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- PDB-8u70: Crystal structure of malaria transmission-blocking anti-Pfs48/45 ... -

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基本情報

登録情報
データベース: PDB / ID: 8u70
タイトルCrystal structure of malaria transmission-blocking anti-Pfs48/45 antibody RUPA-58.
要素
  • Antibody RUPA-58 Heavy chain
  • Antibody RUPA-58 Kappa chain
キーワードIMMUNE SYSTEM / Pfs48/45 / human transmission-blocking antibodies / Malaria
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.09 Å
データ登録者Hailemariam, S. / Ivanochko, D. / Julien, J.P.
資金援助 カナダ, 米国, 5件
組織認可番号国
Canadian Institutes of Health Research (CIHR)428410 カナダ
CIFAR Azrieli Global Scholars カナダ
Ontario Early Researcher Awards カナダ
Canada Research Chairs カナダ
Bill & Melinda Gates FoundationOPP1170236 米国
引用ジャーナル: Nat Struct Mol Biol / 年: 2025
タイトル: Structural elucidation of full-length Pfs48/45 in complex with potent monoclonal antibodies isolated from a naturally exposed individual.
著者: Iga Kucharska / Danton Ivanochko / Sophia Hailemariam / Maartje R Inklaar / Hee Ryung Kim / Karina Teelen / Rianne Stoter / Marga van de Vegte-Bolmer / Geert-Jan van Gemert / Anthony Semesi / ...著者: Iga Kucharska / Danton Ivanochko / Sophia Hailemariam / Maartje R Inklaar / Hee Ryung Kim / Karina Teelen / Rianne Stoter / Marga van de Vegte-Bolmer / Geert-Jan van Gemert / Anthony Semesi / Brandon McLeod / Ahyoung Ki / Won-Kyu Lee / John L Rubinstein / Matthijs M Jore / Jean-Philippe Julien /
要旨: Biomedical interventions that block the transmission of Plasmodium falciparum (Pf) from humans to mosquitoes may be critical for malaria elimination. Pfs48/45, a gamete-surface protein essential for ...Biomedical interventions that block the transmission of Plasmodium falciparum (Pf) from humans to mosquitoes may be critical for malaria elimination. Pfs48/45, a gamete-surface protein essential for Pf development in the mosquito midgut, is a target of clinical-stage transmission-blocking vaccines and monoclonal antibodies (mAbs) that disrupt Pf transmission to mosquitoes. Antibodies directed to domain 3 of Pfs48/45 have been structurally and functionally described; however, in-depth information about other inhibitory epitopes on Pfs48/45 is currently limited. Here, we present a cryo-electron microscopy structure of full-length Pfs48/45 in complex with potent human mAbs targeting all three domains. Our data indicate that although Pfs48/45 domains 1 and 2 are rigidly coupled, there is substantial conformational flexibility between domains 2 and 3. Characterization of mAbs against domain 1 revealed the presence of a conformational epitope class that is largely conserved across Pf field isolates and is associated with recognition by potent antibodies. Our study provides insights into epitopes across full-length Pfs48/45 and has implications for the design of next-generation malaria interventions.
履歴
登録2023年9月14日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年9月18日Provider: repository / タイプ: Initial release
改定 1.12024年11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
改定 1.22025年6月11日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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: Antibody RUPA-58 Kappa chain
C: Antibody RUPA-58 Kappa chain
E: Antibody RUPA-58 Kappa chain
I: Antibody RUPA-58 Kappa chain
K: Antibody RUPA-58 Kappa chain
B: Antibody RUPA-58 Heavy chain
D: Antibody RUPA-58 Heavy chain
F: Antibody RUPA-58 Heavy chain
J: Antibody RUPA-58 Heavy chain
L: Antibody RUPA-58 Heavy chain
G: Antibody RUPA-58 Kappa chain
H: Antibody RUPA-58 Heavy chain


分子量 (理論値)分子数
合計 (水以外)287,31912
ポリマ－287,31912
非ポリマー00
水00
1
A: Antibody RUPA-58 Kappa chain
B: Antibody RUPA-58 Heavy chain


分子量 (理論値)分子数
合計 (水以外)47,8862
ポリマ－47,8862
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-23 kcal/mol
Surface area19530 Å2
手法PISA
2
C: Antibody RUPA-58 Kappa chain
D: Antibody RUPA-58 Heavy chain


分子量 (理論値)分子数
合計 (水以外)47,8862
ポリマ－47,8862
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-21 kcal/mol
Surface area19720 Å2
手法PISA
3
E: Antibody RUPA-58 Kappa chain
F: Antibody RUPA-58 Heavy chain


分子量 (理論値)分子数
合計 (水以外)47,8862
ポリマ－47,8862
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-23 kcal/mol
Surface area20020 Å2
手法PISA
4
I: Antibody RUPA-58 Kappa chain
J: Antibody RUPA-58 Heavy chain


分子量 (理論値)分子数
合計 (水以外)47,8862
ポリマ－47,8862
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-21 kcal/mol
Surface area19840 Å2
手法PISA
5
K: Antibody RUPA-58 Kappa chain
L: Antibody RUPA-58 Heavy chain


分子量 (理論値)分子数
合計 (水以外)47,8862
ポリマ－47,8862
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-22 kcal/mol
Surface area19380 Å2
手法PISA
6
G: Antibody RUPA-58 Kappa chain
H: Antibody RUPA-58 Heavy chain


分子量 (理論値)分子数
合計 (水以外)47,8862
ポリマ－47,8862
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-20 kcal/mol
Surface area19930 Å2
手法PISA
単位格子
Length a, b, c (Å)164.513, 164.513, 92.276
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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要素

#1: 抗体
Antibody RUPA-58 Kappa chain


分子量: 23470.133 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / Cell (発現宿主): epithelial / 細胞株 (発現宿主): 293F / 発現宿主: Homo sapiens (ヒト) / 組織 (発現宿主): embryonic kidney
#2: 抗体
Antibody RUPA-58 Heavy chain


分子量: 24416.352 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / Cell (発現宿主): epithelial / 細胞株 (発現宿主): 239F / 発現宿主: Homo sapiens (ヒト) / 組織 (発現宿主): embryonic kidney
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: 2.51 Å3/Da / 溶媒含有率: 51.04 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: 0.2 M sodium acetate, 30% PEG 8000, 0.1 M sodium cacodylate, 20% ethylene glycol

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データ収集

回折平均測定温度: 80 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 23-ID-D / 波長: 1.0332 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2022年6月25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: 1.0332 Å / 相対比: 1
反射解像度: 3.09→29.46 Å / Num. obs: 51007 / % possible obs: 99.7 % / 冗長度: 9.5 % / Biso Wilson estimate: 51.7 Å2 / CC1/2: 0.957 / Rpim(I) all: 0.152 / Net I/σ(I): 3.6
反射 シェル解像度: 3.09→3.2 Å / 冗長度: 9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5024 / CC1/2: 0.336 / Rpim(I) all: 0.517 / % possible all: 99

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解析

ソフトウェア
名称バージョン分類
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
PHENIX(1.20.1_4487)精密化
精密化構造決定の手法: 分子置換 / 解像度: 3.09→29.46 Å / SU ML: 0.47 / 交差検証法: FREE R-VALUE / σ(F): 1.38 / 位相誤差: 28.66 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2631 1798 3.53 %
Rwork0.2231 --
obs0.2245 51007 99.92 %
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: 3.09→29.46 Å
タンパク質核酸リガンド溶媒全体
原子数19914 0 0 0 19914
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00420388
X-RAY DIFFRACTIONf_angle_d0.90727720
X-RAY DIFFRACTIONf_dihedral_angle_d14.357356
X-RAY DIFFRACTIONf_chiral_restr0.0563096
X-RAY DIFFRACTIONf_plane_restr0.0073552
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.170.3531360.3173739X-RAY DIFFRACTION100
3.17-3.270.37741360.31293755X-RAY DIFFRACTION100
3.27-3.370.38711340.30693850X-RAY DIFFRACTION100
3.37-3.490.3611480.28163762X-RAY DIFFRACTION100
3.49-3.630.30731380.24983820X-RAY DIFFRACTION100
3.63-3.80.27141330.23153778X-RAY DIFFRACTION100
3.8-40.24811460.22853780X-RAY DIFFRACTION100
4-4.250.2551360.20023763X-RAY DIFFRACTION100
4.25-4.570.23921350.18293824X-RAY DIFFRACTION100
4.57-5.030.2351380.1883783X-RAY DIFFRACTION100
5.03-5.750.23781500.19423807X-RAY DIFFRACTION100
5.76-7.230.24451390.23083784X-RAY DIFFRACTION100
7.23-29.460.19741290.19293764X-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)
15.82393.740.79892.11382.19874.47540.3480.16680.20770.1215-0.55790.1771-0.1949-0.06620.15540.47480.0368-0.03770.42470.01970.281613.69324.6559-8.3264
24.58771.7983-1.56514.205-1.63291.8717-0.43130.51960.0458-0.82720.08120.0570.0213-0.20830.10540.503-0.0404-0.08460.41820.00940.29854.866220.281-7.5144
33.23741.1290.17820.77510.19820.1858-0.0214-0.03440.0354-0.0673-0.0775-0.00510.13220.13310.08060.44310.0852-0.00020.39370.03620.295619.517527.98811.9196
46.2676-1.88142.77682.442-0.94392.97460.0950.0322-0.50680.3866-0.1578-0.13410.23210.4993-0.14220.4555-0.01320.00760.60270.09120.58938.133326.32979.3455
56.0713-1.80282.76821.7892-0.89161.98770.24660.37140.63310.2087-0.4914-0.42140.30150.55390.28340.3863-0.0520.09860.74630.13760.43948.114930.99516.995
62.86820.1252.7899.26591.28663.43940.1063-0.401-0.40940.8693-0.2142-0.18510.1282-0.0269-0.01090.50780.0131-0.0340.3650.02520.3926-20.459775.684114.9914
71.1118-0.91120.66435.70691.15583.0681-0.056-0.1598-0.08170.514-0.26120.44030.1039-0.02420.24970.3464-0.09920.02510.46520.04820.3803-23.498384.834711.7109
82.28941.898-0.9437.62651.5482.40370.1321-0.0510.00080.593-0.3480.66070.3227-0.50960.21880.41960.0506-0.01840.50860.05450.3368-26.591677.32368.8009
90.28580.19490.28275.05022.62211.72040.04550.1131-0.10450.3760.09580.09080.44760.0611-0.07710.4265-0.03420.00960.47430.02490.39-18.340362.83311.1107
104.612-1.8062-0.20873.47372.82112.5379-0.05570.0874-0.35530.8394-0.0284-0.25680.734-0.2131-0.22610.59580.01130.00990.5775-0.07240.6578-17.87149.80262.0167
116.9046-2.84681.40526.4536-2.2533.88520.41450.6833-0.0743-0.4726-0.38570.99270.4898-0.09070.1280.5178-0.1301-0.04550.4921-0.16060.5865-17.582653.52911.4208
121.2812-0.4295-1.99914.0862.9975.87970.3315-0.12260.0730.19370.2668-1.32280.0981.1747-0.59610.28690.0693-0.02870.76-0.0850.6635-11.579247.4293-5.5875
136.4021-3.5968-3.50617.59483.96136.5924-0.6142-0.7951-0.76470.92860.8745-0.52052.00870.96140.01470.69560.21290.03370.6514-0.02110.4732-13.043439.7238-0.618
145.4508-2.3457-3.70476.11183.34198.0061-1.301-0.2878-0.5061.60160.39711.02652.21360.58490.58870.96330.0010.11550.5210.10020.6925-20.517540.40643.6916
154.304-1.4267-0.62922.99550.53882.00780.1523-0.27240.1889-0.1403-0.86670.7403-0.14080.90090.20090.58610.01440.02130.5221-0.08670.4325-8.991526.797562.4003
163.5087-0.638-0.72153.46090.29011.2713-0.1891-0.34520.32050.52180.0932-0.1091-0.07640.1020.04370.503-0.0337-0.10790.4526-0.01130.36330.627325.784559.0162
173.4673-0.8963-0.30993.7851.42211.6843-0.1792-0.30960.6377-0.33230.20.0723-0.2686-0.08580.16420.47160.0357-0.04720.38980.03030.3274-8.228328.436756.9821
187.67991.50263.16610.22770.48121.7593-0.66170.43391.1524-0.12670.00970.5964-0.30150.45720.7670.6154-0.0245-0.10480.3775-0.01820.8674-36.875333.251546.2979
194.8021.08590.37223.49661.43282.8792-0.17270.01730.9257-0.0511-0.25530.9919-0.3296-0.25030.4190.56970.0212-0.11920.4315-0.00670.5853-33.881630.404148.068
203.34451.7583-0.0441.739-0.04960.0104-0.11310.77020.70270.1723-0.0960.9259-0.18030.03890.53390.60540.1132-0.15910.6319-0.13430.732-46.951530.646148.9969
217.01263.76841.81472.58041.44950.9617-0.4908-0.52630.7844-0.038-0.36661.07980.0874-0.2810.68060.50860.1381-0.08110.6693-0.0621.0418-40.770737.987654.9879
222.1046-1.00981.31134.2561-0.11485.5349-0.0490.4059-0.4075-0.1287-0.1502-0.23090.03520.54730.13710.27990.04220.11130.5690.02330.4694-57.231241.123417.5326
233.7701-4.4167-2.15965.91292.1383.8739-0.2532-0.1453-0.02030.27970.1207-0.07540.49950.17690.21580.4079-0.00380.06990.41270.08380.3894-56.547933.876720.1109
244.87591.5533-1.33544.7402-3.22466.2385-0.10990.6404-0.241-0.36680.29530.05451.0096-0.2427-0.14270.6211-0.0039-0.01460.5027-0.09180.46-61.47715.276127.6445
252.02311.15790.81636.2464-0.45044.3443-0.29150.40740.47680.50980.1318-0.1421-0.08280.3612-0.18050.4848-0.13610.05410.48550.01270.4096-56.862156.4653-4.5938
264.51330.53931.31333.94291.23877.53870.01930.2315-0.4704-0.19680.0483-0.68430.06510.5983-0.03550.3348-0.0404-0.00390.37690.05840.4297-57.367148.8169-10.4209
271.77510.2697-0.38020.46710.7681.6722-0.2699-0.11110.35260.494-0.2042-0.3837-1.2490.62810.00950.8281-0.546-0.10630.90070.51151.0836-41.954366.4003-11.8011
282.87770.0695-0.3053.7783-2.52763.45630.1910.13770.51510.8777-0.084-0.167-1.06570.2796-0.09970.7635-0.20490.07120.5480.06320.8553-43.618681.7135-26.7723
294.07851.34671.23791.69120.50671.73320.02220.17060.12170.0466-0.1-0.0113-0.1230.12940.07620.36510.00460.02070.35430.05250.26219.725316.598814.3648
302.90762.4411-0.51547.64620.04251.74920.2494-0.59260.46280.9217-0.3332-0.1976-0.11460.04760.04470.5652-0.0425-0.10580.5074-0.00950.45629.743130.959222.3552
312.9999-1.8902-0.58173.80321.54372.3580.60930.117-0.1503-0.5083-0.09460.1264-0.1675-0.0269-0.12140.4481-0.03780.0010.34430.00050.5435-13.040780.6779-13.5506
322.7046-0.90080.83372.78091.17051.7211-0.0204-0.16060.017-0.33890.16830.0087-0.127-0.1283-0.12030.3288-0.02740.03760.37670.04760.4311-13.060190.287-6.0833
333.1899-1.27720.30313.56130.56461.35010.0375-0.24530.4942-0.5809-0.1094-1.0249-0.47860.1659-0.21630.4705-0.06010.01140.5294-0.01980.5951-3.79690.3369-7.01
343.1092-1.74490.34223.63380.45221.7128-0.00610.19730.21050.1333-0.1843-0.4328-0.01080.4267-0.16260.3664-0.13050.01340.42130.04530.5521-7.004184.9681-11.4408
352.1956-0.5317-0.28172.52640.48951.5855-0.118-0.13810.14980.60270.14420.02060.2216-0.0314-0.05470.3713-0.0448-0.00230.41430.03460.4107-15.898284.3923-4.8477
361.80120.1296-0.02854.77240.99443.6130.1658-0.1079-0.45750.0773-0.08011.04280.9189-0.6168-0.0510.5717-0.1487-0.17540.542-0.00230.8097-21.822748.9761-11.0207
371.07410.8358-0.92784.93770.59644.64040.2431-0.3662-0.2494-0.2885-0.18460.54840.3802-0.5347-0.15570.333-0.066-0.05140.4454-0.04680.634-20.72158.4345-11.2418
380.41130.1828-0.80794.56080.49553.6332-0.04820.31780.0827-0.57130.21520.91720.5051-0.4645-0.09470.5596-0.0631-0.19030.5737-0.04040.6592-23.347355.4691-20.7466
394.6460.15221.49112.60050.12261.01270.0596-0.0859-0.1236-0.084-0.0063-0.1185-0.2325-0.151-0.01820.4626-0.0048-0.01970.37710.00870.2472-1.47814.339840.6553
404.6157-0.8348-0.06242.7870.84664.09640.05730.57310.8852-0.8119-0.07730.4071-1.0496-0.1791-0.03970.713-0.0184-0.09040.6160.17970.7761-30.028435.019834.7221
411.42170.57090.60054.8938-0.15951.08420.1746-0.4407-0.28080.4666-0.2157-0.4206-0.331-0.11540.02650.404-0.00620.07680.40430.01650.4131-65.798237.089543.5193
422.62920.78080.18164.2483-1.00671.1268-0.03780.02240.1940.0190.16550.20820.1081-0.04-0.01360.2634-0.01860.03820.45450.00730.278-68.298446.263336.1427
431.79330.78150.00144.2139-0.643-0.0085-0.07220.10260.14510.02920.17850.39770.14270.1658-0.04340.43680.0570.06440.4186-0.04960.3675-72.637141.576738.6071
441.4344-0.54360.5387.2915-1.41771.670.09220.1285-0.2439-0.3101-0.0605-0.24210.28350.14190.02840.31970.08430.00080.4846-0.00330.2282-60.339224.959135.6469
452.98552.577-1.13482.82630.31433.6790.03810.0870.0538-0.35370.2585-0.2931-0.16540.5847-0.26830.6122-0.0304-0.11270.3975-0.05410.5147-51.630914.995141.8229
463.13882.8191-0.39423.09990.14523.880.19070.0956-0.40160.3855-0.0166-0.3360.43020.1154-0.10530.51470.0568-0.00080.375-0.02390.4385-55.02439.477742.6602
472.18170.5406-0.97316.8123-1.82252.6736-0.14021.00070.6444-0.46610.0797-0.9670.611-0.22180.00480.4168-0.13050.05050.5086-0.08020.3934-64.835655.2117-34.218
482.42660.6699-0.98115.6765-2.18381.68170.1022-0.0390.04190.0273-0.01610.0657-0.06080.2882-0.14250.3105-0.0179-0.05180.3831-0.01540.2819-70.637147.2165-27.0437
493.22080.1661-0.13676.6388-2.10381.64750.0475-0.00870.2167-0.11180.17870.31560.17320.0027-0.2350.3719-0.1331-0.02580.32010.03950.2819-72.084653.6003-32.2129
502.56590.1885-0.46942.57980.76450.3901-0.2475-0.2483-0.31960.54030.1011-0.60070.0809-0.01680.15930.43530.0159-0.07180.45880.02170.3907-63.134545.9653-23.02
511.34880.9234-2.14474.2937-0.722.1068-0.4854-0.51410.4783-0.29620.0772-0.7205-0.2470.51910.02180.5308-0.07210.11740.55140.13190.7483-46.804674.4664-36.0553
523.23072.5039-1.53156.1919-0.43624.22850.08-0.16180.075-0.4549-0.0503-0.85930.06410.4398-0.00190.40320.00860.09820.4860.12320.5855-47.781468.4629-33.4178
536.09082.6775-3.66726.2127-1.22493.97090.12570.107-0.0076-1.0706-0.3109-1.03020.3125-00.06590.729-0.08620.13990.6840.16760.5885-45.623767.2878-43.3585
541.35222.90390.60656.3039-0.34434.93080.13670.4873-0.3083-0.4434-0.04130.28210.91080.3586-0.06720.72010.2392-0.14430.6639-0.12910.5912.615875.02995.582
551.21691.8806-0.8814.6171-1.99221.321-0.03320.2267-0.7136-0.2876-0.2569-0.26930.601-0.06440.28180.97170.1255-0.17390.7499-0.21570.907610.554962.821414.6557
562.98341.8672-1.94672.2593-1.3613.076-0.86240.755-0.5189-0.51390.630.21780.3005-0.71550.1230.958-0.0116-0.04420.7333-0.12521.236-4.143346.810921.3425
577.36122.6791-3.73482.6088-1.83953.7506-1.8982.1233-0.9039-2.18641.8306-0.36850.4595-1.03540.88471.9961-0.1543-0.1960.5638-0.08541.1493-1.070138.139715.1909
584.397-0.56610.32962.56010.34223.06090.23950.2723-0.61960.0235-0.07310.02030.39530.1414-0.15780.40890.0621-0.05910.3146-0.06830.43218.180783.037827.4724
592.23370.5599-0.03410.4002-1.07332.19410.2356-0.2187-1.2875-0.3024-0.1480.73160.73020.2355-0.15351.0621-0.0199-0.38210.66750.16491.83495.931949.739734.1206
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 150 )
4X-RAY DIFFRACTION4chain 'A' and (resid 151 through 186 )
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 211 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 18 )
7X-RAY DIFFRACTION7chain 'C' and (resid 19 through 75 )
8X-RAY DIFFRACTION8chain 'C' and (resid 76 through 90 )
9X-RAY DIFFRACTION9chain 'C' and (resid 91 through 128 )
10X-RAY DIFFRACTION10chain 'C' and (resid 129 through 150 )
11X-RAY DIFFRACTION11chain 'C' and (resid 151 through 172 )
12X-RAY DIFFRACTION12chain 'C' and (resid 173 through 186 )
13X-RAY DIFFRACTION13chain 'C' and (resid 187 through 198 )
14X-RAY DIFFRACTION14chain 'C' and (resid 199 through 211 )
15X-RAY DIFFRACTION15chain 'E' and (resid 1 through 18 )
16X-RAY DIFFRACTION16chain 'E' and (resid 19 through 75 )
17X-RAY DIFFRACTION17chain 'E' and (resid 76 through 113 )
18X-RAY DIFFRACTION18chain 'E' and (resid 114 through 150 )
19X-RAY DIFFRACTION19chain 'E' and (resid 151 through 186 )
20X-RAY DIFFRACTION20chain 'E' and (resid 187 through 197 )
21X-RAY DIFFRACTION21chain 'E' and (resid 198 through 211 )
22X-RAY DIFFRACTION22chain 'I' and (resid 1 through 75 )
23X-RAY DIFFRACTION23chain 'I' and (resid 76 through 113 )
24X-RAY DIFFRACTION24chain 'I' and (resid 114 through 211 )
25X-RAY DIFFRACTION25chain 'K' and (resid 1 through 25 )
26X-RAY DIFFRACTION26chain 'K' and (resid 26 through 102 )
27X-RAY DIFFRACTION27chain 'K' and (resid 103 through 113 )
28X-RAY DIFFRACTION28chain 'K' and (resid 114 through 211 )
29X-RAY DIFFRACTION29chain 'B' and (resid 1 through 145 )
30X-RAY DIFFRACTION30chain 'B' and (resid 146 through 213 )
31X-RAY DIFFRACTION31chain 'D' and (resid 1 through 17 )
32X-RAY DIFFRACTION32chain 'D' and (resid 18 through 59 )
33X-RAY DIFFRACTION33chain 'D' and (resid 60 through 72 )
34X-RAY DIFFRACTION34chain 'D' and (resid 73 through 87 )
35X-RAY DIFFRACTION35chain 'D' and (resid 88 through 119 )
36X-RAY DIFFRACTION36chain 'D' and (resid 120 through 145 )
37X-RAY DIFFRACTION37chain 'D' and (resid 146 through 188 )
38X-RAY DIFFRACTION38chain 'D' and (resid 189 through 213 )
39X-RAY DIFFRACTION39chain 'F' and (resid 1 through 111 )
40X-RAY DIFFRACTION40chain 'F' and (resid 112 through 213 )
41X-RAY DIFFRACTION41chain 'J' and (resid 1 through 17 )
42X-RAY DIFFRACTION42chain 'J' and (resid 18 through 59 )
43X-RAY DIFFRACTION43chain 'J' and (resid 60 through 95 )
44X-RAY DIFFRACTION44chain 'J' and (resid 96 through 145 )
45X-RAY DIFFRACTION45chain 'J' and (resid 146 through 165 )
46X-RAY DIFFRACTION46chain 'J' and (resid 166 through 213 )
47X-RAY DIFFRACTION47chain 'L' and (resid 1 through 17 )
48X-RAY DIFFRACTION48chain 'L' and (resid 18 through 72 )
49X-RAY DIFFRACTION49chain 'L' and (resid 73 through 87 )
50X-RAY DIFFRACTION50chain 'L' and (resid 88 through 111 )
51X-RAY DIFFRACTION51chain 'L' and (resid 112 through 145 )
52X-RAY DIFFRACTION52chain 'L' and (resid 146 through 188 )
53X-RAY DIFFRACTION53chain 'L' and (resid 189 through 213 )
54X-RAY DIFFRACTION54chain 'G' and (resid 1 through 38 )
55X-RAY DIFFRACTION55chain 'G' and (resid 39 through 150 )
56X-RAY DIFFRACTION56chain 'G' and (resid 151 through 197 )
57X-RAY DIFFRACTION57chain 'G' and (resid 198 through 211 )
58X-RAY DIFFRACTION58chain 'H' and (resid 1 through 119 )
59X-RAY DIFFRACTION59chain 'H' and (resid 120 through 213 )

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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