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- PDB-5y9f: Crystal structure of HPV59 pentamer in complex with the Fab fragm... -

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基本情報

登録情報
データベース: PDB / ID: 5y9f
タイトルCrystal structure of HPV59 pentamer in complex with the Fab fragment of antibody 28F10
要素
  • Major capsid protein L1
  • heavy chain of Fab fragment of antibody 28F10
  • light chains of Fab fragment of antibody 28F10
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / capsid protein / immune complex / STRUCTURAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Polyomavirus Vp1; Chain A / Double-stranded DNA virus, group I, capsid / Immunoglobulins / Immunoglobulin-like / 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 59 (パピローマウイルス)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 解像度: 3.35 Å
データ登録者Li, S.W. / Li, Z.H.
資金援助 中国, 3件
組織認可番号
National Natural Science Foundation of China31670935 中国
National Natural Science Foundation of China81671645 中国
National Natural Science Foundation of China81571996 中国
引用ジャーナル: mBio / : 2017
タイトル: Crystal Structures of Two Immune Complexes Identify Determinants for Viral Infectivity and Type-Specific Neutralization of Human Papillomavirus.
著者: Zhihai Li / Daning Wang / Ying Gu / Shuo Song / Maozhou He / Jingjie Shi / Xinlin Liu / Shuangping Wei / Jinjin Li / Hai Yu / Qingbing Zheng / Xiaodong Yan / Timothy S Baker / Jun Zhang / ...著者: Zhihai Li / Daning Wang / Ying Gu / Shuo Song / Maozhou He / Jingjie Shi / Xinlin Liu / Shuangping Wei / Jinjin Li / Hai Yu / Qingbing Zheng / Xiaodong Yan / Timothy S Baker / Jun Zhang / Jason S McLellan / Shaowei Li / Ningshao Xia /
要旨: Persistent, high-risk human papillomavirus (HPV) infection is the primary cause of cervical cancer. Neutralizing antibodies elicited by L1-only virus-like particles (VLPs) can block HPV infection; ...Persistent, high-risk human papillomavirus (HPV) infection is the primary cause of cervical cancer. Neutralizing antibodies elicited by L1-only virus-like particles (VLPs) can block HPV infection; however, the lack of high-resolution structures has limited our understanding of the mode of virus infection and the requirement for type specificity at the molecular level. Here, we describe two antibodies, A12A3 and 28F10, that specifically bind to and neutralize HPV58 and HPV59, respectively, through two distinct binding stoichiometries. We show that the epitopes of A12A3 are clustered in the DE loops of two adjacent HPV58 L1 monomers, whereas 28F10 recognizes the HPV59 FG loop of a single monomer. Via structure-based mutagenesis and analysis of antibody binding, we further identified the residues HPV58 D154, S168, and N170 and HPV59 M267, Q270, E273, Y276, K278, and R283, which play critical roles in virus infection. By substituting these strategic epitope residues into other HPV genotypes, we could then redirect the type-specific binding of the antibodies to these genotypes, thus highlighting the importance of these specific residues, HPV58 R161, S168, and N308 and HPV59 Q270, E273, and D281. Overall, our findings provide molecular insights into potential structural determinants of HPV required for infectivity and type specificity. High-risk human papillomaviruses (HPVs) are considered the major causative pathogens of cancers that affect epithelial mucosa, such as cervical cancer. However, because of the lack of high-resolution structural information on the sites of neutralization, we have yet to determine the precise mode of HPV infection and how different types of HPV cause infection. Our crystal structures in this study have uncovered discrete binding stoichiometries for two different antibodies. We show that one A12A3 Fab binds to the center of one HPV58 pentamer, whereas five 28F10 Fabs bind along the top fringe of one HPV59 pentamer. Furthermore, through targeted epitope analysis, we show that 6 to 7 discontinuous residues of the L1 major capsid protein of HPV are determinants, at least in part, for virus infection and type specificity. This knowledge will help us to unravel the process of HPV infection and can potentially be used to drive the development of therapeutics that target neutralization-sensitive sites.
履歴
登録2017年8月24日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02017年10月25日Provider: repository / タイプ: Initial release
改定 1.12024年11月13日Group: Data collection / Database references / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: 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
K: light chains of Fab fragment of antibody 28F10
L: heavy chain of Fab fragment of antibody 28F10
O: light chains of Fab fragment of antibody 28F10
P: heavy chain of Fab fragment of antibody 28F10
Q: light chains of Fab fragment of antibody 28F10
R: heavy chain of Fab fragment of antibody 28F10
S: light chains of Fab fragment of antibody 28F10
T: heavy chain of Fab fragment of antibody 28F10
M: light chains of Fab fragment of antibody 28F10
N: heavy chain of Fab fragment of antibody 28F10
c: light chains of Fab fragment of antibody 28F10
d: heavy chain of Fab fragment of antibody 28F10
V: heavy chain of Fab fragment of antibody 28F10
W: light chains of Fab fragment of antibody 28F10
X: heavy chain of Fab fragment of antibody 28F10
Y: light chains of Fab fragment of antibody 28F10
Z: heavy chain of Fab fragment of antibody 28F10
a: light chains of Fab fragment of antibody 28F10
b: heavy chain of Fab fragment of antibody 28F10
U: light chains of Fab fragment of antibody 28F10


分子量 (理論値)分子数
合計 (水以外)1,040,00930
ポリマ-1,040,00930
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
K: light chains of Fab fragment of antibody 28F10
L: heavy chain of Fab fragment of antibody 28F10
O: light chains of Fab fragment of antibody 28F10
P: heavy chain of Fab fragment of antibody 28F10
Q: light chains of Fab fragment of antibody 28F10
R: heavy chain of Fab fragment of antibody 28F10
S: light chains of Fab fragment of antibody 28F10
T: heavy chain of Fab fragment of antibody 28F10
M: light chains of Fab fragment of antibody 28F10
N: heavy chain of Fab fragment of antibody 28F10


分子量 (理論値)分子数
合計 (水以外)520,00515
ポリマ-520,00515
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
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
c: light chains of Fab fragment of antibody 28F10
d: heavy chain of Fab fragment of antibody 28F10
V: heavy chain of Fab fragment of antibody 28F10
W: light chains of Fab fragment of antibody 28F10
X: heavy chain of Fab fragment of antibody 28F10
Y: light chains of Fab fragment of antibody 28F10
Z: heavy chain of Fab fragment of antibody 28F10
a: light chains of Fab fragment of antibody 28F10
b: heavy chain of Fab fragment of antibody 28F10
U: light chains of Fab fragment of antibody 28F10


分子量 (理論値)分子数
合計 (水以外)520,00515
ポリマ-520,00515
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)116.265, 417.233, 134.942
Angle α, β, γ (deg.)90.00, 111.02, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Major capsid protein L1


分子量: 55962.355 Da / 分子数: 10 / 断片: UNP RESIDUES 10-508 / 変異: C175S / 由来タイプ: 組換発現
由来: (組換発現) Human papillomavirus type 59 (パピローマウイルス)
遺伝子: ORF putative L1, L1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q81971
#2: 抗体
light chains of Fab fragment of antibody 28F10


分子量: 24133.754 Da / 分子数: 10 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ)
#3: 抗体
heavy chain of Fab fragment of antibody 28F10


分子量: 23904.793 Da / 分子数: 10 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ)
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: 2.94 Å3/Da / 溶媒含有率: 58.21 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.5
詳細: 2% tacsimate, 0.1 M sodium citrate, pH 5.5, 17% (w/v) PEG 3350

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データ収集

回折平均測定温度: 80 K
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: 0.9792 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2014年9月16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: 0.9792 Å / 相対比: 1
反射解像度: 3.35→50 Å / Num. obs: 161106 / % possible obs: 94.5 % / 冗長度: 3.2 % / Net I/σ(I): 8.5

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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
精密化解像度: 3.35→36.528 Å / SU ML: 0.45 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 27.03 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2612 8042 4.99 %
Rwork0.23 --
obs0.2316 161016 94.05 %
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: 3.35→36.528 Å
タンパク質核酸リガンド溶媒全体
原子数66832 0 0 0 66832
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00268573
X-RAY DIFFRACTIONf_angle_d0.64993356
X-RAY DIFFRACTIONf_dihedral_angle_d13.1140741
X-RAY DIFFRACTIONf_chiral_restr0.04510376
X-RAY DIFFRACTIONf_plane_restr0.00411946
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3496-3.38760.36362140.32624444X-RAY DIFFRACTION81
3.3876-3.42750.3222810.30375109X-RAY DIFFRACTION94
3.4275-3.46920.34032590.29815087X-RAY DIFFRACTION94
3.4692-3.51310.3292570.29735142X-RAY DIFFRACTION94
3.5131-3.55930.34242440.28885129X-RAY DIFFRACTION95
3.5593-3.6080.34582510.29195088X-RAY DIFFRACTION94
3.608-3.65950.31052780.28465129X-RAY DIFFRACTION94
3.6595-3.71410.30172210.2815121X-RAY DIFFRACTION95
3.7141-3.77210.32092420.26725189X-RAY DIFFRACTION94
3.7721-3.83390.30122620.26815138X-RAY DIFFRACTION95
3.8339-3.89990.29252720.25865089X-RAY DIFFRACTION94
3.8999-3.97070.27982590.25865133X-RAY DIFFRACTION94
3.9707-4.0470.29642510.2435121X-RAY DIFFRACTION95
4.047-4.12950.2662750.23965117X-RAY DIFFRACTION94
4.1295-4.21920.26332760.2345102X-RAY DIFFRACTION94
4.2192-4.31720.24172520.22365133X-RAY DIFFRACTION95
4.3172-4.42490.25532760.22185078X-RAY DIFFRACTION95
4.4249-4.54440.25722740.21885126X-RAY DIFFRACTION95
4.5444-4.67780.23922940.20555123X-RAY DIFFRACTION94
4.6778-4.82850.20562810.19145147X-RAY DIFFRACTION95
4.8285-5.00070.22842700.19535091X-RAY DIFFRACTION94
5.0007-5.20030.23212810.19975124X-RAY DIFFRACTION95
5.2003-5.43630.2272700.20545131X-RAY DIFFRACTION94
5.4363-5.72190.25212610.21385124X-RAY DIFFRACTION94
5.7219-6.07880.24483190.23125091X-RAY DIFFRACTION95
6.0788-6.54570.27732580.23265123X-RAY DIFFRACTION94
6.5457-7.19990.27132690.22245126X-RAY DIFFRACTION94
7.1999-8.23130.25512880.21485123X-RAY DIFFRACTION95
8.2313-10.33160.21172990.1785176X-RAY DIFFRACTION95
10.3316-36.53050.23293080.20265120X-RAY DIFFRACTION94
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)
10.70020.1057-0.43850.25980.10580.6865-0.0842-0.0149-0.00690.101-0.0998-0.0442-0.02140.0434-0.00790.4233-0.1290.01130.4164-0.17560.6036135.9502112.748712.5429
20.32960.08950.0350.5165-0.19380.5703-0.090.0240.1105-0.06210.0964-0.1903-0.0270.08100.3595-0.0802-0.02520.5646-0.22310.6471134.8705110.044814.5291
30.6130.7286-0.53771.1554-0.38490.8936-0.218-0.4677-0.2373-0.2389-0.2926-0.2813-0.28410.4596-1.13930.272-0.0351-0.30790.5632-0.34940.5495133.929101.460444.9308
40.42540.1293-0.30610.13870.00080.2968-0.1261-0.2766-0.23890.04840.03920.1649-0.28580.3322-0.00660.53680.0037-0.12480.6863-0.19250.5418135.753999.749743.6036
50.3435-0.1863-0.07010.3280.04930.2112-0.12230.1268-0.14650.2077-0.22480.23810.242-0.1366-0.01130.4698-0.02520.06220.5711-0.2030.5227121.665976.655131.5756
60.3383-0.2922-0.13750.1968-0.00940.3258-0.0506-0.06650.05810.19490.1031-0.02010.0123-0.0032-00.47520.0009-0.04190.5307-0.14520.4185120.742384.418836.6135
70.13210.35540.02321.11450.06710.3682-0.0811-0.1329-0.0447-0.14740.0625-0.6951-0.09620.4976-0.86980.1795-0.1488-0.37010.6915-0.52870.1207136.859100.751641.6918
80.2384-0.3265-0.1830.60670.05330.3490.04650.12190.1716-0.05960.09630.03590.0225-0.08280.01150.44470.0580.0030.4902-0.03080.36598.4743122.5529-3.2998
90.2593-0.15850.42240.292-0.2220.64690.0556-0.0306-0.23030.165-0.0685-0.01270.14950.192700.4297-0.03680.02270.5314-0.08050.3921120.682102.7975-6.6134
100.3550.04010.04650.62410.1778-0.04780.05890.02350.1492-0.14650.0718-0.1301-0.09240.145700.5425-0.06890.08120.571-0.1560.394119.7574106.8447-2.8631
110.1417-0.05430.00920.1840.115-0.0184-0.07230.08330.0486-0.26520.10860.2361-0.08090.032400.64310.03240.080.4603-0.05280.44297.7722122.4469-2.5358
120.652-0.03320.28720.4410.44240.3057-0.1853-0.1250.00840.09410.29050.08520.1126-0.15630.07760.34770.02160.07750.5621-0.08950.359675.792499.881219.9133
130.3010.30220.26660.51980.13950.3408-0.03370.1777-0.0355-0.1685-0.0216-0.1246-0.00580.217200.5235-0.04540.08170.6196-0.08280.397694.357992.232-2.3797
140.2637-0.034-0.10660.23570.197-0.0286-0.00770.03930.0097-0.08070.0395-0.0221-0.0255-0.0826-00.47960.0131-0.00580.5562-0.0330.316284.977598.386110.8827
150.218-0.2138-0.17210.09740.10610.4971-0.1354-0.1925-0.34410.15380.10210.1820.01640.0757-0.00280.5104-0.0062-0.06090.524-0.06360.334398.648284.392349.9995
160.2396-0.1173-0.09890.5492-0.18980.7543-0.1144-0.4747-0.11070.16770.1394-0.2437-0.10960.327-0.00280.59410.0328-0.14340.6795-0.09760.182998.428989.250247.71
170.3968-0.49980.15850.7141-0.38280.33720.15520.1141-0.1117-0.0901-0.09270.09710.13610.033500.456-0.0916-0.00090.4815-0.06720.365195.107676.08121.1509
180.0988-0.0556-0.14580.5190.47270.6232-0.0343-0.027-0.01990.0154-0.0079-0.085-0.0343-0.0772-00.4771-0.0030.00440.5038-0.09040.401796.135883.842137.0583
190.62110.0021-0.44770.0788-0.05730.212-0.0054-0.0614-0.10850.1161-0.1553-0.1790.11310.1326-0.00380.60620.0514-0.02160.49380.26980.7254115.4063-72.763755.0603
200.7873-0.0897-0.16730.2497-0.17460.10630.03540.00430.0169-0.3270.08210.28540.0084-0.07680.00010.6458-0.0308-0.07680.44850.08670.5318102.114-52.502737.561
210.5420.1616-0.08290.2558-0.03650.004-0.03930.0085-0.0488-0.1207-0.0879-0.07910.113-0.0086-00.6138-0.0551-0.03790.45470.11780.5416100.034-56.53640.8064
220.07140.10320.03640.1872-0.24750.3736-0.072-0.0524-0.221-0.0173-0.0429-0.4131-0.05680.1204-0.00530.5109-0.0068-0.03020.50450.27520.7184115.3825-72.597556.0651
230.2212-0.2051-0.39770.6004-0.14090.75020.09030.1206-0.089-0.16010.12950.0525-0.0287-0.17030.01320.443-0.0487-0.28230.41890.09380.595877.6104-62.014840.7371
240.42540.1881-0.48770.1077-0.02860.0681-0.00670.1027-0.1013-0.16270.04420.0152-0.019-0.147300.5496-0.0414-0.18320.48790.15780.644476.9946-59.314942.9293
250.350.3365-0.11830.2969-0.19540.22260.0742-0.20610.35610.1179-0.15220.1039-0.0422-0.1625-0.18920.46920.01650.00220.5830.48081.059555.2204-48.494663.193
260.1702-0.1001-0.19340.1121-0.22231.023-0.19490.1617-0.0361-0.0147-0.0109-0.00330.1376-0.4523-0.21650.3487-0.0612-0.0070.60390.3630.851859.0576-50.916266.0836
270.3056-0.24450.25180.172-0.21030.73960.3433-0.27680.10850.2854-0.22860.189-0.50550.36170.06490.6047-0.02190.04470.53110.24230.736575.4119-26.052564.6661
280.33040.15920.29830.04620.12070.2450.13110.00940.21170.11360.09880.1766-0.0595-0.166200.65210.05260.16260.44060.24880.828172.413-33.773568.8906
290.28670.04040.11750.07170.09560.0962-0.07830.1795-0.0048-0.09050.3180.07570.1309-0.368200.52-0.0486-0.03750.63720.29830.612465.576-43.607547.4536
300.20580.170.18560.1780.17520.2711-0.11430.1449-0.28650.03570.2451-0.02290.0837-0.69320.00370.5508-0.0544-0.0740.72720.21540.881249.9997-54.739272.436
310.3752-0.2652-0.39480.3212-0.00410.41850.0809-0.18920.13180.29570.20720.0132-0.2761-0.15880.00010.787-0.12210.12820.5860.06020.558179.6923-35.926293.3621
32-0.0052-0.0708-0.06930.48320.16360.1210.31990.07910.25390.051-0.1075-0.2141-0.12860.088500.8007-0.12810.01670.55520.16210.7759101.8454-26.092875.658
330.16340.2916-0.17140.0238-0.44310.94960.0752-0.05420.01430.29170.08360.0631-0.2163-0.06840.0030.7337-0.10350.08040.490.0670.58989.8967-33.734185.3797
340.3120.5330.1310.587-0.0011-0.05950.1329-0.14330.0456-0.0787-0.05780.02270.04390.26630.01420.6054-0.1675-0.08710.67050.21090.5493114.8361-46.935780.0565
350.19720.19370.05750.3735-0.2650.44830.1187-0.0837-0.10190.0596-0.1724-0.0825-0.04430.1987-0.00010.5117-0.1372-0.11050.57630.1740.5654116.7184-48.867573.8924
360.3058-0.16140.03280.13020.18970.42820.0138-0.0297-0.2016-0.6088-0.1715-0.0375-0.0879-0.087700.53420.02240.01930.5346-0.07910.7196158.132354.73235.6509
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1240.0009-0.01090.00910.0184-0.01550.0155-0.07030.3584-0.24510.18830.20080.1325-0.2403-0.17460.00010.89460.1374-0.04320.6833-0.0850.859448.606610.417411.3246
1250.1517-0.02860.03270.0692-0.08780.07930.0798-0.278-0.16860.01360.0217-0.2698-0.0078-0.18660.00010.86370.217-0.10620.81460.15421.001543.914729.598111.3938
1260.4840.00080.25810.2203-0.11410.21330.2374-0.143-0.1498-0.0433-0.00070.0126-0.06780.127800.70310.08630.06540.66440.27310.92952.4343-4.36936.7154
1270.6988-0.5939-0.5830.64650.11711.261-0.33610.2797-0.5108-0.26940.17690.93690.24680.1106-0.56930.59120.0277-0.42810.71970.13241.215634.445116.032212.7651
1280.1912-0.3454-0.24020.58540.41110.2685-0.41240.3516-0.31010.08260.0960.53650.7121-0.3456-0.05680.6621-0.0747-0.20830.96670.09011.168632.396912.834514.1042
1290.0271-0.0433-0.04670.05090.06080.06940.08040.2067-0.1011-0.0634-0.129-0.2235-0.3677-0.1891-0.00991.88460.03530.56030.90980.41062.169785.157325.28655.2026
1300.0139-0.00720.05440.10980.04940.2897-0.21450.23580.6755-0.0930.05730.0840.2438-0.14350.09241.12070.00230.34571.2010.70451.750692.186610.693754.3264
1310.21750.0942-0.02010.0398-0.00850.01360.1292-0.00380.2534-0.304-0.2674-0.07470.32320.2357-0.02251.01320.16530.31170.65370.25332.698280.847117.705764.8516
132-0.00010.0038-0.01120.0057-0.01280.0115-0.1743-0.12180.47-0.3193-0.37420.477-0.36250.147401.31950.1687-0.03581.02620.28931.603680.07412.839554.4327
1330.2103-0.13790.04740.1095-0.06720.0696-0.1316-0.01750.2486-0.1658-0.12050.0761-0.04560.1091-0.09931.56620.29570.26420.44160.41142.319283.099218.164360.5214
1340.1454-0.0590.09810.03-0.05310.06870.1339-0.7621-0.29240.4636-0.1716-0.3922-1.1061-0.4415-0.00541.78610.33430.24871.14230.17482.405582.673240.510764.4538
1350.0626-0.04970.0460.0257-0.02860.0150.0134-0.4560.3713-1.07830.2127-0.3568-0.0634-0.0156-0.00011.85610.1299-0.18791.7785-0.25173.152591.377751.366871.3723
1360.00650.0367-0.02530.1316-0.15270.1380.360.04320.2439-0.23420.2181-0.19080.0994-0.0512-0.00011.72550.12930.0161.1749-0.12152.854587.786246.823672.4297
1370.00780.00170.01860.00120.00720.01920.15410.0708-0.0961-0.3596-0.02670.21540.1932-0.0308-0.00012.5256-0.3819-0.3612.26820.24442.346694.090457.970268.9509
138-0.007-0.0005-0.0052-0.00010.01040.01370.26250.0336-0.0808-0.20230.13920.30980.0377-0.071302.6125-0.56590.27111.6742-0.38712.520187.497758.738564.3519
139-0.0009-0.06160.08030.1780.04260.46180.00860.04640.1712-0.1566-0.2704-0.1130.0497-0.0039-0.53431.2824-0.02440.63460.1751-0.4671.946789.533415.216378.7784
1400.28710.0963-0.39110.5953-0.94331.71480.8850.18940.47480.79011.0551-0.07380.3094-0.13820.29262.47060.4753-0.26251.5067-0.61383.266279.590646.86582.3825
1410.0533-0.09030.16510.1953-0.23940.36860.1863-0.05350.6162-0.27540.23490.0571-0.35460.20210.15531.3198-0.44880.09340.70.0311.315131.32059.15161.3383
1420.0531-0.1124-0.01460.13470.0298-0.0034-0.06790.42420.46640.2555-0.0079-0.45930.1420.398601.7004-0.57320.19111.8983-0.01942.4881160.268424.088257.6421
1430.37870.1864-0.23180.28210.10550.38850.677-0.22940.61010.02990.14810.1495-0.14220.28391.440.238-1.2726-0.03780.3636-0.36680.7165139.6728-10.60267.0225
1440.24440.1109-0.3850.0397-0.15220.6043-0.4778-0.0623-0.14950.1765-0.2455-0.3776-0.23380.1224-0.74551.0922-0.8651-0.09441.3611-0.42322.0653163.083117.193472.2477
1450.02250.04180.05250.0520.09430.1120.20220.30010.12590.30710.3142-0.294-0.03430.53440.0031.16390.00230.10661.06710.31681.2933103.7591-20.5006-4.1988
1460.024-0.0069-0.01140.0845-0.07340.06020.42240.2239-0.09130.3605-0.6068-0.1499-0.02340.34050.00031.0385-0.0643-0.11180.97690.16040.525698.9436-26.89614.8265
1470.02130.023-0.02170.0181-0.02050.04260.09230.62820.01540.0780.1215-0.1065-0.13760.5946-0.00010.7791-0.1206-0.15171.15260.11720.8994107.3316-28.60625.7997
1480.0368-0.00730.02650.01010.00110.0161-0.27970.35680.2610.17050.2531-0.0403-0.20490.0777-00.968-0.03030.05061.03660.22850.5666101.0135-28.2823-0.0305
1490.0318-0.0186-0.02980.0492-0.040.22940.05990.18770.2726-0.03620.16080.05660.13230.03730.69910.7570.25470.31411.38430.65510.44199.9991-19.9112-20.5565
1500.08270.0618-0.08060.0374-0.07470.09470.22820.10020.55850.11180.33030.3707-0.2597-0.1742-0.00021.86230.04650.23291.86890.40011.457689.5055-13.2317-29.0962
1510.03870.0882-0.05940.1898-0.12380.08040.055-0.0984-0.00760.05440.12390.04220.02250.31610.05551.3482-0.1027-0.15911.97150.35380.503299.0605-23.3923-22.5296
1520.04870.0393-0.03370.0444-0.02630.0206-0.07850.07820.0994-0.0607-0.10490.0313-0.0104-0.3233-0.19332.31780.2065-0.19682.34190.53210.615384.1374-13.9777-31.0887
1530.01460.0090.01770.00820.01220.0060.0577-0.24920.05580.08370.2141-0.17840.12030.482-0.00022.36020.1215-0.50461.82390.48551.632689.321-6.3695-32.5871
1540.0214-0.0095-0.0239-0.00630.01080.0250.2366-0.04520.1783-0.03180.35160.015-0.04990.0066-0.00021.84430.00720.18221.8172-0.04161.073197.4648-7.0884-33.5159
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 181 )
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 473 )
3X-RAY DIFFRACTION3chain 'B' and (resid 20 through 56 )
4X-RAY DIFFRACTION4chain 'B' and (resid 57 through 125 )
5X-RAY DIFFRACTION5chain 'B' and (resid 126 through 181 )
6X-RAY DIFFRACTION6chain 'B' and (resid 182 through 335 )
7X-RAY DIFFRACTION7chain 'B' and (resid 336 through 473 )
8X-RAY DIFFRACTION8chain 'C' and (resid 20 through 125 )
9X-RAY DIFFRACTION9chain 'C' and (resid 126 through 181 )
10X-RAY DIFFRACTION10chain 'C' and (resid 182 through 312 )
11X-RAY DIFFRACTION11chain 'C' and (resid 313 through 473 )
12X-RAY DIFFRACTION12chain 'D' and (resid 20 through 125 )
13X-RAY DIFFRACTION13chain 'D' and (resid 126 through 181 )
14X-RAY DIFFRACTION14chain 'D' and (resid 182 through 473 )
15X-RAY DIFFRACTION15chain 'E' and (resid 20 through 86 )
16X-RAY DIFFRACTION16chain 'E' and (resid 87 through 125 )
17X-RAY DIFFRACTION17chain 'E' and (resid 126 through 181 )
18X-RAY DIFFRACTION18chain 'E' and (resid 182 through 473 )
19X-RAY DIFFRACTION19chain 'F' and (resid 20 through 125 )
20X-RAY DIFFRACTION20chain 'F' and (resid 126 through 181 )
21X-RAY DIFFRACTION21chain 'F' and (resid 182 through 312 )
22X-RAY DIFFRACTION22chain 'F' and (resid 313 through 473 )
23X-RAY DIFFRACTION23chain 'G' and (resid 20 through 181 )
24X-RAY DIFFRACTION24chain 'G' and (resid 182 through 473 )
25X-RAY DIFFRACTION25chain 'H' and (resid 20 through 86 )
26X-RAY DIFFRACTION26chain 'H' and (resid 87 through 125 )
27X-RAY DIFFRACTION27chain 'H' and (resid 126 through 181 )
28X-RAY DIFFRACTION28chain 'H' and (resid 182 through 335 )
29X-RAY DIFFRACTION29chain 'H' and (resid 336 through 383 )
30X-RAY DIFFRACTION30chain 'H' and (resid 384 through 473 )
31X-RAY DIFFRACTION31chain 'I' and (resid 20 through 125 )
32X-RAY DIFFRACTION32chain 'I' and (resid 126 through 181 )
33X-RAY DIFFRACTION33chain 'I' and (resid 182 through 473 )
34X-RAY DIFFRACTION34chain 'J' and (resid 20 through 160 )
35X-RAY DIFFRACTION35chain 'J' and (resid 161 through 473 )
36X-RAY DIFFRACTION36chain 'K' and (resid 1 through 80 )
37X-RAY DIFFRACTION37chain 'K' and (resid 81 through 123 )
38X-RAY DIFFRACTION38chain 'K' and (resid 124 through 217 )
39X-RAY DIFFRACTION39chain 'L' and (resid 2 through 119 )
40X-RAY DIFFRACTION40chain 'L' and (resid 120 through 145 )
41X-RAY DIFFRACTION41chain 'L' and (resid 146 through 223 )
42X-RAY DIFFRACTION42chain 'O' and (resid 1 through 37 )
43X-RAY DIFFRACTION43chain 'O' and (resid 38 through 66 )
44X-RAY DIFFRACTION44chain 'O' and (resid 67 through 80 )
45X-RAY DIFFRACTION45chain 'O' and (resid 81 through 101 )
46X-RAY DIFFRACTION46chain 'O' and (resid 102 through 144 )
47X-RAY DIFFRACTION47chain 'O' and (resid 145 through 163 )
48X-RAY DIFFRACTION48chain 'O' and (resid 164 through 177 )
49X-RAY DIFFRACTION49chain 'O' and (resid 178 through 192 )
50X-RAY DIFFRACTION50chain 'O' and (resid 193 through 203 )
51X-RAY DIFFRACTION51chain 'O' and (resid 204 through 218 )
52X-RAY DIFFRACTION52chain 'P' and (resid 2 through 17 )
53X-RAY DIFFRACTION53chain 'P' and (resid 18 through 40 )
54X-RAY DIFFRACTION54chain 'P' and (resid 41 through 51 )
55X-RAY DIFFRACTION55chain 'P' and (resid 52 through 98 )
56X-RAY DIFFRACTION56chain 'P' and (resid 99 through 119 )
57X-RAY DIFFRACTION57chain 'P' and (resid 120 through 134 )
58X-RAY DIFFRACTION58chain 'P' and (resid 135 through 148 )
59X-RAY DIFFRACTION59chain 'P' and (resid 149 through 165 )
60X-RAY DIFFRACTION60chain 'P' and (resid 166 through 191 )
61X-RAY DIFFRACTION61chain 'P' and (resid 192 through 203 )
62X-RAY DIFFRACTION62chain 'P' and (resid 204 through 220 )
63X-RAY DIFFRACTION63chain 'Q' and (resid 1 through 18 )
64X-RAY DIFFRACTION64chain 'Q' and (resid 19 through 80 )
65X-RAY DIFFRACTION65chain 'Q' and (resid 81 through 163 )
66X-RAY DIFFRACTION66chain 'Q' and (resid 164 through 217 )
67X-RAY DIFFRACTION67chain 'R' and (resid 2 through 64 )
68X-RAY DIFFRACTION68chain 'R' and (resid 65 through 134 )
69X-RAY DIFFRACTION69chain 'R' and (resid 135 through 165 )
70X-RAY DIFFRACTION70chain 'R' and (resid 166 through 222 )
71X-RAY DIFFRACTION71chain 'S' and (resid 1 through 53 )
72X-RAY DIFFRACTION72chain 'S' and (resid 54 through 126 )
73X-RAY DIFFRACTION73chain 'S' and (resid 127 through 218 )
74X-RAY DIFFRACTION74chain 'T' and (resid 2 through 119 )
75X-RAY DIFFRACTION75chain 'T' and (resid 120 through 149 )
76X-RAY DIFFRACTION76chain 'T' and (resid 150 through 203 )
77X-RAY DIFFRACTION77chain 'T' and (resid 204 through 220 )
78X-RAY DIFFRACTION78chain 'M' and (resid 1 through 18 )
79X-RAY DIFFRACTION79chain 'M' and (resid 19 through 53 )
80X-RAY DIFFRACTION80chain 'M' and (resid 54 through 80 )
81X-RAY DIFFRACTION81chain 'M' and (resid 81 through 101 )
82X-RAY DIFFRACTION82chain 'M' and (resid 102 through 126 )
83X-RAY DIFFRACTION83chain 'M' and (resid 127 through 144 )
84X-RAY DIFFRACTION84chain 'M' and (resid 145 through 163 )
85X-RAY DIFFRACTION85chain 'M' and (resid 164 through 192 )
86X-RAY DIFFRACTION86chain 'M' and (resid 193 through 203 )
87X-RAY DIFFRACTION87chain 'M' and (resid 204 through 217 )
88X-RAY DIFFRACTION88chain 'N' and (resid 2 through 17 )
89X-RAY DIFFRACTION89chain 'N' and (resid 18 through 60 )
90X-RAY DIFFRACTION90chain 'N' and (resid 61 through 108 )
91X-RAY DIFFRACTION91chain 'N' and (resid 109 through 119 )
92X-RAY DIFFRACTION92chain 'N' and (resid 120 through 138 )
93X-RAY DIFFRACTION93chain 'N' and (resid 139 through 149 )
94X-RAY DIFFRACTION94chain 'N' and (resid 150 through 183 )
95X-RAY DIFFRACTION95chain 'N' and (resid 184 through 220 )
96X-RAY DIFFRACTION96chain 'c' and (resid 1 through 37 )
97X-RAY DIFFRACTION97chain 'c' and (resid 38 through 101 )
98X-RAY DIFFRACTION98chain 'c' and (resid 102 through 163 )
99X-RAY DIFFRACTION99chain 'c' and (resid 164 through 218 )
100X-RAY DIFFRACTION100chain 'd' and (resid 2 through 17 )
101X-RAY DIFFRACTION101chain 'd' and (resid 18 through 40 )
102X-RAY DIFFRACTION102chain 'd' and (resid 41 through 51 )
103X-RAY DIFFRACTION103chain 'd' and (resid 52 through 83 )
104X-RAY DIFFRACTION104chain 'd' and (resid 84 through 98 )
105X-RAY DIFFRACTION105chain 'd' and (resid 99 through 134 )
106X-RAY DIFFRACTION106chain 'd' and (resid 135 through 155 )
107X-RAY DIFFRACTION107chain 'd' and (resid 156 through 172 )
108X-RAY DIFFRACTION108chain 'd' and (resid 173 through 203 )
109X-RAY DIFFRACTION109chain 'd' and (resid 204 through 222 )
110X-RAY DIFFRACTION110chain 'V' and (resid 2 through 17 )
111X-RAY DIFFRACTION111chain 'V' and (resid 18 through 64 )
112X-RAY DIFFRACTION112chain 'V' and (resid 65 through 119 )
113X-RAY DIFFRACTION113chain 'V' and (resid 120 through 149 )
114X-RAY DIFFRACTION114chain 'V' and (resid 150 through 165 )
115X-RAY DIFFRACTION115chain 'V' and (resid 166 through 176 )
116X-RAY DIFFRACTION116chain 'V' and (resid 177 through 191 )
117X-RAY DIFFRACTION117chain 'V' and (resid 192 through 203 )
118X-RAY DIFFRACTION118chain 'V' and (resid 204 through 220 )
119X-RAY DIFFRACTION119chain 'W' and (resid 1 through 18 )
120X-RAY DIFFRACTION120chain 'W' and (resid 19 through 80 )
121X-RAY DIFFRACTION121chain 'W' and (resid 81 through 101 )
122X-RAY DIFFRACTION122chain 'W' and (resid 102 through 126 )
123X-RAY DIFFRACTION123chain 'W' and (resid 127 through 163 )
124X-RAY DIFFRACTION124chain 'W' and (resid 164 through 177 )
125X-RAY DIFFRACTION125chain 'W' and (resid 178 through 219 )
126X-RAY DIFFRACTION126chain 'X' and (resid 2 through 134 )
127X-RAY DIFFRACTION127chain 'X' and (resid 135 through 165 )
128X-RAY DIFFRACTION128chain 'X' and (resid 166 through 220 )
129X-RAY DIFFRACTION129chain 'Y' and (resid 1 through 18 )
130X-RAY DIFFRACTION130chain 'Y' and (resid 19 through 37 )
131X-RAY DIFFRACTION131chain 'Y' and (resid 38 through 53 )
132X-RAY DIFFRACTION132chain 'Y' and (resid 54 through 80 )
133X-RAY DIFFRACTION133chain 'Y' and (resid 81 through 101 )
134X-RAY DIFFRACTION134chain 'Y' and (resid 102 through 126 )
135X-RAY DIFFRACTION135chain 'Y' and (resid 127 through 163 )
136X-RAY DIFFRACTION136chain 'Y' and (resid 164 through 192 )
137X-RAY DIFFRACTION137chain 'Y' and (resid 193 through 203 )
138X-RAY DIFFRACTION138chain 'Y' and (resid 204 through 217 )
139X-RAY DIFFRACTION139chain 'Z' and (resid 2 through 138 )
140X-RAY DIFFRACTION140chain 'Z' and (resid 139 through 220 )
141X-RAY DIFFRACTION141chain 'a' and (resid 1 through 126 )
142X-RAY DIFFRACTION142chain 'a' and (resid 127 through 217 )
143X-RAY DIFFRACTION143chain 'b' and (resid 2 through 119 )
144X-RAY DIFFRACTION144chain 'b' and (resid 120 through 220 )
145X-RAY DIFFRACTION145chain 'U' and (resid 1 through 18 )
146X-RAY DIFFRACTION146chain 'U' and (resid 19 through 53 )
147X-RAY DIFFRACTION147chain 'U' and (resid 54 through 80 )
148X-RAY DIFFRACTION148chain 'U' and (resid 81 through 101 )
149X-RAY DIFFRACTION149chain 'U' and (resid 102 through 126 )
150X-RAY DIFFRACTION150chain 'U' and (resid 127 through 163 )
151X-RAY DIFFRACTION151chain 'U' and (resid 164 through 177 )
152X-RAY DIFFRACTION152chain 'U' and (resid 178 through 192 )
153X-RAY DIFFRACTION153chain 'U' and (resid 193 through 203 )
154X-RAY DIFFRACTION154chain 'U' and (resid 204 through 217 )

+
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

-
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

+
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

+
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。

-
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