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- PDB-6igf: Crystal structure of Human Papillomavirus type 52 pentamer -

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基本情報

登録情報
データベース: PDB / ID: 6igf
タイトルCrystal structure of Human Papillomavirus type 52 pentamer
要素Major capsid protein L1
キーワードSTRUCTURAL PROTEIN / Human Papillomavirus type 52 capsid protein
機能・相同性
機能・相同性情報


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
類似検索 - 分子機能
Major capsid L1 (late) superfamily, Papillomavirus / Polyomavirus Vp1; Chain A / Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Double-stranded DNA virus, group I, capsid / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Major capsid protein L1
類似検索 - 構成要素
生物種Human papillomavirus type 52 (パピローマウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.751 Å
データ登録者Li, Z.H. / Song, S. / He, M.Z. / Gu, Y. / Li, S.W.
資金援助 中国, 6件
組織認可番号
National Natural Science Foundation of China81701637 中国
National Science Foundation (China)81701637 中国
National Natural Science Foundation of ChinaU1705283 中国
National Natural Science Foundation of ChinaU1705283 中国
National Natural Science Foundation of China31670935 中国
National Science Foundation (China)31670935 中国
引用ジャーナル: Nat Commun / : 2018
タイトル: Rational design of a triple-type human papillomavirus vaccine by compromising viral-type specificity.
著者: Zhihai Li / Shuo Song / Maozhou He / Daning Wang / Jingjie Shi / Xinlin Liu / Yunbing Li / Xin Chi / Shuangping Wei / Yurou Yang / Zhiping Wang / Jinjin Li / Huilian Qian / Hai Yu / Qingbing ...著者: Zhihai Li / Shuo Song / Maozhou He / Daning Wang / Jingjie Shi / Xinlin Liu / Yunbing Li / Xin Chi / Shuangping Wei / Yurou Yang / Zhiping Wang / Jinjin Li / Huilian Qian / Hai Yu / Qingbing Zheng / Xiaodong Yan / Qinjian Zhao / Jun Zhang / Ying Gu / Shaowei Li / Ningshao Xia /
要旨: Sequence variability in surface-antigenic sites of pathogenic proteins is an important obstacle in vaccine development. Over 200 distinct genomic sequences have been identified for human ...Sequence variability in surface-antigenic sites of pathogenic proteins is an important obstacle in vaccine development. Over 200 distinct genomic sequences have been identified for human papillomavirus (HPV), of which more than 18 are associated with cervical cancer. Here, based on the high structural similarity of L1 surface loops within a group of phylogenetically close HPV types, we design a triple-type chimera of HPV33/58/52 using loop swapping. The chimeric VLPs elicit neutralization titers comparable with a mix of the three wild-type VLPs both in mice and non-human primates. This engineered region of the chimeric protein recapitulates the conformational contours of the antigenic surfaces of the parental-type proteins, offering a basis for this high immunity. Our stratagem is equally successful in developing other triplet-type chimeras (HPV16/35/31, HPV56/66/53, HPV39/68/70, HPV18/45/59), paving the way for the development of an improved HPV prophylactic vaccine against all carcinogenic HPV strains. This technique may also be extrapolated to other microbes.
履歴
登録2018年9月25日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02018年11月28日Provider: repository / タイプ: Initial release
改定 1.12019年1月2日Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22023年11月22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: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
F: Major capsid protein L1
G: Major capsid protein L1
H: Major capsid protein L1
I: Major capsid protein L1
J: Major capsid protein L1


分子量 (理論値)分子数
合計 (水以外)595,33710
ポリマ-595,33710
非ポリマー00
00
1
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1


分子量 (理論値)分子数
合計 (水以外)297,6685
ポリマ-297,6685
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area35650 Å2
ΔGint-212 kcal/mol
Surface area77310 Å2
手法PISA
2
F: Major capsid protein L1
G: Major capsid protein L1
H: Major capsid protein L1
I: Major capsid protein L1
J: Major capsid protein L1


分子量 (理論値)分子数
合計 (水以外)297,6685
ポリマ-297,6685
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area35700 Å2
ΔGint-215 kcal/mol
Surface area75750 Å2
手法PISA
単位格子
Length a, b, c (Å)306.768, 105.070, 196.903
Angle α, β, γ (deg.)90.00, 125.80, 90.00
Int Tables number5
Space group name H-MC121

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要素

#1: タンパク質
Major capsid protein L1


分子量: 59533.676 Da / 分子数: 10 / 由来タイプ: 組換発現
由来: (組換発現) Human papillomavirus type 52 (パピローマウイルス)
遺伝子: L1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): ER2566 / 参照: UniProt: Q05138

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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: 2.16 Å3/Da / 溶媒含有率: 43.16 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 8% tasimate, 17.5% (w/v) PEG 3350

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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: SSRF / ビームライン: BL17U1 / 波長: 0.9795 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2016年7月8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: 0.9795 Å / 相対比: 1
反射解像度: 2.75→50 Å / Num. obs: 131803 / % possible obs: 99.9 % / 冗長度: 7.6 % / Rsym value: 0.199 / Net I/σ(I): 12.1
反射 シェル解像度: 2.75→2.8 Å / Num. unique obs: 6516 / Rsym value: 1.238

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.11.1_2575: ???)精密化
HKL-2000データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5Y9E
解像度: 2.751→42.95 Å / SU ML: 0.36 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 26.97
Rfactor反射数%反射
Rfree0.2352 6697 5.08 %
Rwork0.1868 --
obs0.1893 131736 99.79 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 2.751→42.95 Å
タンパク質核酸リガンド溶媒全体
原子数33243 0 0 0 33243
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00634119
X-RAY DIFFRACTIONf_angle_d0.92446217
X-RAY DIFFRACTIONf_dihedral_angle_d12.4720242
X-RAY DIFFRACTIONf_chiral_restr0.0554918
X-RAY DIFFRACTIONf_plane_restr0.0066017
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7506-2.78180.3572120.28114042X-RAY DIFFRACTION97
2.7818-2.81450.38492280.28214099X-RAY DIFFRACTION100
2.8145-2.84890.30192160.26634187X-RAY DIFFRACTION100
2.8489-2.88490.33362200.2644099X-RAY DIFFRACTION100
2.8849-2.92290.32322020.27124202X-RAY DIFFRACTION100
2.9229-2.96290.31882400.25934094X-RAY DIFFRACTION100
2.9629-3.00520.31271930.2564236X-RAY DIFFRACTION100
3.0052-3.05010.31151760.25474160X-RAY DIFFRACTION100
3.0501-3.09770.34462360.25524186X-RAY DIFFRACTION100
3.0977-3.14850.26682200.23644097X-RAY DIFFRACTION100
3.1485-3.20270.30672220.23184177X-RAY DIFFRACTION100
3.2027-3.2610.32042120.21944175X-RAY DIFFRACTION100
3.261-3.32370.28322350.22734133X-RAY DIFFRACTION100
3.3237-3.39150.28282450.23314180X-RAY DIFFRACTION100
3.3915-3.46520.2642040.21934144X-RAY DIFFRACTION100
3.4652-3.54580.29122220.20084162X-RAY DIFFRACTION100
3.5458-3.63440.25062120.18214147X-RAY DIFFRACTION100
3.6344-3.73260.20762330.18244207X-RAY DIFFRACTION100
3.7326-3.84240.22452340.17764141X-RAY DIFFRACTION100
3.8424-3.96630.24152310.17474134X-RAY DIFFRACTION100
3.9663-4.1080.21032310.15824198X-RAY DIFFRACTION100
4.108-4.27230.18432240.15184144X-RAY DIFFRACTION100
4.2723-4.46650.18622500.1434166X-RAY DIFFRACTION100
4.4665-4.70180.19382010.13464180X-RAY DIFFRACTION100
4.7018-4.99590.15852460.1194204X-RAY DIFFRACTION100
4.9959-5.3810.1672170.13094186X-RAY DIFFRACTION100
5.381-5.92120.20922470.15694178X-RAY DIFFRACTION100
5.9212-6.77520.22082210.16694205X-RAY DIFFRACTION100
6.7752-8.52510.19352140.15634270X-RAY DIFFRACTION100
8.5251-42.95560.20182530.18664306X-RAY DIFFRACTION100
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0313-0.0507-0.01770.06140.07130.0676-0.06590.06610.0601-0.1795-0.0017-0.0933-0.0546-0.0777-0.00010.3520.04-0.03380.49530.06680.3202-65.47627.224611.8346
20.0305-0.00940.01890.0352-0.04230.0584-0.0090.1180.0583-0.1595-0.10460.01130.0053-0.0197-0.06390.36780.134-0.09780.7130.15080.1369-71.606810.31483.0907
30.02750.02030.01430.0730.02620.10390.07480.06550.04170.0185-0.10140.0236-0.0393-0.0767-0.03010.27230.0742-0.06010.45920.03270.2574-82.11126.52315.1421
40.00170.00490.00840.0333-0.02180.03180.00250.06160.0558-0.1426-0.01990.04850.01120.03460.00510.4061-0.02930.070.37860.18350.3028-51.444525.645413.7214
50.3151-0.13910.18110.119-0.01130.2153-0.03990.45870.0702-0.132-0.08160.05090.1384-0.162-0.11020.3265-0.0664-0.04020.4762-0.13330.2115-79.6981-9.140312.2407
60.25370.0397-0.24840.0069-0.03730.2884-0.08870.2256-0.0938-0.0387-0.28630.25330.187-0.059-0.18930.3586-0.113-0.12440.787-0.17020.4049-102.1919-6.32444.7408
70.0926-0.10120.05810.1839-0.00310.090.0430.11310.1549-0.2145-0.1950.0043-0.071-0.0256-0.17440.28040.1463-0.05130.36270.26870.3194-84.272228.241621.7603
80.0491-0.0550.03860.13890.11380.28620.06290.0510.0902-0.0967-0.0133-0.0024-0.1188-0.05390.09970.31130.0852-0.00440.40340.11690.2985-78.56724.867725.6901
90.02330.00290.01590.00380.04240.04870.07850.07820.1199-0.03-0.04160.03510.0613-0.08940.00230.30810.02850.01440.1850.10890.3596-68.101629.905634.3503
100.41920.0329-0.02950.26190.00840.09060.13390.12980.3977-0.0272-0.1091-0.0556-0.0349-0.00080.01850.20130.08770.01450.18920.13440.163-70.402821.784728.2086
110.0427-0.0307-0.02510.06940.08050.08050.1420.2730.2092-0.1926-0.23920.1713-0.0212-0.1201-0.01860.29560.0788-0.04820.36760.11550.4266-97.606132.761526.6231
120.01980.0006-0.0460.0810.06330.0379-0.0796-0.04740.23070.00040.11730.06910.0999-0.14160.00150.31770.08850.04580.24860.01980.2749-84.768920.349865.0537
130.0134-0.01390.00540.0148-0.00830.0072-0.0779-0.04850.10390.0711-0.0449-0.122-0.1560.079700.2657-0.04290.01930.21370.01340.3581-54.555726.962552.2484
140.07050.0151-0.01990.04730.02590.04180.0033-0.06280.1151-0.02650.0355-0.0605-0.094-0.02890.02920.20450.06440.04530.07660.03730.1904-78.180123.920461.1655
150.01640.02730.02430.06710.00330.020.00470.04110.12110.01470.0289-0.04880.02630.0640.00020.23420.0152-0.03850.25140.01220.2414-52.32486.405848.956
160.0648-0.01350.05730.0669-0.02240.0406-0.0791-0.1350.13140.0590.0638-0.05680.02980.01350.00160.20650.0074-0.03890.2020.02670.1485-58.57468.357458.2016
170.00870.0160.0090.01330.01090.0095-0.13260.08620.10590.101-0.0560.0075-0.03160.084700.19990.0486-0.02940.31350.00410.2891-36.134-10.445148.4347
180.17180.04610.11580.03670.02560.12110.0160.0744-0.05740.0072-0.01630.1035-0.08520.06560.05270.2270.04130.010.12660.07530.2218-74.897113.115554.1661
190.0827-0.04790.07920.1610.03250.08780.0661-0.03440.07610.054-0.0115-0.1553-0.2073-0.00020.03440.2995-0.04070.03690.17440.09090.337-62.413728.300743.101
200.1831-0.0788-0.0990.03060.05780.14940.1017-0.13920.18050.1510.16260.1595-0.36880.00220.03870.26180.08640.00960.26240.04570.2804-82.284324.416668.274
210.13680.0965-0.09990.0713-0.02530.2762-0.1056-0.0324-0.2090.2793-0.0889-0.04320.32460.3214-0.07690.48920.16130.08680.20910.05260.5213-3.2821-45.145268.9753
22-0.0010.00080.001-0.00260.00370.0204-0.0664-0.15010.00220.16950.01720.04710.0144-0.10040.00020.54830.05710.18470.48350.07770.57-20.9399-46.089576.7418
230.01550.0346-0.0218-0.00740.01050.1776-0.10410.0882-0.13620.01370.08170.01810.1280.25470.00560.390.20450.01620.4172-0.02290.465615.0218-39.886948.0753
240.05280.0367-0.00110.0375-0.01620.02350.05130.0992-0.1392-0.0126-0.00940.00430.15050.08690.03950.51360.19550.06320.3043-0.03260.604110.8929-51.371948.3428
250.0515-0.0610.04230.0979-0.08090.0603-0.05820.1014-0.08460.11160.0251-0.00540.18720.130.02260.34520.15190.01590.3108-0.07630.40426.6883-39.3443.9447
260.0675-0.0986-0.06660.17530.00150.4029-0.1179-0.1425-0.19140.1656-0.01030.06360.33350.3757-0.28040.39320.27140.04560.10870.1680.5129-1.747-44.982267.6912
270.0095-0.0002-0.00060.00850.00820.0038-0.0695-0.08310.05360.0067-0.0348-0.0054-0.0034-0.006-0.00010.48680.14330.0420.37660.04380.5265-13.7912-33.3578.0889
280.0191-0.00040.0259-0.0031-0.00820.02370.0421-0.03970.04680.21610.05530.0899-0.05890.13-0.00010.26040.05190.02490.26130.07180.3025-9.5585-9.20982.9116
290.0138-0.0113-0.01330.02730.0040.0121-0.1249-00.05440.2028-0.1453-0.1262-0.06650.10370.00010.29370.0845-0.08340.55610.02540.323823.8942-7.7174.0076
300.00170.01260.0080.03420.05290.07230.0986-0.01990.06770.3142-0.06180.07760.03170.01010.04110.3336-0.04510.18950.3148-0.01020.26-8.7195-1.215590.1661
310.19480.2149-0.15780.2044-0.1190.07740.05410.0712-0.09670.149-0.0874-0.0139-0.03720.1338-0.03520.22180.1216-0.00610.39010.03350.270718.236-18.692563.2032
320.01730.0310.02460.1137-0.00430.0018-0.1268-0.2436-0.13910.17990.0752-0.00830.09880.2615-0.00190.29090.1209-0.04040.39730.0790.306912.8494-23.226571.2316
330.0122-0.0011-0.00550.0041-0.01320.0838-0.05280.0086-0.0075-0.0112-0.106-0.1132-0.04350.05-0.02630.43740.2781-0.06120.5689-0.02810.46330.7679-44.600456.1374
340.1102-0.0287-0.04520.2449-0.00030.0912-0.0502-0.0046-0.01830.11150.0474-0.00160.12060.2695-0.00570.25280.0194-0.00430.38830.04640.25739.3141-7.077767.7054
350.15450.08360.03280.07880.03160.02350.0363-0.14330.15190.275-0.050.1301-0.13530.1786-0.03180.28080.01630.03820.28050.04580.1653-5.5793-6.357486.3979
360.14460.1360.04940.14290.00660.1831-0.17250.1245-0.2385-0.1643-0.0167-0.03750.18740.0997-0.05380.47340.1330.00170.3502-0.15610.5901-14.8377-44.279230.121
370.02010.0234-0.01840.0211-0.01190.0120.0232-0.0404-0.0062-0.07690.07030.06640.15840.01260.09280.43670.0852-0.02750.1986-0.21590.6409-17.0763-50.669527.9622
380.03870.0290.0070.16070.010.15150.01640.2133-0.212-0.1468-0.0996-0.00730.2040.1979-0.02160.33170.1394-0.02550.4579-0.1920.38974.8305-32.641624.7058
390.0053-0.02180.02740.1237-0.07190.07250.06310.1194-0.137-0.09320.03260.00440.11360.02040.03320.4180.1194-0.05930.5177-0.16240.43370.4082-31.506321.8873
400.00330.0030.00060.0090.01540.0206-0.03910.1450.0338-0.05860.04350.05640.06470.0494-00.29380.09460.06830.61260.00290.342725.0529-14.239513.9633
410.06370.13670.02160.1969-0.03910.2407-0.24210.1528-0.1178-0.2741-0.05990.06310.22490.1164-0.36650.29870.20440.03450.0883-0.22410.404-2.9547-41.35836.0349
420.0055-0.0141-0.00950.00940.00610.0043-0.03890.0433-0.0597-0.01550.0540.01480.13640.047-00.51780.0488-0.09880.4385-0.27270.6732-25.1505-45.716817.6002
430.00520.00040.00180.007-0.00990.0092-0.00120.0087-0.02030.02350.04330.06890.0385-0.02310.00010.52450.05150.04360.244-0.0180.6695-24.7113-46.291244.0914
440.04990.02560.04230.09540.00250.091-0.03460.1440.082-0.131-0.02050.07050.03780.23670.00040.32260.0613-0.07010.4897-0.06780.3144-8.2293-8.666615.7314
450.01030.0212-0.02770.0382-0.05630.0683-0.06940.0748-0.0012-0.3360.03940.1363-0.01050.0992-0.03650.30010.0774-0.18240.5463-0.05690.3327-27.6002-3.706711.5036
460.01810.0046-0.01910.13530.02950.00990.04660.17430.0124-0.1484-0.031-0.02610.01430.1297-00.26020.0645-0.03670.4609-0.04060.289310.764-9.639326.5012
470.00650.02710.03840.01430.06540.09150.10180.18260.0979-0.0391-0.117-0.0530.05240.158400.23990.01010.04350.50590.0360.27146.882.549324.3411
480.15220.1681-0.06620.33050.02370.18960.01180.23750.0072-0.0893-0.02380.0073-0.01950.15880.00420.16110.0747-0.02750.3753-0.05460.22154.9727-7.678525.7057
490.0478-0.03580.03450.0318-0.00790.0317-0.01880.2697-0.0625-0.22-0.01650.17650.0397-0.033300.32510.0419-0.11440.4932-0.03610.3115-21.6181-2.142814.8813
500.0274-0.03250.01710.0358-0.02390.01170.05680.0592-0.04410.10010.00610.03110.08590.0861-0.00010.2549-0.03620.01430.24650.04750.2627-12.50217.336753.5228
510.00050.011-0.00150.00550.01240.0791-0.06060.06640.1376-0.0619-0.087-0.1181-0.14150.1348-0.00050.2204-0.0711-0.04630.40580.11460.424818.921513.797940.0794
520.01710.00890.01810.01140.0160.06260.0010.07260.07190.09730.02150.0475-0.14270.06170.00530.2857-0.00130.03450.18880.09740.3861-14.336426.769748.8406
530.0206-0.0428-0.12590.0245-0.03570.11260.0260.03970.00170.0058-0.06030.0391-0.07910.1787-00.24030.026-0.01850.4096-0.01570.296515.4076-0.524547.5773
540.01070.0116-0.01240.0097-0.01890.01030.00240.12650.0091-0.03390.13880.08630.0664-0.1021-00.2657-0.0583-0.00620.3886-0.04260.279918.840111.717666.3501
550.03590.04820.01410.036-0.01980.04270.0387-0.07020.1034-0.0386-0.0398-0.0365-0.11270.2246-00.232-0.0272-0.02380.3415-0.02480.268913.64424.405156.3446
560.0029-0.00290.01230.008-0.00450.0104-0.057-0.0619-0.02860.0655-0.0258-0.0640.02850.1247-0.00020.23810.0511-0.07210.68820.11310.44837.1115-14.100364.8188
570.00390.001-0.00670.032-0.00830.02120.0369-0.0398-0.0415-0.0221-0.0517-0.0202-0.01290.0595-00.20810.0339-0.010.35250.00520.28663.4541-4.106845.968
580.0162-0.04780.04870.1021-0.08670.08320.0599-0.03150.0826-0.0073-0.03350.0064-0.14710.2249-0.010.2414-0.07310.02850.31380.0220.27611.700313.726745.3486
590.0691-0.02650.01130.0390.02190.01080.18530.14380.04260.0013-0.02120.0721-0.1776-0.0610.0120.2704-0.0540.0040.2260.03320.2649-10.494618.173843.5484
600.39370.17920.0580.4238-0.10030.2891-0.1489-0.011-0.15830.0354-0.1579-0.03940.3389-0.3003-0.56650.5836-0.36370.18690.0884-0.31250.3498-75.9982-33.946832.4026
610.6019-0.16840.30810.17750.12680.3208-0.0250.32290.1764-0.0948-0.1953-0.12690.5547-0.2631-0.42040.4558-0.25940.00820.131-0.3361-0.0206-73.3157-26.299227.2758
620.0182-0.04420.00710.09170.01370.0639-0.03260.0336-0.08750.0003-0.150.06370.1407-0.0387-0.25730.4286-0.15630.02830.301-0.38880.0602-65.7651-24.863612.7388
630.4455-0.24650.11280.32550.08930.10990.0990.30180.1883-0.1744-0.24-0.23420.2207-0.2317-0.23850.3064-0.1208-0.0610.1877-0.2111-0.0628-68.4997-12.84417.4935
640.06270.0607-0.11030.3272-0.06890.3747-0.16170.0638-0.06670.0171-0.1553-0.11060.6069-0.1373-0.59880.4758-0.19120.04810.2826-0.27060.1955-70.4287-28.743836.1733
650.0059-0.02060.00850.036-0.02580.0155-0.099-0.0095-0.1946-0.00830.04180.00520.3269-0.1755-0.04470.7055-0.35240.12750.4581-0.2290.4223-89.8373-39.173933.6295
660.00170.02090.06560.1792-0.09880.5328-0.09650.02450.05160.0592-0.1077-0.01680.29520.2324-0.10040.2764-0.02040.01560.1265-0.04720.2266-63.7728-14.724465.3814
670.01520.00010.01340.02440.01080.01380.0154-0.0815-0.04220.08310.0936-0.01770.0322-0.0643-0.00020.31860.01610.0320.30760.0410.2109-79.7135-19.649879.2816
680.12550.03380.06520.0358-0.04060.2025-0.01560.1153-0.06650.0705-0.0298-0.01110.14160.1867-0.00480.28980.02320.00810.06070.0010.1587-58.14-14.384147.5968
690.0549-0.05580.12390.188-0.16390.2787-0.11750.0043-0.154-0.0015-0.11250.00930.23570.1523-0.16510.3230.02320.07090.0657-0.04070.2419-60.097-22.411647.9515
700.0074-0.01680.0120.02480.01390.0522-0.03290.1082-0.0350.02360.009-0.00380.02120.0533-0.02260.44510.13350.03640.3385-0.0750.1327-45.0899-25.498921.4085
710.0124-0.0359-0.07070.07570.06380.2023-0.0231-0.0294-0.01210.001-0.0068-0.03270.08480.096300.228-0.0078-0.01980.1934-0.00390.1777-63.5469-7.447957.9372
720.00190.03740.03070.01780.03280.17830.0108-0.1073-0.04440.1378-0.0582-0.0719-0.0176-0.0749-0.03620.35970.00150.08590.11290.06620.27-76.7132-20.726172.6361
730.3898-0.01460.07380.5341-0.0880.22420.01570.13380.0135-0.1207-0.06560.07810.0658-0.2137-0.11380.3302-0.0464-0.07710.6483-0.16550.2496-87.3893-7.45755.3126
740.0030.00470.00480.0053-0.00330.00760.02-0.01780.0108-0.12950.0160.11240.0419-0.0393-00.4569-0.1436-0.14710.7786-0.12260.4901-107.4599-11.02713.1413
750.1245-0.0590.01040.16940.08660.11560.07680.125-0.0888-0.187-0.12730.08480.1086-0.2338-0.10130.2425-0.1012-0.12080.4042-0.11020.1988-82.7715-6.040111.2998
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 129 through 174 )
2X-RAY DIFFRACTION2chain 'H' and (resid 175 through 231 )
3X-RAY DIFFRACTION3chain 'H' and (resid 232 through 265 )
4X-RAY DIFFRACTION4chain 'H' and (resid 266 through 295 )
5X-RAY DIFFRACTION5chain 'H' and (resid 296 through 386 )
6X-RAY DIFFRACTION6chain 'H' and (resid 387 through 477 )
7X-RAY DIFFRACTION7chain 'I' and (resid 20 through 73 )
8X-RAY DIFFRACTION8chain 'I' and (resid 74 through 148 )
9X-RAY DIFFRACTION9chain 'I' and (resid 149 through 197 )
10X-RAY DIFFRACTION10chain 'I' and (resid 198 through 386 )
11X-RAY DIFFRACTION11chain 'I' and (resid 387 through 477 )
12X-RAY DIFFRACTION12chain 'J' and (resid 18 through 46 )
13X-RAY DIFFRACTION13chain 'J' and (resid 47 through 73 )
14X-RAY DIFFRACTION14chain 'J' and (resid 74 through 128 )
15X-RAY DIFFRACTION15chain 'J' and (resid 129 through 174 )
16X-RAY DIFFRACTION16chain 'J' and (resid 175 through 265 )
17X-RAY DIFFRACTION17chain 'J' and (resid 266 through 295 )
18X-RAY DIFFRACTION18chain 'J' and (resid 296 through 343 )
19X-RAY DIFFRACTION19chain 'J' and (resid 344 through 386 )
20X-RAY DIFFRACTION20chain 'J' and (resid 387 through 477 )
21X-RAY DIFFRACTION21chain 'A' and (resid 20 through 85 )
22X-RAY DIFFRACTION22chain 'A' and (resid 86 through 112 )
23X-RAY DIFFRACTION23chain 'A' and (resid 113 through 174 )
24X-RAY DIFFRACTION24chain 'A' and (resid 175 through 231 )
25X-RAY DIFFRACTION25chain 'A' and (resid 232 through 317 )
26X-RAY DIFFRACTION26chain 'A' and (resid 318 through 454 )
27X-RAY DIFFRACTION27chain 'A' and (resid 455 through 476 )
28X-RAY DIFFRACTION28chain 'B' and (resid 15 through 46 )
29X-RAY DIFFRACTION29chain 'B' and (resid 47 through 73 )
30X-RAY DIFFRACTION30chain 'B' and (resid 74 through 98 )
31X-RAY DIFFRACTION31chain 'B' and (resid 99 through 148 )
32X-RAY DIFFRACTION32chain 'B' and (resid 149 through 265 )
33X-RAY DIFFRACTION33chain 'B' and (resid 266 through 295 )
34X-RAY DIFFRACTION34chain 'B' and (resid 296 through 386 )
35X-RAY DIFFRACTION35chain 'B' and (resid 387 through 478 )
36X-RAY DIFFRACTION36chain 'C' and (resid 19 through 56 )
37X-RAY DIFFRACTION37chain 'C' and (resid 57 through 98 )
38X-RAY DIFFRACTION38chain 'C' and (resid 99 through 184 )
39X-RAY DIFFRACTION39chain 'C' and (resid 185 through 265 )
40X-RAY DIFFRACTION40chain 'C' and (resid 266 through 295 )
41X-RAY DIFFRACTION41chain 'C' and (resid 296 through 386 )
42X-RAY DIFFRACTION42chain 'C' and (resid 387 through 454 )
43X-RAY DIFFRACTION43chain 'C' and (resid 455 through 478 )
44X-RAY DIFFRACTION44chain 'D' and (resid 20 through 73 )
45X-RAY DIFFRACTION45chain 'D' and (resid 74 through 98 )
46X-RAY DIFFRACTION46chain 'D' and (resid 99 through 148 )
47X-RAY DIFFRACTION47chain 'D' and (resid 149 through 197 )
48X-RAY DIFFRACTION48chain 'D' and (resid 198 through 386 )
49X-RAY DIFFRACTION49chain 'D' and (resid 387 through 475 )
50X-RAY DIFFRACTION50chain 'E' and (resid 15 through 46 )
51X-RAY DIFFRACTION51chain 'E' and (resid 47 through 73 )
52X-RAY DIFFRACTION52chain 'E' and (resid 74 through 98 )
53X-RAY DIFFRACTION53chain 'E' and (resid 99 through 163 )
54X-RAY DIFFRACTION54chain 'E' and (resid 164 through 184 )
55X-RAY DIFFRACTION55chain 'E' and (resid 185 through 265 )
56X-RAY DIFFRACTION56chain 'E' and (resid 266 through 295 )
57X-RAY DIFFRACTION57chain 'E' and (resid 296 through 317 )
58X-RAY DIFFRACTION58chain 'E' and (resid 318 through 406 )
59X-RAY DIFFRACTION59chain 'E' and (resid 407 through 481 )
60X-RAY DIFFRACTION60chain 'F' and (resid 20 through 73 )
61X-RAY DIFFRACTION61chain 'F' and (resid 74 through 174 )
62X-RAY DIFFRACTION62chain 'F' and (resid 175 through 231 )
63X-RAY DIFFRACTION63chain 'F' and (resid 232 through 314 )
64X-RAY DIFFRACTION64chain 'F' and (resid 315 through 386 )
65X-RAY DIFFRACTION65chain 'F' and (resid 387 through 478 )
66X-RAY DIFFRACTION66chain 'G' and (resid 20 through 73 )
67X-RAY DIFFRACTION67chain 'G' and (resid 74 through 98 )
68X-RAY DIFFRACTION68chain 'G' and (resid 99 through 174 )
69X-RAY DIFFRACTION69chain 'G' and (resid 175 through 265 )
70X-RAY DIFFRACTION70chain 'G' and (resid 266 through 295 )
71X-RAY DIFFRACTION71chain 'G' and (resid 296 through 386 )
72X-RAY DIFFRACTION72chain 'G' and (resid 387 through 476 )
73X-RAY DIFFRACTION73chain 'H' and (resid 20 through 73 )
74X-RAY DIFFRACTION74chain 'H' and (resid 74 through 98 )
75X-RAY DIFFRACTION75chain 'H' and (resid 99 through 128 )

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万見について

-
お知らせ

-
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