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- PDB-6bpa: 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: 6bpa
タイトルPlasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to monoclonal antibody 3E9
要素
  • Monoclonal antibody 3E9 Fab heavy chain
  • Monoclonal antibody 3E9 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 / BROMIDE ION / 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: 2.53 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 3E9 Fab heavy chain
C: Monoclonal antibody 3E9 Fab light chain
D: Reticulocyte binding protein 2, putative
E: Monoclonal antibody 3E9 Fab heavy chain
F: Monoclonal antibody 3E9 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)179,6677
ポリマ－179,5876
非ポリマー801
水9,764542
1
A: Reticulocyte binding protein 2, putative
B: Monoclonal antibody 3E9 Fab heavy chain
C: Monoclonal antibody 3E9 Fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)89,8744
ポリマ－89,7943
非ポリマー801
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 3E9 Fab heavy chain
F: Monoclonal antibody 3E9 Fab light chain


分子量 (理論値)分子数
合計 (水以外)89,7943
ポリマ－89,7943
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)59.070, 177.100, 178.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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: pET32-a(+) / 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 3E9 Fab heavy chain


分子量: 27243.787 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 3E9 Fab light chain


分子量: 26030.107 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: 化合物 ChemComp-BR / BROMIDE ION / ブロミド


分子量: 79.904 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Br
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 542 / 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: 2.83 Å3/Da / 溶媒含有率: 56.55 %
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 / pH: 5.5
詳細: 0.2 M KBr, 15% (w/v) PEG 4,000 and 0.05 M sodium citrate/citric acid

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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
反射解像度: 2.53→59.54 Å / Num. obs: 63529 / % possible obs: 99.8 % / 冗長度: 6.7 % / CC1/2: 0.993 / Net I/σ(I): 9.9
反射 シェル解像度: 2.53→2.59 Å / 冗長度: 6.4 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4411 / CC1/2: 0.552 / % possible all: 99.3

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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: 2.53→56.051 Å / SU ML: 0.34 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 23.32
Rfactor反射数%反射
Rfree0.2246 1039 1.64 %
Rwork0.1942 --
obs0.1947 63452 99.73 %
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: 123.9 Å2 / Biso mean: 44.0516 Å2 / Biso min: 7.18 Å2
精密化ステップサイクル: final / 解像度: 2.53→56.051 Å
タンパク質核酸リガンド溶媒全体
原子数11516 0 1 542 12059
Biso mean--67.28 38.18 -
残基数----1448
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00411779
X-RAY DIFFRACTIONf_angle_d0.63215961
X-RAY DIFFRACTIONf_chiral_restr0.0411778
X-RAY DIFFRACTIONf_plane_restr0.0042031
X-RAY DIFFRACTIONf_dihedral_angle_d3.3657099
LS精密化 シェル

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

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.53-2.66340.32891430.27958751889499
2.6634-2.83020.27731370.25428802893999
2.8302-3.04880.29441210.234687938914100
3.0488-3.35550.2691530.218688819034100
3.3555-3.8410.22761390.183389069045100
3.841-4.83880.18741630.154389939156100
4.8388-56.06520.17891830.16692879470100
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)
10.52080.2506-0.18630.1858-0.10921.9111-0.87050.1631-0.3860.65610.0389-0.16470.92960.61080.66781.07660.3164-0.01131.08020.21911.08584.1239-41.326697.1414
24.7870.28750.30371.90320.2212.2860.0914-0.22050.3598-0.15270.60960.25430.6098-0.6001-0.52140.57950.0581-0.17570.55640.00630.52733.3117-31.68483.2741
32.8301-1.0796-0.53032.61610.72350.22320.4284-1.1543-0.58420.51080.18790.12190.55160.9262-0.60580.8551-0.0536-0.29471.09550.12420.86018.6244-33.3203102.5939
40.5799-0.44120.05763.99530.77760.4881-0.1628-0.35160.36490.83890.4479-1.28920.50340.3253-0.46870.65970.0875-0.18340.8152-0.06040.759115.1764-35.120988.7194
51.2297-0.27191.92722.6331.17459.7076-0.2831-0.14940.36290.1114-0.45090.2174-1.09640.32280.01990.4044-0.07590.01020.2456-0.03340.4461-23.2801-37.594369.4435
64.4172-0.19211.95782.4997-0.20411.3839-0.4572-0.49050.23540.23110.12190.344-0.9456-0.63410.04570.55330.00120.06150.47380.02160.4796-28.3775-40.998179.6734
70.7025-0.3886-1.01883.62820.04431.65230.1528-0.3073-0.18680.4213-0.04360.0890.1843-0.0245-0.12010.335-0.1004-0.05920.32470.02670.2599-23.1783-50.891170.3837
82.61160.01233.03121.34571.83715.89920.2212-0.5639-0.59180.48370.0516-0.14640.0129-0.6923-0.10950.4291-0.06460.0310.4660.07550.2924-27.3105-45.989175.8725
91.29570.0361-1.06931.55251.28674.9360.0412-0.08210.27320.1826-0.0113-0.1159-0.32840.3191-0.12040.2994-0.0404-0.05380.342-0.00580.2513-19.9078-42.846569.7234
104.0383-0.1926-3.1412.95951.06192.7838-0.663-0.60090.6007-0.28260.3029-0.7541-0.02820.07520.20520.607-0.0832-0.18940.6953-0.03830.6964.7242-22.460390.4615
114.59741.2674-0.73073.1624-0.40982.09860.43940.14330.0451-0.16630.11070.22390.2924-0.1634-0.3720.5416-0.0097-0.14710.6037-0.06650.3936-6.9867-26.40788.9117
124.7151-2.9203-1.14274.6549-0.87731.44140.23130.48520.467-0.01810.1226-0.6913-0.34120.1056-0.27570.6776-0.0625-0.21230.605-0.05140.5958-3.3577-18.016682.718
134.64080.46120.22184.0371-0.16771.7509-0.1202-0.388-0.09860.5387-0.0723-0.26160.0767-0.43210.2950.652-0.1362-0.08310.5901-0.02260.3851-10.8948-35.522790.0232
144.4446-0.4111-0.60421.33110.49651.7788-0.11750.31610.7299-0.49740.0742-0.621-0.75970.18150.08560.781-0.1473-0.29750.7146-0.05390.9888.3015-16.185182.6651
156.31043.702-3.51364.2191-3.30473.60151.3152-1.24980.70741.2157-0.8916-0.066-1.17-0.0346-0.61890.9118-0.275-0.08470.52980.06681.03434.607-10.170688.1485
162.79991.55361.13173.70460.47243.66320.1823-1.16141.0535-0.1974-0.4370.7816-0.5147-0.11920.22990.5561-0.0728-0.12590.6725-0.09490.6741-7.4359-16.112593.0998
175.55560.8646-0.09552.0394-1.46965.5292-0.22670.0070.02730.35840.62830.044-0.04830.1068-0.46740.3877-0.00230.08760.3546-0.06780.209728.7304-33.696818.8479
185.278-2.91772.17013.9518-1.25411.87760.21340.6479-0.0129-0.7209-0.01260.24880.1017-0.1413-0.15520.4667-0.07560.00680.48710.07460.268113.0635-22.17077.5049
191.9829-2.02731.17424.387-1.71652.29860.37750.3684-0.1245-0.9248-0.06550.12690.43210.1267-0.08350.4266-0.03920.08950.457-0.03770.328430.4265-38.715411.6751
204.532-2.25112.7044.3542-3.07965.1546-0.3426-0.53340.63610.0668-0.2083-0.636-0.343-0.23570.40710.312-0.06270.04460.49640.00610.39340.4481-37.856421.117
215.158-4.96052.04645.78-1.66470.98260.40010.9151.0532-0.8915-0.6266-0.9081-0.05330.3460.19720.6122-0.15030.07320.60590.0960.431222.611-16.47515.0396
222.94380.61360.76051.16340.10064.892-0.18680.36670.3756-0.69490.1170.14050.0997-0.1855-0.09480.42140.004-0.09140.37620.04010.3291.9824-16.829215.5581
233.2035-0.94393.94794.2365-1.05484.94830.4738-0.5335-0.71510.54780.3060.70230.15080.1662-0.38230.2780.0195-0.00610.35460.01460.295515.7338-36.733534.5235
245.8097-7.41574.2489.5479-5.30923.2385-0.009-0.3480.24851.2289-0.08010.58260.6059-0.5254-0.18060.45540.01380.0110.55080.04510.312828.9196-40.871540.8871
252.97920.14270.71944.5999-2.48854.78110.131-0.09030.2050.3433-0.4539-0.65850.19140.18120.12460.22830.0457-0.01550.34810.01790.413937.159-47.801939.0277
263.6837-2.6274.72446.1161-1.68217.186-0.17280.78810.115-0.73860.4595-0.9088-0.09920.52020.24270.2436-0.01290.04380.2921-0.02710.315529.6079-37.789828.265
271.4461-1.28851.01313.4903-1.66391.949-0.09350.19080.0657-0.2280.05130.0197-0.27470.08330.04350.3124-0.0416-0.03630.27310.00620.24812.0542-21.356520.7826
284.4585-4.18894.42394.9371-5.0565.23560.1619-0.6955-0.4837-0.4610.66580.91150.483-0.144-0.62630.38640.07550.00540.40.04950.403529.1424-53.84335.0389
295.1970.3468-2.84110.29750.50283.04270.03620.17810.6203-0.11450.30030.5881-0.0173-0.2763-0.50330.23210.0353-0.06770.29350.05090.3761-17.244-23.107442.9744
305.7051-1.9289-0.30666.3554-0.21962.5438-0.04150.47690.2457-0.93880.14630.2167-0.74140.0024-0.13840.3324-0.0274-0.05680.41710.03240.286-7.6961-22.080728.6243
315.78330.71230.38183.02281.04295.00910.0479-0.58590.25090.34440.1072-0.09820.1879-0.06910.08070.2290.0541-0.07310.2634-0.04560.2815-5.5039-24.938847.4911
323.4387-0.17043.37522.595-1.84719.3172-0.20850.3792-0.1459-0.5471-0.0522-0.05450.68850.6670.2790.2818-0.0257-0.04660.23930.00030.2821-4.4446-33.669536.6205
332.77470.5702-2.08383.2233-0.94936.9547-0.0970.1198-0.0808-0.22170.0550.20860.7292-0.11120.04880.21880.0257-0.02620.2253-0.00490.3259-13.1465-31.640640.301
346.54682.6897-5.64675.1782-1.42478.0278-0.01880.10610.10580.150.0185-0.13890.64-0.24850.11940.1914-0.05050.03090.2855-0.01610.3432-11.6895-24.88550.5168
351.1193-0.8249-1.43721.121.49432.210.0349-0.1131-0.0403-0.1263-0.07190.1117-0.10860.04810.02540.23550.0103-0.04260.23620.02810.2169-13.0406-17.12348.0034
362.76112.09091.97568.78582.43963.17340.0432-0.2621-0.15820.474-0.0614-0.1742-0.2583-0.09930.02360.31510.02770.04630.2259-0.00170.1772-21.9582-3.037263.7985
373.6543-1.59121.28293.81241.46863.1145-0.1263-0.0015-0.31750.15640.3180.22420.08250.0205-0.12220.18690.02760.03030.18310.01820.249-18.0845-4.676458.3655
382.9084-0.610.2634.91611.2262.45750.05240.12820.49020.3606-0.1292-0.3351-0.2598-0.24970.0460.2377-0.02520.01890.26430.01320.2991-20.10084.973861.4187
391.53240.3997-0.21653.12722.4562.1854-0.39790.43110.2593-0.3130.16290.7621-0.02680.37580.05150.25290.0278-0.02560.26560.04160.2823-27.2231-6.880152.8398
405.03181.41364.92127.14342.44388.28480.1096-0.4251-0.3022-0.2423-0.64371.0178-0.816-0.83560.61690.26880.08590.01430.31660.04710.3751-29.55246.622864.0405
413.0389-2.552-0.58642.24181.00433.50150.004-0.37960.23361.10830.1632-0.62650.05750.37750.03620.2464-0.0163-0.00770.4005-0.06640.248511.023-16.266556.7575
422.4052.08320.72263.8823-3.58118.81430.05340.0409-0.3682-0.3376-0.0123-0.85370.47440.7350.05720.22140.0227-0.00690.38630.05210.330815.1192-28.642147.537
432.36480.6539-0.38843.26960.25564.20750.1505-0.01010.3148-0.2023-0.19210.1581-0.4111-0.0876-0.0830.26870.00230.01660.2829-0.03330.31346.4903-13.972843.6927
442.9867-0.6053-0.58853.94541.6462.3872-0.097-0.45880.5902-0.28870.4470.162-0.37530.3031-0.18260.2278-0.0710.01870.3751-0.12530.41612.2408-12.791850.4245
458.6835-5.9218-6.17724.67683.0559.8536-0.12360.3613-0.02720.0441-0.40270.51780.10020.1057-0.20010.23370.0388-0.07720.1904-0.04470.29986.1243-23.588847.1708
462.87510.8798-0.19564.23480.03781.9172-0.0641-0.29780.14580.1843-0.05560.26720.05460.32730.02510.2221-0.0155-0.08230.2777-0.02140.20434.842-23.39650.635
472.7248-1.2168-1.83362.11730.67953.3598-0.1163-0.16730.40230.03040.10580.08490.0156-0.1296-0.00810.2497-0.06310.00680.2615-0.02960.1498-17.4413-0.644170.2264
487.05490.9819-4.03851.0328-0.97543.97820.0331-0.5968-0.15830.4453-0.0389-0.07440.15650.5979-0.03710.2973-0.0306-0.02430.2521-0.05710.2213-10.9153-3.394775.8317
498.75892.2639-2.6934.82980.31522.9558-0.54130.5086-0.2063-0.39920.4658-0.19780.4984-0.01970.1790.21450.0186-0.05980.3397-0.0410.2719-8.9219-6.040367.5778
505.2239-0.0034-0.83883.96151.25495.3889-0.06610.0527-0.60930.7361-0.12770.51490.4293-0.42560.25790.3947-0.00210.08560.34720.01480.3325-26.1853-6.82477.5179
512.0734-1.25421.13541.3843-0.3565.9824-0.0377-0.72860.34860.1766-0.1128-0.2634-0.28480.3464-0.18130.43720.0013-0.09530.38440.00120.3404-16.7217-0.983181.472
528.35051.8258-1.21672.3073-0.75923.37420.1448-1.46610.53450.16920.0979-0.1144-0.14220.4529-0.41420.40230.0373-0.02730.4055-0.09390.3567-13.35093.444980.2445
533.449-1.35932.15283.2417-0.42881.16560.0881-0.1393-0.1060.0104-0.1878-0.19030.14650.11220.00390.2605-0.0322-0.05820.2738-0.01150.2689-39.7924-75.203949.8835
546.4681-3.54752.3224.9224-2.33056.06840.10580.3942-0.2234-1.136-0.1015-0.13520.65570.7457-0.23020.5976-0.0131-0.04940.3794-0.05740.5842-19.8956-89.74158.1442
553.2966-2.89984.46727.1185-3.06046.1250.91780.6374-1.2559-0.0002-0.3533-0.4470.73520.7106-0.63620.4753-0.0387-0.08970.361-0.02370.6773-36.872-89.530748.6584
562.7320.3397-0.12983.3384-2.58414.13320.14760.46870.3197-0.9339-0.23530.41390.2598-0.41050.06470.39720.0228-0.08070.4055-0.07780.3566-54.2753-63.674333.0724
574.9314-0.9106-0.09916.593-1.95264.26820.1625-0.65470.80610.13870.07240.4187-0.0258-0.62790.07340.31840.03280.04670.4002-0.05110.4946-58.2272-64.080142.5084
586.2225-1.2423.29142.5461-1.74523.14630.4553-0.5493-0.5090.2475-0.26970.02780.3917-0.1985-0.22930.4555-0.08630.01050.40180.00690.4015-42.5967-84.624256.1205
592.7257-1.8377-0.20932.806-0.37361.88980.0592-0.0702-0.304-0.1335-0.0573-0.27470.54410.0049-0.0280.3833-0.0175-0.14180.2890.00940.4755-17.8888-81.165162.4681
608.9716-4.78540.35054.6361-0.75061.50210.020.51150.83570.0282-0.2283-0.2627-0.18720.12460.08350.28130.0148-0.02590.2496-0.00420.2599-33.7573-53.530748.2726
613.83510.12020.24977.51540.78292.6747-0.0448-0.39980.4367-0.08590.06290.5781-0.2263-0.42120.04240.25030.041-0.01760.3039-0.07120.3835-51.5541-47.351139.577
627.9144-2.74953.80014.6966-2.60262.89020.4137-0.48990.1944-0.0358-0.40390.1590.228-0.55-0.11840.2812-0.01810.01680.329-0.07750.2587-39.5443-62.541250.9615
631.7122-2.12281.94053.3316-2.33721.69620.0978-0.0311-0.19530.25420.0303-0.00030.15720.0532-0.14450.356-0.0508-0.05910.30040.04370.3715-25.1782-73.900260.0287
644.8964-1.93230.13444.038-4.16355.5420.23440.15910.6508-0.6298-0.464-0.2406-0.01710.62710.21210.39120.0302-0.09480.2878-0.04950.3884-44.434-49.792232.5835
654.9156-0.46870.42173.13153.73844.5798-0.7442-0.5375-1.1710.932-0.2095-0.7630.78210.81660.14830.2445-0.0333-0.54590.43910.23990.7609-1.3445-57.220768.4915
662.22850.2046-0.08583.6392-0.33770.67530.04910.1801-0.305-0.0304-0.0253-0.64520.1057-0.0701-0.10010.30810.0093-0.07280.37120.07380.4673-3.1068-54.21760.1155
675.5412-2.1309-1.65293.1602-1.26513.86920.3453-0.0015-0.0889-0.1317-0.3256-0.3474-0.1936-0.30720.0380.2041-0.0114-0.01320.21860.08480.2923-10.1195-49.643657.5652
682.15561.2753-0.35823.4366-0.663.82570.22580.24040.0765-0.5573-0.1836-0.39620.06770.1987-0.00330.26550.0347-0.03940.30940.03090.4077-5.6539-48.916452.4668
692.29212.80730.80349.34360.74353.68590.04340.0575-0.0133-0.658-0.0158-1.0212-0.12580.529-0.19560.30070.0257-0.03480.34750.05730.53170.6824-50.499257.2082
708.39666.1031-2.57594.5431-0.99966.8680.27720.25430.3646-0.14370.08630.0658-0.3076-0.2898-0.12840.2451-0.025-0.00280.41520.10990.5118-3.7661-43.808964.5057
710.5996-0.6017-0.37561.28170.92920.729-0.0649-0.16040.33770.26310.0917-0.38380.05380.3383-0.14950.4193-0.0833-0.19440.41970.0950.5322-1.5447-43.321174.1069
723.6507-1.3593-2.83322.87111.57772.3168-0.3695-0.34660.05390.63030.0316-0.54450.22030.70330.11010.58270.0473-0.20910.77090.04110.73218.2831-34.889285.0143
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain E and resid 182:188)E182 - 188
2X-RAY DIFFRACTION2(chain E and resid 189:209)E189 - 209
3X-RAY DIFFRACTION3(chain E and resid 210:222)E210 - 222
4X-RAY DIFFRACTION4(chain E and resid 223:239)E223 - 239
5X-RAY DIFFRACTION5(chain F and resid 23:35)F23 - 35
6X-RAY DIFFRACTION6(chain F and resid 36:45)F36 - 45
7X-RAY DIFFRACTION7(chain F and resid 46:84)F46 - 84
8X-RAY DIFFRACTION8(chain F and resid 85:107)F85 - 107
9X-RAY DIFFRACTION9(chain F and resid 108:130)F108 - 130
10X-RAY DIFFRACTION10(chain F and resid 131:152)F131 - 152
11X-RAY DIFFRACTION11(chain F and resid 153:165)F153 - 165
12X-RAY DIFFRACTION12(chain F and resid 166:187)F166 - 187
13X-RAY DIFFRACTION13(chain F and resid 188:197)F188 - 197
14X-RAY DIFFRACTION14(chain F and resid 198:208)F198 - 208
15X-RAY DIFFRACTION15(chain F and resid 209:217)F209 - 217
16X-RAY DIFFRACTION16(chain F and resid 218:233)F218 - 233
17X-RAY DIFFRACTION17(chain A and resid 170:186)A170 - 186
18X-RAY DIFFRACTION18(chain A and resid 187:217)A187 - 217
19X-RAY DIFFRACTION19(chain A and resid 218:266)A218 - 266
20X-RAY DIFFRACTION20(chain A and resid 267:285)A267 - 285
21X-RAY DIFFRACTION21(chain A and resid 286:309)A286 - 309
22X-RAY DIFFRACTION22(chain A and resid 310:337)A310 - 337
23X-RAY DIFFRACTION23(chain A and resid 338:350)A338 - 350
24X-RAY DIFFRACTION24(chain A and resid 351:357)A351 - 357
25X-RAY DIFFRACTION25(chain A and resid 358:378)A358 - 378
26X-RAY DIFFRACTION26(chain A and resid 379:384)A379 - 384
27X-RAY DIFFRACTION27(chain A and resid 385:448)A385 - 448
28X-RAY DIFFRACTION28(chain A and resid 449:466)A449 - 466
29X-RAY DIFFRACTION29(chain B and resid 20:40)B20 - 40
30X-RAY DIFFRACTION30(chain B and resid 41:51)B41 - 51
31X-RAY DIFFRACTION31(chain B and resid 52:65)B52 - 65
32X-RAY DIFFRACTION32(chain B and resid 66:81)B66 - 81
33X-RAY DIFFRACTION33(chain B and resid 82:106)B82 - 106
34X-RAY DIFFRACTION34(chain B and resid 107:115)B107 - 115
35X-RAY DIFFRACTION35(chain B and resid 116:152)B116 - 152
36X-RAY DIFFRACTION36(chain B and resid 153:174)B153 - 174
37X-RAY DIFFRACTION37(chain B and resid 175:199)B175 - 199
38X-RAY DIFFRACTION38(chain B and resid 200:219)B200 - 219
39X-RAY DIFFRACTION39(chain B and resid 220:232)B220 - 232
40X-RAY DIFFRACTION40(chain B and resid 233:241)B233 - 241
41X-RAY DIFFRACTION41(chain C and resid 23:44)C23 - 44
42X-RAY DIFFRACTION42(chain C and resid 45:53)C45 - 53
43X-RAY DIFFRACTION43(chain C and resid 54:83)C54 - 83
44X-RAY DIFFRACTION44(chain C and resid 84:108)C84 - 108
45X-RAY DIFFRACTION45(chain C and resid 109:113)C109 - 113
46X-RAY DIFFRACTION46(chain C and resid 114:127)C114 - 127
47X-RAY DIFFRACTION47(chain C and resid 128:154)C128 - 154
48X-RAY DIFFRACTION48(chain C and resid 155:176)C155 - 176
49X-RAY DIFFRACTION49(chain C and resid 177:196)C177 - 196
50X-RAY DIFFRACTION50(chain C and resid 197:210)C197 - 210
51X-RAY DIFFRACTION51(chain C and resid 211:220)C211 - 220
52X-RAY DIFFRACTION52(chain C and resid 221:234)C221 - 234
53X-RAY DIFFRACTION53(chain D and resid 170:202)D170 - 202
54X-RAY DIFFRACTION54(chain D and resid 203:216)D203 - 216
55X-RAY DIFFRACTION55(chain D and resid 217:242)D217 - 242
56X-RAY DIFFRACTION56(chain D and resid 243:265)D243 - 265
57X-RAY DIFFRACTION57(chain D and resid 266:279)D266 - 279
58X-RAY DIFFRACTION58(chain D and resid 280:304)D280 - 304
59X-RAY DIFFRACTION59(chain D and resid 305:337)D305 - 337
60X-RAY DIFFRACTION60(chain D and resid 338:355)D338 - 355
61X-RAY DIFFRACTION61(chain D and resid 356:378)D356 - 378
62X-RAY DIFFRACTION62(chain D and resid 379:393)D379 - 393
63X-RAY DIFFRACTION63(chain D and resid 394:449)D394 - 449
64X-RAY DIFFRACTION64(chain D and resid 450:465)D450 - 465
65X-RAY DIFFRACTION65(chain E and resid 20:29)E20 - 29
66X-RAY DIFFRACTION66(chain E and resid 30:57)E30 - 57
67X-RAY DIFFRACTION67(chain E and resid 58:78)E58 - 78
68X-RAY DIFFRACTION68(chain E and resid 79:93)E79 - 93
69X-RAY DIFFRACTION69(chain E and resid 94:107)E94 - 107
70X-RAY DIFFRACTION70(chain E and resid 108:115)E108 - 115
71X-RAY DIFFRACTION71(chain E and resid 116:162)E116 - 162
72X-RAY DIFFRACTION72(chain E and resid 163:181)E163 - 181

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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