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- PDB-4q6i: Crystal structure of murine 2D5 Fab, a potent anti-CD4 HIV-1-neut... -

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基本情報

登録情報
データベース: PDB / ID: 4q6i
タイトルCrystal structure of murine 2D5 Fab, a potent anti-CD4 HIV-1-neutralizing antibody in complex with CD4
要素
  • Heavy chain of murine 2D5 Fab
  • Light chain of murine 2D5 Fab
  • T-cell surface glycoprotein CD4
キーワードIMMUNE SYSTEM / Ig fold / Antibody / anti-CD4 / HIV-1 neutralization / CD4
機能・相同性
機能・相同性情報


helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / cellular response to ionomycin / response to methamphetamine hydrochloride / T cell selection / MHC class II protein binding / interleukin-15-mediated signaling pathway / cellular response to granulocyte macrophage colony-stimulating factor stimulus ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / cellular response to ionomycin / response to methamphetamine hydrochloride / T cell selection / MHC class II protein binding / interleukin-15-mediated signaling pathway / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of monocyte differentiation / Alpha-defensins / Nef Mediated CD4 Down-regulation / regulation of T cell activation / response to vitamin D / Other interleukin signaling / extracellular matrix structural constituent / T cell receptor complex / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / macrophage differentiation / immunoglobulin binding / T cell differentiation / Co-inhibition by PD-1 / positive regulation of calcium ion transport into cytosol / Binding and entry of HIV virion / positive regulation of interleukin-2 production / coreceptor activity / positive regulation of T cell proliferation / positive regulation of calcium-mediated signaling / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / Vpu mediated degradation of CD4 / MHC class II protein complex binding / response to estradiol / transmembrane signaling receptor activity / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / T cell receptor signaling pathway / Clathrin-mediated endocytosis / virus receptor activity / signaling receptor activity / defense response to Gram-negative bacterium / adaptive immune response / response to ethanol / early endosome / cell surface receptor signaling pathway / cell adhesion / immune response / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / symbiont entry into host cell / lipid binding / endoplasmic reticulum membrane / protein kinase binding / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane
類似検索 - 分子機能
CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 ...CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
T-cell surface glycoprotein CD4
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.65 Å
データ登録者Boyington, J.C. / Nabel, G.J. / Mascola, J.R.
引用ジャーナル: Sci Transl Med / 年: 2014
タイトル: Neutralizing antibodies to HIV-1 envelope protect more effectively in vivo than those to the CD4 receptor.
著者: Pegu, A. / Yang, Z.Y. / Boyington, J.C. / Wu, L. / Ko, S.Y. / Schmidt, S.D. / McKee, K. / Kong, W.P. / Shi, W. / Chen, X. / Todd, J.P. / Letvin, N.L. / Huang, J. / Nason, M.C. / Hoxie, J.A. / ...著者: Pegu, A. / Yang, Z.Y. / Boyington, J.C. / Wu, L. / Ko, S.Y. / Schmidt, S.D. / McKee, K. / Kong, W.P. / Shi, W. / Chen, X. / Todd, J.P. / Letvin, N.L. / Huang, J. / Nason, M.C. / Hoxie, J.A. / Kwong, P.D. / Connors, M. / Rao, S.S. / Mascola, J.R. / Nabel, G.J.
履歴
登録2014年4月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年7月23日Provider: repository / タイプ: Initial release
改定 1.12024年11月6日Group: Data collection / Database references / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Light chain of murine 2D5 Fab
B: Heavy chain of murine 2D5 Fab
C: T-cell surface glycoprotein CD4
D: Light chain of murine 2D5 Fab
E: Heavy chain of murine 2D5 Fab
F: Light chain of murine 2D5 Fab
G: Heavy chain of murine 2D5 Fab
H: Heavy chain of murine 2D5 Fab
I: T-cell surface glycoprotein CD4
J: T-cell surface glycoprotein CD4
K: T-cell surface glycoprotein CD4
L: Light chain of murine 2D5 Fab


分子量 (理論値)分子数
合計 (水以外)287,96012
ポリマ－287,96012
非ポリマー00
水00
1
A: Light chain of murine 2D5 Fab
B: Heavy chain of murine 2D5 Fab
K: T-cell surface glycoprotein CD4


分子量 (理論値)分子数
合計 (水以外)71,9903
ポリマ－71,9903
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: Light chain of murine 2D5 Fab
E: Heavy chain of murine 2D5 Fab
J: T-cell surface glycoprotein CD4


分子量 (理論値)分子数
合計 (水以外)71,9903
ポリマ－71,9903
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
F: Light chain of murine 2D5 Fab
G: Heavy chain of murine 2D5 Fab
I: T-cell surface glycoprotein CD4


分子量 (理論値)分子数
合計 (水以外)71,9903
ポリマ－71,9903
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
C: T-cell surface glycoprotein CD4
H: Heavy chain of murine 2D5 Fab
L: Light chain of murine 2D5 Fab


分子量 (理論値)分子数
合計 (水以外)71,9903
ポリマ－71,9903
非ポリマー00
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)149.547, 149.547, 183.867
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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要素

#1: 抗体
Light chain of murine 2D5 Fab


分子量: 24157.643 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ)
#2: 抗体
Heavy chain of murine 2D5 Fab


分子量: 24830.010 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ)
#3: タンパク質
T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


分子量: 23002.369 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CD4 / 細胞株 (発現宿主): HEK293 / 発現宿主: homo sapiens (ヒト) / 参照: UniProt: P01730
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: 3.57 Å3/Da / 溶媒含有率: 65.55 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.5
詳細: 1.5 M (NH4)2SO4, 200 mM MgCl2, 150 mM NaCl, 100 mM NaAc pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 22-BM / 波長: 1 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2009年4月2日
放射モノクロメーター: Si(111) / 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: 3.65→30 Å / Num. all: 47683 / Num. obs: 46157 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 3.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.5
反射 シェル解像度: 3.65→3.78 Å / 冗長度: 2.6 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 1.9 / % possible all: 75.4

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解析

ソフトウェア
名称バージョン分類
SERGUIデータ収集
PHASER位相決定
PHENIX(phenix.refine: 1.8.4_1496)精密化
HKL-2000データ削減
HKL-2000データスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 3.65→29.909 Å / SU ML: 0.51 / σ(F): 1.34 / 位相誤差: 30.24 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2571 2207 5.08 %
Rwork0.2262 --
obs0.2278 43407 96.78 %
all-47683 -
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: 3.65→29.909 Å
タンパク質核酸リガンド溶媒全体
原子数19192 0 0 0 19192
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00319649
X-RAY DIFFRACTIONf_angle_d0.78426654
X-RAY DIFFRACTIONf_dihedral_angle_d13.5797170
X-RAY DIFFRACTIONf_chiral_restr0.0283000
X-RAY DIFFRACTIONf_plane_restr0.0043418
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.65-3.72930.3029850.3671840X-RAY DIFFRACTION70
3.7293-3.81580.39421210.35112318X-RAY DIFFRACTION87
3.8158-3.91110.34671430.33732514X-RAY DIFFRACTION96
3.9111-4.01660.35811280.3342657X-RAY DIFFRACTION99
4.0166-4.13450.32041500.30122620X-RAY DIFFRACTION100
4.1345-4.26750.36831310.27542652X-RAY DIFFRACTION100
4.2675-4.41960.2771450.26582654X-RAY DIFFRACTION100
4.4196-4.5960.3051600.25272646X-RAY DIFFRACTION100
4.596-4.80430.25851370.23362637X-RAY DIFFRACTION100
4.8043-5.05650.24661400.22632642X-RAY DIFFRACTION100
5.0565-5.37160.25681530.22472679X-RAY DIFFRACTION100
5.3716-5.78360.25111260.22252680X-RAY DIFFRACTION100
5.7836-6.36050.22981450.22512657X-RAY DIFFRACTION100
6.3605-7.26940.26051400.2212664X-RAY DIFFRACTION100
7.2694-9.11540.21291570.17972668X-RAY DIFFRACTION100
9.1154-29.91040.1991460.15542672X-RAY DIFFRACTION98
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)
14.0880.5422-0.92427.3668-2.10992.5589-0.4233-0.2713-0.06760.68360.46150.9019-0.2275-0.2519-0.00131.38070.08870.25042.1271-0.19461.377-45.0805-47.571185.451
20.9042-0.9174-0.7750.94190.79830.6645-0.9314-0.47830.9181-0.4904-0.3754-1.16790.84940.5983-0.07331.46940.2194-0.29352.5109-0.43951.3882-42.3302-34.7127180.1975
32.1822-2.01-0.05293.2750.72670.2859-0.9545-2.0151.72062.4320.041-0.75451.75750.617-0.09253.68410.4733-0.40723.3038-0.03871.544-32.5398-51.2611216.1599
43.0133-1.87551.9461.4741-1.28811.28390.2064-2.3372-0.20160.64951.2424-0.32450.87540.54170.19392.98530.9476-0.34.5907-0.53641.6232-31.5683-50.3648219.3977
55.36680.95630.48714.2115-1.03180.5788-0.2781-2.5615-0.77941.1796-0.0627-0.1295-0.5688-1.3685-0.00023.56660.7431-0.30483.2594-0.03841.7581-35.1404-47.9446223.6694
61.96551.0198-0.45890.4787-0.18960.08-0.3687-0.17990.96242.85190.9897-1.79591.02872.0230.01562.04780.1393-0.81731.6133-0.54521.8779-19.9749-33.1992191.0115
71.9984-1.5033-0.16461.11060.17310.54750.1078-0.0920.8280.6060.2457-1.0478-0.69910.11120.0021.7362-0.1636-0.06182.0681-0.42111.354-27.9865-34.7851181.9712
84.5653-0.3014-1.00282.9826-1.45743.1559-0.40970.44561.13430.28020.6063-0.92-1.18121.08070.00081.5006-0.1733-0.10641.9249-0.35091.4732-27.9597-31.4319181.8945
94.56913.5281-2.10952.7815-1.60680.9823-0.5702-1.2269-0.47981.8859-0.0838-1.511-1.2493-0.7606-1.24162.57350.0513-0.90222.0952-0.66911.6586-20.0103-31.5176204.214
102.102-2.0936-1.832.08841.82631.5922-1.65610.8996-0.60071.32640.76880.4476-0.04591.3925-0.14612.6429-0.4419-1.07552.47030.44372.4934-23.3802-56.3018223.277
115.28761.9037-3.03311.5437-0.22872.5393-1.0743-2.2823-1.67282.2652-0.7279-3.2731.18960.6927-0.55043.11030.2867-0.68452.4894-0.12022.1256-21.1948-48.3219211.3386
123.41640.2595-2.73751.1513-0.93782.5323-0.4491-0.9475-0.00280.19491.2606-1.14611.05540.1947-0.00113.78120.5217-0.90962.4079-0.42722.14-22.1703-50.9545212.3161
130.07880.21060.14461.13680.96370.80120.5662-1.13342.41191.8074-1.37940.4933-1.2552.073-0.00283.1497-0.2768-0.58492.1871-0.01672.4789-14.0351-52.2146219.1159
145.0914-0.2110.29760.23880.66831.98031.0393-2.2707-1.18250.0261-0.51871.2683-0.1909-0.0449-0.0461.0575-0.06270.09821.2343-0.11421.8484-7.4696-57.750493.7175
150.37570.2109-0.25521.011-0.2150.5312-0.857-1.55710.63942.59880.7431-1.19940.6631.51880.01262.3847-0.118-0.01022.20870.3331.74312.004-57.0439101.18
166.25651.241-2.01126.2727-0.63724.8020.0483-1.3444-0.33590.4424-0.2722-0.18590.10570.2328-0.00111.3585-0.05910.1561.19380.03121.53734.514-52.4791.2458
175.70962.76052.39612.01730.29562.02670.95980.7823-1.18090.0374-0.468-0.07530.18960.08680.00071.48840.04630.20871.01640.03671.6318-22.1515-60.214587.7936
181.03031.37350.15192.5331-0.64781.0673-0.01010.6743-2.20110.75550.55652.04660.8446-1.07360.00371.53810.18170.27281.53040.09141.7045-35.574-60.181987.2347
192.2740.5038-1.81352.85680.28631.5904-0.9587-1.5537-0.08091.34380.5657-0.1908-0.51120.0788-0.00261.3613-0.13590.22121.0016-0.0391.6596-28.3789-57.557191.3801
202.2457-1.24311.07180.6754-0.54431.0534-0.67821.28321.0731-0.63430.66941.98020.0397-1.42450.00282.08110.0992-0.06292.07560.28251.6755-70.166237.8923149.9941
215.63271.59511.67264.1359-2.11313.1218-0.05550.64360.47120.11370.21530.2737-0.6344-0.6730.00231.91890.2165-0.151.17430.10711.3698-63.430735.2676159.4413
222.3548-1.37670.72080.9335-0.05761.1347-0.49920.80421.5094-0.42160.2553-0.0891-0.6968-0.02210.0031.36770.0572-0.26721.66280.24191.8722-60.848537.7036149.8855
232.11860.1628-0.62822.72840.56860.31940.7490.77310.60230.34360.00340.909-0.7534-0.13510.00471.6192-0.0809-0.12281.73450.02541.5307-64.996933.6657147.5096
242.78641.48530.75769.20481.74720.4419-1.46152.17360.1689-0.25162.2315-2.67160.4518-0.49110.11152.7147-0.644-0.2673.4963-0.33561.368-46.770225.3006114.6568
252.17521.3128-2.41931.0394-0.82324.3319-1.36523.74280.3675-1.06811.23751.2381-0.5316-2.1006-0.0812.5013-0.3394-0.31643.970.19281.5644-58.180434.065120.7554
263.2164-3.585-0.45284.7089-0.95262.46310.17191.9733-0.5158-0.8109-0.6828-0.44180.8284-2.6832-0.00262.3871-0.72430.05093.4530.20851.7239-57.195128.3954119.6878
272.50362.33870.25412.59520.60320.2724-1.22732.3278-0.493-1.82191.19841.7997-2.0378-1.01710.00093.3263-0.10260.0483.23380.15971.8924-56.295835.8612111.0729
282.5911-0.152-0.92211.8444-0.23092.9498-0.35681.1976-1.09920.33970.9384-0.87041.09811.50750.02682.0412-0.0691-0.15781.4303-0.16571.5701-51.103312.6775155.6471
292.0047-0.45140.09471.27030.22250.6282-0.231-0.4450.0749-0.4814-0.0171-0.87770.6647-0.5355-0.00061.8985-0.2569-0.26041.0554-0.06491.1365-62.381218.1644153.6423
303.87910.8114-3.34290.66380.12113.9416-0.42760.1233-0.9303-0.0058-0.26590.01220.05940.2667-0.00152.4485-0.02370.07191.2165-0.22371.5433-60.63887.88156.1917
311.55950.4281-0.2311.5959-2.72024.6243-0.8141-0.2438-0.525-0.42030.0147-0.25960.8235-0.255-0.00061.98740.0209-0.00181.1851-0.02131.2273-54.959218.8104152.6251
321.44110.2636-0.79510.5760.57381.33130.25972.19550.2379-0.6422-0.20712.71120.7208-0.37930.00412.3114-0.56080.05152.58680.19931.2621-43.200632.5723116.4845
331.350.0481-0.40982.05371.38721.0843-1.08851.2407-0.24660.99851.21040.0534-0.0373-0.3744-0.00042.6396-0.29930.00352.2324-0.11771.4688-45.671426.7912129.1453
344.29411.5907-0.54160.6375-0.67051.5235-0.26381.9291-1.62281.04210.5731-0.15470.69330.13680.00042.2336-0.12040.29822.2833-0.19141.6571-42.215125.1304124.4782
355.9904-1.10550.36735.66680.04885.6811-0.4207-0.5996-0.07270.82990.2417-0.5544-0.11491.5689-0.00180.90450.0861-0.23261.61260.12271.3869-32.9916-25.30192.6985
360.6792-0.9451-1.42391.46031.63686.213-0.5414-0.34720.18270.08710.0578-0.915-0.59472.2006-0.04660.79030.2039-0.34231.69380.06442.0031-27.3178-23.622190.8468
373.13331.582-1.92025.9727-2.26991.5975-0.0399-1.0071-0.12580.3195-0.7445-0.8061-1.71760.287-0.00131.12210.2606-0.57321.58780.05531.5278-34.6543-24.4763100.3283
386.91575.2704-2.66445.5444-1.75961.04920.893-3.51412.32942.7344-0.88082.4869-0.2023-1.1574-0.07763.4163-0.07810.40522.99120.21261.7053-55.4713-22.7794133.0936
393.8430.96831.68523.93031.2121.76890.345-0.6716-0.52981.9662-0.6403-0.73191.3549-0.476-0.0013.5191-0.0076-0.33692.6462-0.11831.7503-43.592-25.4448128.2755
400.0537-0.2024-0.00884.054-1.46790.54940.61740.4880.80081.8235-0.0086-0.02490.8828-0.1755-0.00122.6295-0.1666-0.02262.6682-0.22211.802-41.602-20.9002137.4535
411.4031.01591.26931.1091.36391.66290.2916-1.0531-0.33452.58471.06213.5437-0.8463-2.03870.09221.57180.26230.61621.18430.24711.6728-58.9927-35.498298.2788
420.921-0.37930.88361.7160.97811.9715-0.58710.6821-1.42690.22230.36820.41310.4915-0.23560.00081.10740.09370.15121.3185-0.031.3807-56.741-32.562484.4343
435.8948-0.7457-3.26085.2131-2.56494.3873-0.035-0.5636-1.35510.6392-0.21740.32460.9141-0.616-0.00491.2310.12350.11841.06190.20441.4083-51.1428-41.908491.9495
442.08520.27140.92461.7283-1.08421.20550.02050.2270.43630.68810.60790.3428-0.09310.40560.00420.8740.34390.07671.34880.06181.2885-47.4664-29.001387.0877
451.9488-1.4325-0.09771.16390.5692.1669-0.1263-1.77780.45530.8319-0.1496-0.08210.07880.15120.00292.0791-0.00940.44271.9238-0.38051.5138-56.4158-25.5823122.2614
460.3530.04990.69092.6482.1422.46690.2093-0.67910.522-0.0514-0.70780.2318-0.7764-1.73140.00042.82240.24750.38322.2789-0.18411.8183-57.0976-19.8473121.1596
471.32612.31940.8784.27962.84512.08850.21591.1591-2.3515-1.23040.6103-0.98930.43731.7353-0.6381.2362-0.0802-0.21391.0167-0.51131.97416.2894-65.063157.0448
481.54180.6781.11720.57270.10151.19450.79850.0079-0.50570.4117-0.78780.35160.7796-0.0689-0.0021.0374-0.0231-0.01020.67220.04271.623917.0437-62.372671.0781
492.91140.0119-0.66642.35990.46792.691-0.13120.4494-0.7752-0.2377-0.27090.3463-0.0645-0.1853-0.00150.87280.1355-0.21110.7532-0.30521.685911.1437-59.67957.9467
501.22160.06570.78621.1482-0.50592.25350.829-0.29320.52140.8262-0.94750.0627-1.20811.8636-0.02251.86220.1843-0.1622.0577-0.50991.315323.7834-52.382936.6399
510.577-0.24550.10650.8471-0.44670.2625-1.35360.4191-0.5008-0.05641.1640.1944-0.35470.82-0.00461.94390.2966-0.00412.2899-0.08081.623623.3464-44.625539.4709
522.916-2.5727-0.55082.34970.03582.00021.17842.2547-0.7391-1.2174-0.219-0.6529-0.84840.92230.00811.80980.4682-0.14771.9213-0.54711.628517.4239-52.910234.6169
534.96221.6041-0.02656.0499-3.45652.12771.06920.7811-1.41470.508-1.763-1.4637-1.2040.7629-0.00052.59280.24450.34061.7213-0.23781.262532.082-49.733634.7758
540.31840.6419-0.03751.2257-0.13250.15011.02672.2277-0.18160.5416-0.12193.76950.0679-0.3776-0.03041.86970.13920.24042.8199-0.40872.070631.6457-53.535228.5879
552.07542.2466-0.06083.2146-0.68520.4092-0.19561.2255-0.6189-1.549-0.01640.12430.34690.05280.0051.37940.2284-0.10721.6066-0.16511.5554-41.1518-38.404158.7509
561.8199-0.57150.4652.51162.80063.8871-0.9461-0.35760.2102-0.16150.51351.34750.67420.21180.00210.96660.1981-0.13461.1705-0.1161.525-42.903-29.993767.8327
573.62481.4036-1.20175.45642.02541.8117-0.76180.94751.4905-0.7827-0.8434-0.8854-0.83760.3356-0.00911.11420.19260.20261.4914-0.28611.8266-37.3808-31.035461.1304
582.8714-2.92740.04083.71380.87790.2963-0.5088-0.1373-0.73220.36550.72490.50930.1739-0.26650.011.13540.17420.19521.35-0.22941.6366-31.5404-48.370568.3755
590.307-0.18860.52160.4056-0.67531.34360.4011.5778-0.25380.7762-0.31010.96480.7619-3.35330.0860.9351-0.0665-0.20281.2758-0.33032.1276-32.4995-59.150867.4999
603.4985-4.83853.596.6838-4.96253.68361.6806-1.8016-1.5913-1.3036-0.94672.83720.35532.11890.30651.1584-0.2988-0.02342.0043-0.632.4045-21.9408-68.035960.8888
610.20830.12890.46371.87450.03991.07541.29880.6954-2.01780.1163-1.4211-0.27830.4673-0.51910.11941.07760.24640.14521.396-0.52921.872-17.4382-67.375467.9782
620.43350.613-0.1611.44470.01940.13810.11060.6889-1.1774-0.0816-0.24220.9763-0.4114-0.2862-0.00451.35310.2723-0.11411.4216-0.44731.5874-25.8927-59.453161.7243
632.4252-1.644-0.78322.16281.04770.43590.01480.9131-0.5087-0.6474-0.1077-0.2659-0.2981-0.49440.00340.9972-0.22070.20071.2786-0.32271.6515-17.8051-60.456865.2406
641.20580.74471.15623.54621.00181.0557-0.4396-0.9415-0.58220.6067-0.1656-0.02350.6814-0.64050.00242.1402-0.07420.00951.93960.12861.4005-66.714817.5496188.9853
651.25010.4165-1.34330.7166-0.2541.49430.8304-1.0828-0.72760.2536-0.2-1.60141.25690.558-0.00072.5107-0.0956-0.07271.575-0.03941.3952-59.979223.7428180.3224
661.32141.3285-0.32221.5266-0.32820.07910.5614-0.86263.38950.28220.57160.22620.0291-1.1340.6832.13030.0187-0.07791.3974-0.15091.3923-68.337627.4509180.482
672.59782.429-0.86742.3108-0.15942.90660.2422-0.18830.64650.6341-0.5344-0.50580.38440.5913-02.4054-0.07910.10251.6504-0.02151.4415-68.475118.2139184.4044
684.2301-0.42631.28552.3781-0.42390.98330.72410.7756-0.9609-0.1408-0.39550.05810.4408-0.5392-0.00052.097-0.1440.18891.75840.1531.497-98.502711.6553179.0987
692.1629-0.3232-2.40261.2905-0.3062.945-1.0739-2.38050.71120.55490.7578-0.2017-0.4107-0.0502-0.00332.0756-0.25920.06711.19070.08641.4765-96.654414.2379183.3773
700.8727-1.08020.56891.4411-0.75290.37081.04860.85370.9111-2.5811-1.30110.65770.4632-0.1067-0.00472.1170.48140.13892.2899-0.13591.5018-44.7397-25.6435154.5287
713.1073.82561.75554.7032.17030.9954-1.03653.2157-1.607-0.40281.0207-2.3030.90480.60970.24531.3090.10980.46172.3615-0.00971.5414-30.1014-38.5755147.1692
720.2024-0.56410.54761.5633-1.51221.4398-0.5425-0.8387-0.93730.65310.6099-1.394-0.598-0.21320.00231.5278-0.12570.22911.8915-0.11291.5735-35.2184-40.1477159.9575
731.84770.221-0.15972.8835-1.68451.02950.01480.7932-2.0813-1.2937-0.0192-0.06120.10390.5750.00021.7679-0.3483-0.1142.13-0.09771.7718-40.7391-39.5603153.1674
740.5738-1.46410.80864.1054-2.61671.8073-0.4040.0435-0.4771-0.9523-0.4807-0.569-0.52850.386-0.00351.7529-0.25920.06882.0483-0.14271.4742-39.793-31.4518159.0539
750.89940.5005-0.02221.81221.35291.4354-0.8105-1.59730.12850.40760.7523-0.2145-0.14481.01580.00041.8698-0.1494-0.05681.85550.1311.2519-54.8995-17.6518161.8268
762.9537-2.90020.80792.7983-0.65671.2045-0.21440.66252.8737-0.8673-0.2587-2.2269-0.82280.617-0.0522.3815-0.53680.24931.7383-0.06651.4192-54.0999-9.0278157.0648
774.8499-0.6165-1.1524.5634-3.51083.0360.09890.5751.2537-0.19820.1593-0.39480.07010.2209-0.00192.2402-0.21840.06751.4128-0.13841.2477-62.4094-10.6533157.6321
781.7956-0.08440.55270.08020.3922.7950.08221.09141.1798-1.590.0012.3062-0.5584-1.45590.00251.85740.4739-0.12881.4778-0.05191.95570.234-36.758158.4591
796.06180.45442.53942.8903-2.57966.61140.3418-0.12170.27510.1922-0.41790.9729-1.9203-0.1495-0.03651.34270.309-0.09980.5628-0.12931.49698.073-41.823868.0322
802.2221-1.4513-1.12371.15510.68380.8249-0.12560.1942-0.206-0.7591-0.47320.1207-0.0701-0.3235-3.7962.10450.9645-0.2257-0.1671-0.14321.64122.4353-34.959666.8244
813.51870.639-0.98323.20972.37462.30330.31810.65540.5985-0.9189-0.23790.8515-1.0995-0.341401.31840.3619-0.25160.7466-0.03681.68016.8189-39.991556.8433
822.5262.2321-0.95642.111-0.99780.55170.05061.0571-0.1337-1.24271.16970.2559-0.25981.68460.20792.37120.5022-0.42512.8997-0.59151.425419.9568-47.983525.7677
833.85681.1197-1.50492.3218-2.07942.8786-0.05151.5211-0.7148-0.9028-0.22510.7210.362-1.0511-0.00032.42130.2796-0.55122.2256-0.19811.872111.215-45.133228.1851
842.91242.49331.10782.12760.81931.3885-1.02020.0709-0.1643-1.43852.41411.2953-0.64470.8948-0.00063.16180.3931-0.25742.47050.23481.87513.9264-39.653619.4772
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 101 )
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 128 )
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 139 )
5X-RAY DIFFRACTION5chain 'A' and (resid 140 through 214 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 17 )
7X-RAY DIFFRACTION7chain 'B' and (resid 18 through 51 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 106 )
9X-RAY DIFFRACTION9chain 'B' and (resid 107 through 119 )
10X-RAY DIFFRACTION10chain 'B' and (resid 120 through 134 )
11X-RAY DIFFRACTION11chain 'B' and (resid 135 through 157 )
12X-RAY DIFFRACTION12chain 'B' and (resid 158 through 202 )
13X-RAY DIFFRACTION13chain 'B' and (resid 203 through 215 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 14 )
15X-RAY DIFFRACTION15chain 'C' and (resid 15 through 26 )
16X-RAY DIFFRACTION16chain 'C' and (resid 27 through 88 )
17X-RAY DIFFRACTION17chain 'C' and (resid 89 through 140 )
18X-RAY DIFFRACTION18chain 'C' and (resid 141 through 154 )
19X-RAY DIFFRACTION19chain 'C' and (resid 155 through 182 )
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 25 )
21X-RAY DIFFRACTION21chain 'D' and (resid 26 through 75 )
22X-RAY DIFFRACTION22chain 'D' and (resid 76 through 90 )
23X-RAY DIFFRACTION23chain 'D' and (resid 91 through 113 )
24X-RAY DIFFRACTION24chain 'D' and (resid 114 through 128 )
25X-RAY DIFFRACTION25chain 'D' and (resid 129 through 150 )
26X-RAY DIFFRACTION26chain 'D' and (resid 151 through 188 )
27X-RAY DIFFRACTION27chain 'D' and (resid 189 through 214 )
28X-RAY DIFFRACTION28chain 'E' and (resid 1 through 33 )
29X-RAY DIFFRACTION29chain 'E' and (resid 34 through 51 )
30X-RAY DIFFRACTION30chain 'E' and (resid 52 through 87 )
31X-RAY DIFFRACTION31chain 'E' and (resid 88 through 119 )
32X-RAY DIFFRACTION32chain 'E' and (resid 120 through 134 )
33X-RAY DIFFRACTION33chain 'E' and (resid 135 through 168 )
34X-RAY DIFFRACTION34chain 'E' and (resid 169 through 215 )
35X-RAY DIFFRACTION35chain 'F' and (resid 1 through 61 )
36X-RAY DIFFRACTION36chain 'F' and (resid 62 through 75 )
37X-RAY DIFFRACTION37chain 'F' and (resid 76 through 113 )
38X-RAY DIFFRACTION38chain 'F' and (resid 114 through 128 )
39X-RAY DIFFRACTION39chain 'F' and (resid 129 through 188 )
40X-RAY DIFFRACTION40chain 'F' and (resid 189 through 214 )
41X-RAY DIFFRACTION41chain 'G' and (resid 1 through 17 )
42X-RAY DIFFRACTION42chain 'G' and (resid 18 through 33 )
43X-RAY DIFFRACTION43chain 'G' and (resid 34 through 87 )
44X-RAY DIFFRACTION44chain 'G' and (resid 88 through 106 )
45X-RAY DIFFRACTION45chain 'G' and (resid 107 through 134 )
46X-RAY DIFFRACTION46chain 'G' and (resid 135 through 215 )
47X-RAY DIFFRACTION47chain 'H' and (resid 1 through 17 )
48X-RAY DIFFRACTION48chain 'H' and (resid 18 through 33 )
49X-RAY DIFFRACTION49chain 'H' and (resid 34 through 134 )
50X-RAY DIFFRACTION50chain 'H' and (resid 135 through 157 )
51X-RAY DIFFRACTION51chain 'H' and (resid 158 through 168 )
52X-RAY DIFFRACTION52chain 'H' and (resid 169 through 184 )
53X-RAY DIFFRACTION53chain 'H' and (resid 185 through 202 )
54X-RAY DIFFRACTION54chain 'H' and (resid 203 through 215 )
55X-RAY DIFFRACTION55chain 'I' and (resid 1 through 26 )
56X-RAY DIFFRACTION56chain 'I' and (resid 27 through 46 )
57X-RAY DIFFRACTION57chain 'I' and (resid 47 through 68 )
58X-RAY DIFFRACTION58chain 'I' and (resid 69 through 119 )
59X-RAY DIFFRACTION59chain 'I' and (resid 120 through 131 )
60X-RAY DIFFRACTION60chain 'I' and (resid 132 through 140 )
61X-RAY DIFFRACTION61chain 'I' and (resid 141 through 154 )
62X-RAY DIFFRACTION62chain 'I' and (resid 155 through 163 )
63X-RAY DIFFRACTION63chain 'I' and (resid 164 through 182 )
64X-RAY DIFFRACTION64chain 'J' and (resid 1 through 26 )
65X-RAY DIFFRACTION65chain 'J' and (resid 27 through 46 )
66X-RAY DIFFRACTION66chain 'J' and (resid 47 through 58 )
67X-RAY DIFFRACTION67chain 'J' and (resid 59 through 102 )
68X-RAY DIFFRACTION68chain 'J' and (resid 103 through 154 )
69X-RAY DIFFRACTION69chain 'J' and (resid 155 through 182 )
70X-RAY DIFFRACTION70chain 'K' and (resid 1 through 14 )
71X-RAY DIFFRACTION71chain 'K' and (resid 15 through 26 )
72X-RAY DIFFRACTION72chain 'K' and (resid 27 through 46 )
73X-RAY DIFFRACTION73chain 'K' and (resid 47 through 68 )
74X-RAY DIFFRACTION74chain 'K' and (resid 69 through 88 )
75X-RAY DIFFRACTION75chain 'K' and (resid 89 through 119 )
76X-RAY DIFFRACTION76chain 'K' and (resid 120 through 140 )
77X-RAY DIFFRACTION77chain 'K' and (resid 141 through 182 )
78X-RAY DIFFRACTION78chain 'L' and (resid 1 through 25 )
79X-RAY DIFFRACTION79chain 'L' and (resid 26 through 61 )
80X-RAY DIFFRACTION80chain 'L' and (resid 62 through 75 )
81X-RAY DIFFRACTION81chain 'L' and (resid 76 through 113 )
82X-RAY DIFFRACTION82chain 'L' and (resid 114 through 139 )
83X-RAY DIFFRACTION83chain 'L' and (resid 140 through 188 )
84X-RAY DIFFRACTION84chain 'L' and (resid 189 through 214 )

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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