0994-0.309-0.39921.8359-0.0941.3829-14.6339-139.485470.3234
292.94282.1912.01927.4415-0.44591.8669-0.2129-0.2540.61761.2966-0.1576-0.4753-0.97520.15140.20891.52770.0616-0.19312.09060.17761.9799-1.2108-133.953559.6953
301.6162-1.4794-2.07481.2911.83642.4611-0.4294-0.2724-1.51721.1162-0.87180.78971.1107-0.25971.36282.09290.2962-0.52712.42410.26822.0397-10.8489-155.398578.443
310.65260.5551.66813.6523-1.00822.79550.35260.1013-1.8127-1.70560.5152-0.17171.32470.37450.49620.28250.65290.57181.8101-0.14661.8215-90.645-115.398532.3446
320.44080.7690.55121.00561.78963.61970.0409-0.10710.02081.2597-0.2347-0.67090.3339-0.1072-0.06571.49570.2395-0.14771.31330.07881.4423-110.8631-90.067944.6166
331.00590.9636-0.70952.77491.21253.2125-0.2656-0.44380.08210.0310.4948-0.13020.2917-1.6467-0.00031.4842-0.1297-0.27471.8676-0.05781.1865-110.8966-81.379441.9972
341.1295-0.618-1.37461.39830.72661.72460.17830.1257-0.11960.6777-0.45530.97160.70340.19730.10471.87210.02530.24311.29070.06531.8011-82.3255-124.859942.6628
351.633-0.38860.62113.44713.36995.9469-0.2151-0.1733-0.5425-0.208-0.1263-0.03420.7983-0.57810.31161.15710.19540.07311.84070.20841.6931-92.1395-128.371864.1339
362.1162-4.2999-0.36359.3828-0.64452.72882.0601-0.243-2.1662-3.37610.9307-1.9618-2.544-0.001-1.92612.9658-0.4284-0.63022.79520.35012.5317-88.6554-110.947797.5013
370.82880.8816-0.770.9371-0.8220.85760.04181.87192.2717-1.5168-1.26740.34141.9402-0.31970.45844.02580.5087-0.23022.19710.62792.4468-90.1806-121.32998.9867
383.05070.0107-0.59813.66182.07243.93470.9150.5429-1.64330.53441.30130.7488-4.3133-1.1373-1.56333.61620.0354-0.58622.01550.17061.9033-94.4308-114.708587.2901
391.26040.3028-2.05550.056-0.50093.3021-0.111-0.66650.67762.69680.59110.79013.6175-1.30460.41623.7947-0.44430.03521.8585-0.03851.2669-103.1173-115.438194.5669
405.86294.0971-3.09683.9518-3.52833.34310.05670.9408-0.84070.53920.91211.6673-0.077-0.728-0.06192.6997-1.70840.82011.8132-0.382.3825-100.9296-121.568579.7827
415.58983.65782.13971.9962-3.05363.37661.56930.5761-0.79910.05031.36582.33331.7614-1.1441.9741.4114-0.9746-0.09023.7789-0.06651.2794-105.4578-124.847892.4714
421.77971.02771.13442.0585-0.61852.96541.2758-0.62950.53260.2180.1941-0.68530.21261.34080.5566-0.62360.42580.56362.04120.50652.1815-98.5252-82.1311-2.142
433.5022-1.02472.26050.611-0.55541.49370.53630.1552-0.3759-0.3502-0.076-0.34880.7341.24560.00290.8586-0.41440.41371.5574-0.29581.4087-116.34-79.4424-2.2093
441.4247-2.15451.85843.3522-2.5476.9497-0.32871.64790.7665-0.4247-0.3334-1.37530.49710.57880.09530.8437-0.2747-0.15232.1078-0.30371.9509-117.563-96.8116-5.2547
454.7599-1.1241-2.03412.0478-2.63515.30030.906-0.4933-0.59631.51320.22990.115-0.91120.7509-0.16690.47160.01290.67971.6979-0.58661.8386-103.4697-94.4186-6.3539
461.0311.9406-0.56353.5476-1.41428.6654-0.92080.24142.5127-0.442-0.37210.3463-0.6999-3.574-0.731-0.0209-0.1835-0.17212.0132-0.92042.6161-123.9699-68.3274-14.1531
470.355-1.3114-0.42236.44493.65582.54490.4897-0.7128-0.2815-0.0761-1.67610.31131.3395-0.70350.34820.5326-0.0908-0.15341.5187-0.21071.1082-125.8329-47.789316.759
483.412-0.57551.04523.91591.64361.5758-0.47120.4018-1.35341.43890.9121.6426-0.6748-0.66020.51030.7771-0.1070.76252.5030.52721.6408-134.2683-58.202712.8489
492.97522.2492-0.75153.23850.33933.8018-0.20890.26621.1656-0.8595-1.07391.7918-2.43510.57070.33751.12130.09890.24491.5181-0.08141.73-125.0987-26.01538.1678
500.16520.77360.14254.0869-1.80151.2215-0.7208-0.5968-0.2990.6031-0.12280.0285-1.00070.2809-0.2651.49590.0264-0.00831.458-0.40791.3714-56.62783.4397106.7187
512.7971.0553-0.08231.30940.93584.95340.2831-0.3919-0.03461.0593-0.2848-0.3079-0.66341.13220.35991.18880.07170.24731.60370.02321.5409-25.22825.514282.6912
524.63132.0911.53884.6488-0.38916.25750.7093-0.1119-0.54361.8202-1.3402-0.43040.12221.09320.66821.48090.97260.16530.9940.59221.5948-26.0484-26.568386.6323
533.69931.63752.49583.97220.58064.2572-1.18210.6868-1.80260.28070.6985-0.73030.38150.5970.23591.01351.16450.07851.84870.71051.514-25.5406-33.284179.4109
541.2854-0.99140.07282.5997-0.23490.99010.0349-0.24940.11170.8971-0.0111-0.1686-0.0251-0.0290.2031.5517-0.3112-0.29941.03980.0591.2158-46.6136-2.6198104.2632
553.8476-3.8263-0.59843.77921.26513.5162-0.4648-1.0781-1.65811.1017-0.02391.07570.8489-0.27990.13512.9451-0.35010.41781.19980.25831.2581-49.4538-22.1131127.2648
561.5781-1.1295-2.20773.83611.25492.85270.39240.1942-0.59740.930.39610.1604-0.4102-0.4257-0.1983.1802-0.09430.04561.1730.31092.1632-45.8885-23.1803117.9766
572.27052.44062.72963.38253.35423.47430.2937-0.74710.0290.43881.1964-2.67820.96841.359-1.46192.4301-0.116-0.39972.1094-0.11452.8668-31.37131.2847135.8293
580.4502-0.0515-0.32940.0221-0.18212.4917-2.1188-1.0634-0.821-0.61221.5521.5427-1.06170.54660.28832.734-0.73990.58522.0301-0.42132.2056-44.7446-53.1076130.5931
595.33162.2159-3.67789.0043-3.58476.8511.5897-0.28120.27454.37520.4355-1.45041.7071-0.08520.90173.3291-1.10760.44091.44930.10892.1398-42.816-41.218132.239
603.217-0.6732-0.50690.9034-2.30617.32-0.7005-0.07430.33674.3228-1.1042-2.89470.7192-1.60280.59923.1367-0.8573-0.20331.51490.04622.6335-34.9228-51.4962130.7037
610.27570.0517-0.20232.232-2.09052.1786-1.41090.0804-0.3280.2574-0.6418-3.02-0.93131.00860.9191.8227-0.3116-0.84082.52521.02573.1741-28.2433-37.7946128.5459
620.2152-1.0796-0.01215.00480.48330.7435-0.29150.81180.36050.6958-0.05381.31870.53480.24060.07830.54250.1676-0.11542.02150.31271.8404-40.199719.117253.5081
632.6168-0.5585-0.23363.97161.48141.1829-0.76712.45182.27540.46660.75181.5272-0.4782-0.4684-0.00791.1819-0.1732-0.34391.10030.63511.9081-27.554815.353747.4693
640.48440.7624-1.06452.2482-1.04132.4644-0.16210.3850.08060.6263-0.6559-0.48990.62760.81880.17120.9082-0.1776-0.85432.00450.47521.1654-18.929524.53156.8055
650.81811.8496-0.18595.1722-0.04520.5780.312-0.45-0.65590.9372-0.61450.0146-0.85930.20880.17041.8531-1.2734-1.94250.5542-0.59351.9063-28.655830.819466.6126
662.54070.8668-1.62111.331-0.47770.990.4818-0.22760.18380.35490.41220.06570.74020.6961-0.09131.0321-0.1038-0.36451.3633-0.13861.5424-31.923428.187755.6762
672.4349-2.70071.54335.3962-0.8563.25320.1196-0.7335-0.1885-0.5977-0.3058-0.82820.1570.31970.09751.5040.62060.58171.87120.36610.8526-18.8495-1.460633.267
681.14790.07050.16560.6431.56363.7017-0.1324-0.53320.9248-0.5279-1.3132-1.85952.70280.8740.81021.9080.61440.2052.16880.62162.2304-15.5123-22.870426.666
694.0892-2.04310.52393.0006-1.09141.62040.02981.4750.1156-0.0319-1.6496-0.1342-0.03852.3366-0.0541.31930.9860.24652.46830.20842.4747-2.1841-20.390833.6737
702.46180.7064-1.45792.51912.50414.1250.59330.0819-0.3936-0.05990.1173-0.20491.46580.9417-0.19961.70020.52780.14841.97030.37781.9448-9.1249-10.10826.5646
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 53 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 182 )
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 239 )
4X-RAY DIFFRACTION4chain 'A' and (resid 240 through 340 )
5X-RAY DIFFRACTION5chain 'A' and (resid 341 through 436 )
6X-RAY DIFFRACTION6chain 'A' and (resid 437 through 678 )
7X-RAY DIFFRACTION7chain 'A' and (resid 679 through 787 )
8X-RAY DIFFRACTION8chain 'A' and (resid 788 through 865 )
9X-RAY DIFFRACTION9chain 'A' and (resid 866 through 942 )
10X-RAY DIFFRACTION10chain 'A' and (resid 943 through 1015 )
11X-RAY DIFFRACTION11chain 'A' and (resid 1016 through 1088 )
12X-RAY DIFFRACTION12chain 'B' and (resid 32 through 38 )
13X-RAY DIFFRACTION13chain 'B' and (resid 39 through 46 )
14X-RAY DIFFRACTION14chain 'B' and (resid 47 through 59 )
15X-RAY DIFFRACTION15chain 'B' and (resid 60 through 81 )
16X-RAY DIFFRACTION16chain 'B' and (resid 82 through 90 )
17X-RAY DIFFRACTION17chain 'B' and (resid 91 through 105 )
18X-RAY DIFFRACTION18chain 'B' and (resid 106 through 122 )
19X-RAY DIFFRACTION19chain 'B' and (resid 123 through 128 )
20X-RAY DIFFRACTION20chain 'B' and (resid 129 through 135 )
21X-RAY DIFFRACTION21chain 'C' and (resid 630 through 690 )
22X-RAY DIFFRACTION22chain 'C' and (resid 691 through 733 )
23X-RAY DIFFRACTION23chain 'C' and (resid 734 through 777 )
24X-RAY DIFFRACTION24chain 'C' and (resid 778 through 819 )
25X-RAY DIFFRACTION25chain 'C' and (resid 820 through 878 )
26X-RAY DIFFRACTION26chain 'C' and (resid 879 through 947 )
27X-RAY DIFFRACTION27chain 'C' and (resid 948 through 993 )
28X-RAY DIFFRACTION28chain 'C' and (resid 994 through 1081 )
29X-RAY DIFFRACTION29chain 'C' and (resid 1082 through 1203 )
30X-RAY DIFFRACTION30chain 'C' and (resid 1204 through 1246 )
31X-RAY DIFFRACTION31chain 'D' and (resid 53 through 168 )
32X-RAY DIFFRACTION32chain 'D' and (resid 169 through 369 )
33X-RAY DIFFRACTION33chain 'D' and (resid 370 through 506 )
34X-RAY DIFFRACTION34chain 'D' and (resid 507 through 865 )
35X-RAY DIFFRACTION35chain 'D' and (resid 866 through 1088 )
36X-RAY DIFFRACTION36chain 'E' and (resid 32 through 46 )
37X-RAY DIFFRACTION37chain 'E' and (resid 47 through 59 )
38X-RAY DIFFRACTION38chain 'E' and (resid 60 through 90 )
39X-RAY DIFFRACTION39chain 'E' and (resid 91 through 122 )
40X-RAY DIFFRACTION40chain 'E' and (resid 123 through 128 )
41X-RAY DIFFRACTION41chain 'E' and (resid 129 through 135 )
42X-RAY DIFFRACTION42chain 'F' and (resid 630 through 690 )
43X-RAY DIFFRACTION43chain 'F' and (resid 691 through 777 )
44X-RAY DIFFRACTION44chain 'F' and (resid 778 through 834 )
45X-RAY DIFFRACTION45chain 'F' and (resid 835 through 896 )
46X-RAY DIFFRACTION46chain 'F' and (resid 897 through 930 )
47X-RAY DIFFRACTION47chain 'F' and (resid 931 through 1146 )
48X-RAY DIFFRACTION48chain 'F' and (resid 1147 through 1203 )
49X-RAY DIFFRACTION49chain 'F' and (resid 1204 through 1246 )
50X-RAY DIFFRACTION50chain 'G' and (resid 53 through 129 )
51X-RAY DIFFRACTION51chain 'G' and (resid 130 through 239 )
52X-RAY DIFFRACTION52chain 'G' and (resid 240 through 304 )
53X-RAY DIFFRACTION53chain 'G' and (resid 305 through 386 )
54X-RAY DIFFRACTION54chain 'G' and (resid 387 through 865 )
55X-RAY DIFFRACTION55chain 'G' and (resid 866 through 942 )
56X-RAY DIFFRACTION56chain 'G' and (resid 943 through 1015 )
57X-RAY DIFFRACTION57chain 'G' and (resid 1016 through 1088 )
58X-RAY DIFFRACTION58chain 'H' and (resid 32 through 51 )
59X-RAY DIFFRACTION59chain 'H' and (resid 52 through 76 )
60X-RAY DIFFRACTION60chain 'H' and (resid 77 through 105 )
61X-RAY DIFFRACTION61chain 'H' and (resid 106 through 135 )
62X-RAY DIFFRACTION62chain 'I' and (resid 630 through 690 )
63X-RAY DIFFRACTION63chain 'I' and (resid 691 through 733 )
64X-RAY DIFFRACTION64chain 'I' and (resid 734 through 819 )
65X-RAY DIFFRACTION65chain 'I' and (resid 820 through 849 )
66X-RAY DIFFRACTION66chain 'I' and (resid 850 through 911 )
67X-RAY DIFFRACTION67chain 'I' and (resid 912 through 1032 )
68X-RAY DIFFRACTION68chain 'I' and (resid 1033 through 1081 )
69X-RAY DIFFRACTION69chain 'I' and (resid 1082 through 1146 )
70X-RAY DIFFRACTION70chain 'I' and (resid 1147 through 1246 )

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万見について

-
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