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- PDB-6bpc: Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound ... -

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基本情報

登録情報
データベース: PDB / ID: 6bpc
タイトルPlasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to monoclonal antibody 4F7
要素
  • Monoclonal antibody 4F7 Fab heavy chain
  • Monoclonal antibody 4F7 Fab light chain
  • Reticulocyte binding protein 2, putative
キーワードCELL INVASION / Plasmodium vivax / invasion / malaria / antibody complex
機能・相同性NBD94 domain / Nucleotide-Binding Domain 94 of RH / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Reticulocyte binding protein 2, putative
機能・相同性情報
生物種Plasmodium vivax (マラリア 病原虫)
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: 2.66 Å
データ登録者Gruszczyk, J. / Chan, L.J. / Tham, W.H.
引用ジャーナル: Nature / 年: 2018
タイトル: Cryo-EM structure of an essential Plasmodium vivax invasion complex.
著者: Jakub Gruszczyk / Rick K Huang / Li-Jin Chan / Sébastien Menant / Chuan Hong / James M Murphy / Yee-Foong Mok / Michael D W Griffin / Richard D Pearson / Wilson Wong / Alan F Cowman / ...著者: Jakub Gruszczyk / Rick K Huang / Li-Jin Chan / Sébastien Menant / Chuan Hong / James M Murphy / Yee-Foong Mok / Michael D W Griffin / Richard D Pearson / Wilson Wong / Alan F Cowman / Zhiheng Yu / Wai-Hong Tham /
要旨: Plasmodium vivax is the most widely distributed malaria parasite that infects humans. P. vivax invades reticulocytes exclusively, and successful entry depends on specific interactions between the P. ...Plasmodium vivax is the most widely distributed malaria parasite that infects humans. P. vivax invades reticulocytes exclusively, and successful entry depends on specific interactions between the P. vivax reticulocyte-binding protein 2b (PvRBP2b) and transferrin receptor 1 (TfR1). TfR1-deficient erythroid cells are refractory to invasion by P. vivax, and anti-PvRBP2b monoclonal antibodies inhibit reticulocyte binding and block P. vivax invasion in field isolates. Here we report a high-resolution cryo-electron microscopy structure of a ternary complex of PvRBP2b bound to human TfR1 and transferrin, at 3.7 Å resolution. Mutational analyses show that PvRBP2b residues involved in complex formation are conserved; this suggests that antigens could be designed that act across P. vivax strains. Functional analyses of TfR1 highlight how P. vivax hijacks TfR1, an essential housekeeping protein, by binding to sites that govern host specificity, without affecting its cellular function of transporting iron. Crystal and solution structures of PvRBP2b in complex with antibody fragments characterize the inhibitory epitopes. Our results establish a structural framework for understanding how P. vivax reticulocyte-binding protein engages its receptor and the molecular mechanism of inhibitory monoclonal antibodies, providing important information for the design of novel vaccine candidates.
履歴
登録2017年11月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年6月20日Provider: repository / タイプ: Initial release
改定 1.12018年6月27日Group: Data collection / Database references / カテゴリ: citation / citation_author / Item: _citation.pdbx_database_id_DOI
改定 1.22018年7月11日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.32018年7月18日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.42023年10月4日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Reticulocyte binding protein 2, putative
B: Monoclonal antibody 4F7 Fab heavy chain
C: Monoclonal antibody 4F7 Fab light chain
D: Reticulocyte binding protein 2, putative
E: Monoclonal antibody 4F7 Fab heavy chain
F: Monoclonal antibody 4F7 Fab light chain


分子量 (理論値)分子数
合計 (水以外)180,5346
ポリマ－180,5346
非ポリマー00
水11,169620
1
A: Reticulocyte binding protein 2, putative
B: Monoclonal antibody 4F7 Fab heavy chain
C: Monoclonal antibody 4F7 Fab light chain


分子量 (理論値)分子数
合計 (水以外)90,2673
ポリマ－90,2673
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: Reticulocyte binding protein 2, putative
E: Monoclonal antibody 4F7 Fab heavy chain
F: Monoclonal antibody 4F7 Fab light chain


分子量 (理論値)分子数
合計 (水以外)90,2673
ポリマ－90,2673
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)70.090, 70.310, 140.363
Angle α, β, γ (deg.)104.180, 100.340, 98.410
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質 Reticulocyte binding protein 2, putative


分子量: 36519.789 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Plasmodium vivax (strain Salvador I) (マラリア 病原虫)
株: Salvador I / 遺伝子: PVX_094255 / プラスミド: pET-32a(+) / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): SHuffle T7 / 参照: UniProt: A5K736
#2: 抗体 Monoclonal antibody 4F7 Fab heavy chain


分子量: 27428.127 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ)
#3: 抗体 Monoclonal antibody 4F7 Fab light chain


分子量: 26319.176 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ)
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 620 / 由来タイプ: 天然 / 式: H2O

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.92 Å3/Da / 溶媒含有率: 68.66 %
結晶化温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.2 M trisodium citrate and 20% (w/v) PEG 3,350

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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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.9537 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2016年7月27日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9537 Å / 相対比: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.12
反射解像度: 2.66→66.55 Å / Num. obs: 67863 / % possible obs: 94.3 % / 冗長度: 3.6 % / CC1/2: 0.982 / Net I/σ(I): 6
反射 シェル解像度: 2.66→2.72 Å / 冗長度: 3.5 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4417 / CC1/2: 0.58 / % possible all: 94.3

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解析

ソフトウェア
名称バージョン分類
PHENIX1.12_2829精密化
Blu-Iceデータ収集
iMOSFLM7.2.1データ削減
Aimless0.2.7データスケーリング
PHENIX1.12_2829位相決定
PHENIX1.12_2829モデル構築
PDB_EXTRACT3.22データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 5W53,5EN2

5w53

5en2


解像度: 2.66→66.308 Å / 交差検証法: FREE R-VALUE / σ(F): 1.39 / 位相誤差: 25.42
Rfactor反射数%反射
Rfree0.2148 1009 1.49 %
Rwork0.1973 --
obs0.1996 67840 94.27 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 131.2 Å2 / Biso mean: 48.8194 Å2 / Biso min: 14.67 Å2
精密化ステップサイクル: final / 解像度: 2.66→66.308 Å
タンパク質核酸リガンド溶媒全体
原子数11425 0 0 620 12045
Biso mean---46.57 -
残基数----1430
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00511686
X-RAY DIFFRACTIONf_angle_d0.67515810
X-RAY DIFFRACTIONf_chiral_restr0.0421735
X-RAY DIFFRACTIONf_plane_restr0.0042008
X-RAY DIFFRACTIONf_dihedral_angle_d4.3427016
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 93 %

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6626-2.8030.34741240.311995949718
2.803-2.97850.30251420.28894509592
2.9785-3.20840.2611320.245996239755
3.2084-3.5310.22561390.211795159654
3.531-4.04150.21151240.184595519675
4.0415-5.08980.16541270.15194919618
5.0898-37.6860.18821460.176594759621
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)
12.2591.53770.43272.1716-1.18875.1422-0.0202-0.07360.0858-0.23670.20640.42190.5301-0.3552-0.26750.2-0.110.08470.17-0.02670.494969.862941.528211.2638
23.7471.197-1.05014.0907-0.95678.41990.0964-0.5395-0.30910.4282-0.3164-0.6924-0.18380.91630.32190.3266-0.0585-0.0330.32590.00050.582584.978339.854523.7028
31.50371.20890.24811.46010.1060.2887-0.06910.0736-0.033-0.0729-0.1118-0.4435-0.20170.20260.08870.2801-0.49810.14470.0179-0.14690.58981.31647.74225.3218
49.2384-5.9507-7.25444.57585.53348.53450.825-1.33471.9425-0.631-0.2590.0222-0.99730.6588-0.63130.3606-0.08950.11150.3728-0.15380.537780.883647.77224.7853
53.03520.0891-1.80981.35630.21686.09580.29690.78760.1474-0.07380.24670.42890.0176-0.9445-0.44220.2194-0.1050.0390.5798-0.01680.729559.066820.7013-7.372
62.41180.5872-0.47941.59360.16472.694-0.20350.6860.20990.0211-0.0920.2907-0.0974-0.32390.19610.2727-0.17640.01410.37190.00410.553162.506212.7419-2.8886
71.71990.55-0.00593.32610.73233.26260.21740.1928-0.22670.14260.0988-0.15810.2427-0.4561-0.33840.1257-0.0737-0.02190.36420.04770.280269.917417.3411-10.0126
83.7578-0.4453-0.49279.38610.97392.9291-0.274-0.0358-0.10140.11490.4842-0.862-0.01270.3258-0.37060.1428-0.04510.04490.30890.05380.300474.825318.5673-6.8671
93.714-0.51490.97334.1350.81448.1332-0.2898-0.0401-0.7901-0.11320.3168-0.31220.4160.0782-0.09730.2044-0.01170.07520.22720.01690.499173.63049.9125-7.2095
100.5744-0.2904-0.68061.20260.52621.2848-0.06030.1941-0.11410.1001-0.02150.1117-0.0051-0.23110.04160.1888-0.0570.05330.2650.0160.386867.256922.71322.2744
113.08522.57420.13862.5440.79561.25670.23930.00670.18920.175-0.0852-0.0038-0.1379-0.0486-0.16460.3053-0.01440.02320.1135-0.03030.343667.092341.82519.1691
124.6016-5.5874-5.41749.05286.49049.7526-0.29670.7185-0.6743-0.2728-0.4442.4445-0.0089-1.12390.73690.3169-0.0253-0.01890.2403-0.01440.377255.838134.913820.6303
134.4814-1.3507-3.84041.653.70278.5285-0.0760.120.1249-0.3869-0.17591.2523-0.5739-0.5850.16840.49310.057-0.01430.18540.08230.557756.758545.330220.6163
142.5876-2.5968-0.73026.22592.83863.0379-0.06450.1129-0.216-0.50120.2810.12670.08260.1468-0.050.3598-0.08740.08990.16740.06540.312467.026730.55314.5857
152.6415-1.39590.66349.283-0.29714.0370.1369-0.25420.5916-0.2262-0.20920.9518-0.7783-0.0470.07640.4682-0.02810.15910.2584-0.03980.633761.919356.163124.8826
165.21440.73961.22910.68081.96285.71830.2816-0.38080.34460.8281-0.30140.4854-0.1418-0.17560.14690.3834-0.0410.06720.24250.03150.220760.411638.320629.006
171.5582-2.07451.3247.1885-2.70112.2652-0.1014-0.14060.02390.41470.252-0.53840.1829-0.021-0.20510.55310.00290.05270.23410.01310.3707128.183145.971848.5171
182.5383-2.98681.00556.7436-1.51631.1678-0.1127-0.4783-0.53330.07860.54160.54180.2224-0.3607-0.35250.6314-0.06020.06990.24320.04490.4592121.547939.33948.5261
190.39271.104-0.39914.8586-2.87397.7592-0.2446-0.1438-0.5499-0.1170.06050.02680.6459-0.11360.15321.2273-0.1635-0.10730.58160.17631.0664133.52888.550755.9716
202.4939-3.01230.25525.6827-1.56570.79050.4520.2787-0.0192-0.4805-0.2649-0.11580.60640.0182-0.16711.0081-0.0078-0.01980.1606-0.05570.5703130.889827.03443.339
214.2672-2.2660.91582.76542.01794.2183-0.19130.2660.0606-1.22710.3267-0.49550.01250.1942-0.11730.49430.00450.14640.1259-0.06030.3964123.638657.036936.4692
223.93570.54433.53772.00940.95444.8653-0.42460.26360.9186-0.52650.0099-0.8422-0.75170.18330.45030.78090.01280.04780.2336-0.03310.6538128.976273.166741.4595
233.4387-1.0718-0.16834.5561-2.99553.8501-0.1356-0.62940.3661.05920.1302-0.4373-0.4448-0.08340.00520.9490.0505-0.14780.3322-0.08340.5562134.339261.859358.2258
244.4596-1.66860.75572.996-0.68063.0102-0.5009-0.3295-0.46610.77530.5705-0.00920.43230.5991-0.06120.9760.1313-0.08910.4740.0240.5624148.985729.091562.6989
250.9306-2.0520.63337.1363-1.64720.4695-0.22550.06150.2485-0.41210.2049-0.90590.46420.23180.0681.03530.1577-0.01640.2286-0.06890.5957141.988832.13155.2618
262.2455-2.27181.52975.4198-4.31083.5827-0.18640.09630.73810.4829-0.1586-1.1144-0.73520.35960.31880.5768-0.08590.01220.3208-0.03510.7422139.136365.589247.1012
271.5382-2.77791.77466.6937-3.12972.8634-0.2083-0.3390.07560.60240.375-0.28570.0672-0.0589-0.20780.75560.0588-0.0390.2535-0.04140.5371135.128243.688656.4738
283.4426-4.02734.77556.3913-7.66019.1797-0.1105-0.5056-0.4816-1.96610.22360.3135-0.4699-0.8985-0.22961.20790.0802-0.13850.4227-0.04770.7291146.19813.129570.0615
292.776-2.93540.91684.30220.14681.711-0.08470.3863-1.04630.0473-0.24020.71160.4239-0.66330.20610.45-0.17010.08610.3655-0.040.580594.203757.749622.6471
302.5129-0.71791.36972.5114-0.47612.71550.0187-0.3779-0.6149-0.0834-0.09810.36450.5426-0.4248-0.0670.3797-0.16340.08790.1839-0.04970.4097102.537457.159928.6549
313.8749-0.39541.12111.98151.00283.2316-0.2222-0.3221-0.30370.1545-0.04290.1873-0.0317-0.5530.10120.2024-0.05840.10580.1457-0.04590.3826103.417764.50532.0869
328.483-1.7682-0.41045.5195-1.16125.3313-0.2153-0.3023-0.23281.0156-0.10170.75260.1332-0.78940.29850.3882-0.04760.08890.4066-0.07130.203697.728760.432234.7901
335.066-2.412-0.5347.215-3.27119.54610.2148-0.70590.30490.4541-0.53550.2098-0.0716-0.52790.32170.3873-0.09290.08870.4203-0.08160.365988.267169.12628.8548
341.6259-0.7350.67961.25780.39340.9574-0.0362-0.0199-0.25330.11910.10150.24150.2774-0.291-0.00030.3752-0.16620.08120.1118-0.08460.307106.19762.232725.6791
351.6441-0.07991.27611.61170.31712.02760.0581-0.53170.27980.38320.02450.1240.2123-0.3059-0.03410.2776-0.2479-0.01960.21820.0060.39985.754162.35913.0212
361.19341.8405-1.2535.8506-2.62339.3726-0.23330.5675-0.0845-0.69090.1807-0.23940.24740.22180.03090.4457-0.19420.08220.41-0.03760.463491.263260.6668-14.9054
372.74120.3932-1.74410.2466-0.71842.29240.04640.0766-0.0943-0.07540.04040.02430.01980.20260.0890.0022-0.19230.1050.07210.0450.503189.324462.74191.0091
380.96920.9793-0.83481.52820.54276.527-0.209-0.2350.0143-0.15470.1423-0.54170.43171.1362-0.02790.223-0.00050.11110.5019-0.02260.445198.487754.6612-1.565
393.61220.9153-1.25772.9436-0.04444.99030.10630.0634-0.3724-0.1348-0.28430.0050.13940.10180.18390.115-0.1119-0.05720.21210.00230.411191.647959.784-1.1428
404.4121-0.77640.85723.29630.26330.99160.2461-0.1364-0.6146-0.93770.20361.00140.7691-0.5849-0.41420.4849-0.16170.00690.2538-0.04160.670886.975653.8481-9.9715
411.68481.5685-0.81834.1819-1.30746.18220.0463-0.14450.55250.52530.17250.3688-0.9421-0.1111-0.14160.6751-0.00040.02650.0869-0.11830.6495109.166479.87728.9121
421.72030.5186-2.05322.5862-2.40953.771-0.17070.53270.7490.38410.4521-0.35880.0082-0.2433-0.36870.3457-0.1208-0.08990.38110.02240.5103113.733978.50568.6382
431.19460.3494-0.02610.1173-0.26782.6555-0.04080.11070.3760.1752-0.0278-0.0753-0.6007-0.1204-0.04620.497-0.08390.0670.0143-0.05340.4881118.758877.156922.2803
443.66030.0662-0.0691.1297-1.56232.1553-0.11010.4817-0.3691-0.3870.03040.13120.212-0.1271-0.13610.43430.04040.08640.1244-0.03150.3109109.972365.434715.2718
452.10180.56690.16262.12880.0183.8597-0.00920.16750.05990.0242-0.0751-0.161-0.21330.20920.09070.222-0.01130.0080.09170.03350.3694117.461169.985919.7292
465.05940.2355-4.57160.4577-0.81476.0744-0.04840.70640.4425-0.10820.3558-0.0288-0.4321-0.1343-0.35370.1291-0.1795-0.09550.26220.19460.5543112.041176.07513.9155
471.7496-0.18441.53512.7243-0.40663.0335-0.10340.31590.0008-0.62460.25060.4059-0.0378-0.07840.03470.2287-0.08130.0270.2087-0.00780.260889.617167.6634-9.6921
484.34450.58234.31383.40550.22464.4029-0.36320.14720.8087-0.1855-0.0356-0.1998-0.42880.00870.24440.306-0.03350.10270.24390.03140.205596.056677.3667-9.733
496.74811.05414.26444.848-1.51053.7052-0.1225-0.63391.40350.1062-0.0790.9419-0.9485-0.94080.2810.50010.1332-0.05590.3674-0.04650.573283.143680.8519-8.9133
505.58122.52652.24151.54870.30972.24120.2396-0.278-0.14210.1123-0.3411-0.30310.0007-0.20050.08240.2621-0.11320.04420.29580.00180.2712101.889871.6554-1.8538
516.089-1.62813.76443.45370.62618.9455-0.0522-0.28540.2817-0.540.23940.6536-0.1457-0.8739-0.14920.3186-0.0209-0.04240.28490.0820.388978.824472.8443-12.9077
524.5828-0.0170.3261.684-0.62532.2348-0.88661.7920.4301-1.00690.72780.133-0.36940.40220.1380.4445-0.08360.00010.45980.07680.272393.90975.8015-17.5703
535.34411.0906-5.52552.5483-2.23437.7436-0.42260.371-0.21540.2126-0.1634-0.0838-0.2258-0.59760.45580.68750.0224-0.12290.4981-0.08620.6066105.29692.2993-38.8596
547.9725-2.5324-2.6751.95861.64142.09510.5070.4466-0.0809-0.4033-0.32610.0738-0.058-0.2803-0.23890.6357-0.04130.06580.48710.04180.329495.89646.9889-37.5539
557.1209-2.1398-2.12941.97951.31682.1240.69920.93570.0138-0.7872-0.38780.1412-0.1905-0.5667-0.20660.5502-0.0586-0.07870.6280.0710.298280.098413.9052-34.0716
567.3897-0.5392-2.12530.22620.79693.21020.49330.04280.8069-0.21980.2434-0.53670.09070.2686-0.62580.7414-0.11640.10860.5481-0.01620.5244115.85788.3176-44.9345
575.8318-0.4498-1.76395.4084-0.02770.5398-0.3515-0.7142-0.29380.27920.3135-0.63590.16040.6230.10830.669-0.0249-0.10161.4296-0.21980.6451122.8306-0.1149-39.1963
586.8978-1.3021-1.01421.46771.59442.64790.3439-0.56710.03520.0297-0.1076-0.2391-0.04050.4796-0.13160.4822-0.1434-0.09890.43140.1240.357390.76169.7148-27.1361
596.4805-0.722-0.87263.74970.56361.09020.35290.6477-0.8546-0.3923-0.49620.55090.1947-0.85230.03230.8071-0.181-0.25020.7301-0.08630.611874.0999-1.0358-39.7709
604.4308-1.0543-2.29344.27731.84682.68170.27670.0196-0.7879-0.1066-0.59240.21.03910.08160.22781.23070.0462-0.03330.7024-0.01110.4972103.8097-14.1271-51.9566
611.7906-1.56240.75484.1338-2.0561.1115-0.1802-0.5589-0.08030.08810.0298-0.17990.23070.98840.05761.03280.3067-0.0291.02850.05120.4931120.1082-9.9735-50.2155
626.4696-0.7529-3.720.54580.91542.7211-0.3863-0.4023-0.72430.0388-0.0330.14350.39470.16260.32371.0504-0.1003-0.08390.4310.06270.475293.2782-8.1984-41.0683
633.7916-1.0955-3.65210.44691.13463.5474-0.0470.0325-0.5791-0.3034-0.11920.21550.4548-0.22780.31010.9189-0.1012-0.18050.53170.0410.478677.4-1.9022-32.6741
647.3604-2.7871-3.68812.67991.31664.3340.81350.7565-0.12530.1087-0.5359-0.0695-0.06-0.4105-0.24820.86150.0243-0.04690.5908-0.06730.4504107.5713-4.0219-54.1906
651.6544-0.2858-0.95073.51650.57543.8267-0.0646-0.01320.4664-0.29980.0423-0.3823-0.8920.20230.11060.4525-0.1826-0.03060.36380.06320.402878.228133.7077-14.0694
663.8286-1.7913-2.31694.6062.36633.3258-0.28231.15460.2495-1.1125-0.0772-0.3324-0.7075-0.30810.07430.6522-0.17860.06220.52130.12850.380577.994628.9361-27.4022
673.46651.5823-2.52595.85731.08863.2994-0.00450.54030.5034-0.8820.23390.0312-0.8047-0.0373-0.20880.6833-0.09160.0140.52640.09640.27477.730336.3405-22.408
680.140.5021-0.28244.18330.70432.14570.01850.25270.2642-0.0428-0.0856-0.0358-0.56660.05540.12950.3533-0.1164-0.02660.3750.03580.314474.438230.9026-13.9698
690.713-0.07130.010.74880.9251.73420.25940.13460.0974-0.18960.06190.1336-0.2693-0.03-0.21970.3456-0.16810.08670.26410.03060.4473.414147.09255.5256
705.6999-3.89643.8713.3499-2.277.4685-0.062-0.30710.0548-0.19060.05990.02610.40110.2216-0.12090.2636-0.03490.01850.16570.03650.380975.736639.888621.6784
710.13840.2147-0.18080.7249-0.39190.36480.08750.04620.0936-0.0408-0.10670.05720.1673-0.0404-0.08110.0361-0.4040.2018-0.07130.09320.56272.970745.52954.4015
728.14312.63960.59215.0283-2.64033.70320.0297-0.4203-1.096-0.4778-0.627-0.67461.33340.9280.59740.49640.0480.03820.24120.08540.425682.93135.189214.9449
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain E and resid 188:208)E188 - 208
2X-RAY DIFFRACTION2(chain E and resid 209:220)E209 - 220
3X-RAY DIFFRACTION3(chain E and resid 221:232)E221 - 232
4X-RAY DIFFRACTION4(chain E and resid 233:237)E233 - 237
5X-RAY DIFFRACTION5(chain F and resid 25:35)F25 - 35
6X-RAY DIFFRACTION6(chain F and resid 36:52)F36 - 52
7X-RAY DIFFRACTION7(chain F and resid 53:63)F53 - 63
8X-RAY DIFFRACTION8(chain F and resid 64:76)F64 - 76
9X-RAY DIFFRACTION9(chain F and resid 77:93)F77 - 93
10X-RAY DIFFRACTION10(chain F and resid 94:145)F94 - 145
11X-RAY DIFFRACTION11(chain F and resid 146:165)F146 - 165
12X-RAY DIFFRACTION12(chain F and resid 166:170)F166 - 170
13X-RAY DIFFRACTION13(chain F and resid 171:186)F171 - 186
14X-RAY DIFFRACTION14(chain F and resid 187:202)F187 - 202
15X-RAY DIFFRACTION15(chain F and resid 203:215)F203 - 215
16X-RAY DIFFRACTION16(chain F and resid 216:235)F216 - 235
17X-RAY DIFFRACTION17(chain A and resid 171:212)A171 - 212
18X-RAY DIFFRACTION18(chain A and resid 213:258)A213 - 258
19X-RAY DIFFRACTION19(chain A and resid 259:265)A259 - 265
20X-RAY DIFFRACTION20(chain A and resid 266:294)A266 - 294
21X-RAY DIFFRACTION21(chain A and resid 295:308)A295 - 308
22X-RAY DIFFRACTION22(chain A and resid 309:321)A309 - 321
23X-RAY DIFFRACTION23(chain A and resid 322:335)A322 - 335
24X-RAY DIFFRACTION24(chain A and resid 336:369)A336 - 369
25X-RAY DIFFRACTION25(chain A and resid 370:395)A370 - 395
26X-RAY DIFFRACTION26(chain A and resid 396:420)A396 - 420
27X-RAY DIFFRACTION27(chain A and resid 421:457)A421 - 457
28X-RAY DIFFRACTION28(chain A and resid 458:466)A458 - 466
29X-RAY DIFFRACTION29(chain B and resid 20:35)B20 - 35
30X-RAY DIFFRACTION30(chain B and resid 36:59)B36 - 59
31X-RAY DIFFRACTION31(chain B and resid 60:77)B60 - 77
32X-RAY DIFFRACTION32(chain B and resid 78:101)B78 - 101
33X-RAY DIFFRACTION33(chain B and resid 102:108)B102 - 108
34X-RAY DIFFRACTION34(chain B and resid 109:128)B109 - 128
35X-RAY DIFFRACTION35(chain B and resid 129:146)B129 - 146
36X-RAY DIFFRACTION36(chain B and resid 147:158)B147 - 158
37X-RAY DIFFRACTION37(chain B and resid 159:174)B159 - 174
38X-RAY DIFFRACTION38(chain B and resid 175:186)B175 - 186
39X-RAY DIFFRACTION39(chain B and resid 187:230)B187 - 230
40X-RAY DIFFRACTION40(chain B and resid 231:237)B231 - 237
41X-RAY DIFFRACTION41(chain C and resid 24:29)C24 - 29
42X-RAY DIFFRACTION42(chain C and resid 30:40)C30 - 40
43X-RAY DIFFRACTION43(chain C and resid 41:58)C41 - 58
44X-RAY DIFFRACTION44(chain C and resid 59:69)C59 - 69
45X-RAY DIFFRACTION45(chain C and resid 70:125)C70 - 125
46X-RAY DIFFRACTION46(chain C and resid 126:130)C126 - 130
47X-RAY DIFFRACTION47(chain C and resid 131:158)C131 - 158
48X-RAY DIFFRACTION48(chain C and resid 159:174)C159 - 174
49X-RAY DIFFRACTION49(chain C and resid 175:183)C175 - 183
50X-RAY DIFFRACTION50(chain C and resid 184:200)C184 - 200
51X-RAY DIFFRACTION51(chain C and resid 201:218)C201 - 218
52X-RAY DIFFRACTION52(chain C and resid 219:235)C219 - 235
53X-RAY DIFFRACTION53(chain D and resid 171:186)D171 - 186
54X-RAY DIFFRACTION54(chain D and resid 187:200)D187 - 200
55X-RAY DIFFRACTION55(chain D and resid 201:229)D201 - 229
56X-RAY DIFFRACTION56(chain D and resid 230:264)D230 - 264
57X-RAY DIFFRACTION57(chain D and resid 265:279)D265 - 279
58X-RAY DIFFRACTION58(chain D and resid 280:313)D280 - 313
59X-RAY DIFFRACTION59(chain D and resid 314:335)D314 - 335
60X-RAY DIFFRACTION60(chain D and resid 336:359)D336 - 359
61X-RAY DIFFRACTION61(chain D and resid 360:381)D360 - 381
62X-RAY DIFFRACTION62(chain D and resid 382:405)D382 - 405
63X-RAY DIFFRACTION63(chain D and resid 406:435)D406 - 435
64X-RAY DIFFRACTION64(chain D and resid 436:461)D436 - 461
65X-RAY DIFFRACTION65(chain E and resid 20:68)E20 - 68
66X-RAY DIFFRACTION66(chain E and resid 69:79)E69 - 79
67X-RAY DIFFRACTION67(chain E and resid 80:102)E80 - 102
68X-RAY DIFFRACTION68(chain E and resid 103:129)E103 - 129
69X-RAY DIFFRACTION69(chain E and resid 130:158)E130 - 158
70X-RAY DIFFRACTION70(chain E and resid 159:165)E159 - 165
71X-RAY DIFFRACTION71(chain E and resid 166:176)E166 - 176
72X-RAY DIFFRACTION72(chain E and resid 177:187)E177 - 187

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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://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