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- PDB-6h6l: Murine norovirus protruding domain (CW3 strain) in complex with t... -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 6h6l
タイトルMurine norovirus protruding domain (CW3 strain) in complex with the CD300lf receptor and glycochenodeoxycholate (GCDCA)
要素
  • CMRF35-like molecule 1
  • Capsid protein
キーワードVIRAL PROTEIN / MNV1 / sCD300lf / GCDCA / bile acid / glycochenodeoxycholate
機能・相同性
機能・相同性情報


interleukin-13-mediated signaling pathway / negative regulation of MyD88-dependent toll-like receptor signaling pathway / negative regulation of apoptotic cell clearance / interleukin-4 receptor binding / positive regulation of interleukin-4-mediated signaling pathway / negative regulation of mast cell activation / ceramide binding / positive regulation of apoptotic cell clearance / TRIF-dependent toll-like receptor signaling pathway / phosphatidylserine binding ...interleukin-13-mediated signaling pathway / negative regulation of MyD88-dependent toll-like receptor signaling pathway / negative regulation of apoptotic cell clearance / interleukin-4 receptor binding / positive regulation of interleukin-4-mediated signaling pathway / negative regulation of mast cell activation / ceramide binding / positive regulation of apoptotic cell clearance / TRIF-dependent toll-like receptor signaling pathway / phosphatidylserine binding / osteoclast differentiation / transmembrane signaling receptor activity / virus receptor activity / host cell cytoplasm / plasma membrane / cytoplasm
類似検索 - 分子機能
SHP2-interacting transmembrane adaptor protein, SIT / Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein ...SHP2-interacting transmembrane adaptor protein, SIT / Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Immunoglobulin V-set domain / Viral coat protein subunit / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Capsid protein / CMRF35-like molecule 1
類似検索 - 構成要素
生物種Murine norovirus 1 (マウスノロウイルス 1)
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: 2.5 Å
データ登録者Kilic, T. / Hansman, G.S.
引用ジャーナル: To Be Published
タイトル: Crystal structures of murine norovirus protruding domain with conjugated bile acid reveal a novel binding pocket.
著者: Kilic, T. / Koromyslova, A. / Malak, V. / Hansman, G.S.
履歴
登録2018年7月27日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年8月14日Provider: repository / タイプ: Initial release
改定 1.12024年1月17日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: CMRF35-like molecule 1
F: CMRF35-like molecule 1
G: CMRF35-like molecule 1
H: CMRF35-like molecule 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)185,02125
ポリマ-182,8748
非ポリマー2,14717
4,197233
1
A: Capsid protein
B: Capsid protein
E: CMRF35-like molecule 1
F: CMRF35-like molecule 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)92,54213
ポリマ-91,4374
非ポリマー1,1059
724
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
2
C: Capsid protein
D: Capsid protein
G: CMRF35-like molecule 1
H: CMRF35-like molecule 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)92,48012
ポリマ-91,4374
非ポリマー1,0428
543
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)87.000, 87.000, 276.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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要素

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タンパク質 , 2種, 8分子 ABCDEFGH

#1: タンパク質
Capsid protein


分子量: 33063.285 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Murine norovirus 1 (マウスノロウイルス 1)
発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: A7U694
#2: タンパク質
CMRF35-like molecule 1 / CLM-1 / CD300 antigen-like family member F / Leukocyte mono-Ig-like receptor 3 / Myeloid-associated ...CLM-1 / CD300 antigen-like family member F / Leukocyte mono-Ig-like receptor 3 / Myeloid-associated immunoglobulin-like receptor 5 / MAIR-V


分子量: 12655.293 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Cd300lf, Clm1, Lmir3 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q6SJQ7

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非ポリマー , 5種, 250分子

#3: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 8 / 由来タイプ: 合成 / : Mg
#4: 化合物
ChemComp-CHO / GLYCOCHENODEOXYCHOLIC ACID / グリコケノデオキシコ-ル酸


分子量: 449.623 Da / 分子数: 4 / 由来タイプ: 合成 / : C26H43NO5 / コメント: 可溶化剤*YM
#5: 化合物
ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 4 / 由来タイプ: 合成 / : Na
#6: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 1 / 由来タイプ: 合成 / : C2H6O2
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 233 / 由来タイプ: 天然 / : 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: 2.86 Å3/Da / 溶媒含有率: 57.06 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.1 M Tris.HCl pH 8.5, 25 %(v/v) PEG 550 MME

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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: ESRF / ビームライン: ID29 / 波長: 1.07227 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2017年11月11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: 1.07227 Å / 相対比: 1
反射解像度: 2.5→46.71 Å / Num. obs: 70179 / % possible obs: 99.7 % / 冗長度: 6.9 % / Biso Wilson estimate: 48.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1031 / Rpim(I) all: 0.0424 / Rrim(I) all: 0.1116 / Net I/σ(I): 14.68
反射 シェル解像度: 2.5→2.59 Å / Rmerge(I) obs: 0.8105 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 6850 / CC1/2: 0.784 / Rpim(I) all: 0.3342 / Rrim(I) all: 0.8778 / % possible all: 98.05

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.13_2998: ???)精密化
XDSVERSION Jun 1, 2017データ削減
XSCALEVERSION Jun 1, 2017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: 5OR7
解像度: 2.5→46.71 Å / SU ML: 0.33 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 23.6
Rfactor反射数%反射
Rfree0.2157 3508 5 %
Rwork0.1892 --
obs0.1906 70169 99.71 %
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: 2.5→46.71 Å
タンパク質核酸リガンド溶媒全体
原子数11918 0 144 233 12295
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00412397
X-RAY DIFFRACTIONf_angle_d0.66417060
X-RAY DIFFRACTIONf_dihedral_angle_d3.1097327
X-RAY DIFFRACTIONf_chiral_restr0.0461981
X-RAY DIFFRACTIONf_plane_restr0.0042201
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5033-2.53760.42291320.36722511X-RAY DIFFRACTION96
2.5376-2.57390.31721400.28722666X-RAY DIFFRACTION100
2.5739-2.61230.31031400.26472654X-RAY DIFFRACTION100
2.6123-2.65310.30561400.24852669X-RAY DIFFRACTION100
2.6531-2.69660.27661420.23642687X-RAY DIFFRACTION100
2.6966-2.74310.26531390.23512646X-RAY DIFFRACTION100
2.7431-2.7930.271410.23112686X-RAY DIFFRACTION100
2.793-2.84670.30441400.22392643X-RAY DIFFRACTION100
2.8467-2.90480.23141420.22422703X-RAY DIFFRACTION100
2.9048-2.96790.26691380.23822626X-RAY DIFFRACTION100
2.9679-3.0370.26951410.23232673X-RAY DIFFRACTION100
3.037-3.11290.24891410.21632681X-RAY DIFFRACTION100
3.1129-3.1970.23311410.21372684X-RAY DIFFRACTION100
3.197-3.29110.25371400.20992651X-RAY DIFFRACTION100
3.2911-3.39730.21911410.19812683X-RAY DIFFRACTION100
3.3973-3.51870.22041410.19222679X-RAY DIFFRACTION100
3.5187-3.65950.24021400.1932654X-RAY DIFFRACTION100
3.6595-3.8260.22341400.18912672X-RAY DIFFRACTION100
3.826-4.02760.20891420.17182686X-RAY DIFFRACTION100
4.0276-4.27980.17051400.15382666X-RAY DIFFRACTION100
4.2798-4.60990.14711420.13932697X-RAY DIFFRACTION100
4.6099-5.07340.18361400.14152665X-RAY DIFFRACTION100
5.0734-5.80630.16511430.16882709X-RAY DIFFRACTION100
5.8063-7.31080.18731400.17062672X-RAY DIFFRACTION100
7.3108-46.71530.18281420.17742698X-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)
12.2291-0.3767-0.55241.67180.25463.02950.0012-0.2631-0.29440.6246-0.0655-0.12260.01860.2383-0.10970.4916-0.0852-0.1470.36680.05980.488356.1791-6.7935-17.4737
21.32150.00340.09361.2214-0.99862.11020.04670.07610.24180.3376-0.1214-0.1318-0.49410.05660.1120.5282-0.0867-0.09460.2730.02810.500652.30358.1333-27.2482
31.98830.5822-0.03482.2417-1.79341.79940.25780.1916-0.1839-0.41730.0169-0.22660.0638-0.098-0.22250.5743-0.0045-0.07530.43530.01090.433642.02831.9701-43.86
41.24890.79230.1512.10950.43721.70370.05260.28270.083-0.0678-0.149-0.1835-0.3140.27040.02340.4727-0.0794-0.05460.42540.12190.508751.660210.8945-38.8184
52.01340.689-1.19572.0114-0.46241.872-0.08180.50160.26180.05460.10030.1839-0.2492-0.0746-0.0060.4186-0.0222-0.04440.33880.05870.501146.18456.32-42.795
61.1230.8752-0.43182.046-0.14671.20660.02890.09710.2230.3043-0.1004-0.3178-0.64670.29390.04520.6326-0.111-0.09730.3240.04780.610460.20614.478-28.8784
70.604-0.54420.89632.1154-0.18191.41580.0191-0.02060.15010.3702-0.1356-0.4398-0.12030.364-0.00250.4802-0.1124-0.16080.43540.06540.576962.3578-1.4594-22.1474
83.5745-0.4996-0.10280.3368-0.70212.05560.1666-0.6407-0.13690.4843-0.2323-0.2427-0.00090.36820.21390.7391-0.1379-0.2970.40810.05890.634264.0056-5.5697-5.8862
93.47220.3644-0.7064.51220.98322.95780.42580.067-0.19420.406-0.3443-1.1051-0.35430.3245-0.06790.6004-0.1222-0.22870.4240.11250.754369.3453-4.7834-14.6846
100.76840.02220.16950.18290.07950.0740.0105-0.3909-0.24670.4263-0.3641-0.1472-0.57230.2014-1.53440.9724-0.2591-0.56180.74170.12690.479467.5251-3.2917-3.522
111.26971.40670.02661.64950.76853.75530.06880.0890.15460.1412-0.2387-0.0271-0.5707-0.00090.23180.4354-0.0064-0.05220.2666-0.00250.40439.8999-3.7939-16.8889
121.43530.2877-0.75150.66250.02461.495-0.12160.0457-0.24090.06840.0459-0.15930.27080.07520.07140.36270.0038-0.03560.2264-0.01640.376543.9563-18.3267-28.0717
134.96832.0944-0.66482.02970.34552.2397-0.14530.62240.2219-0.22440.0927-0.2116-0.1252-0.0660.04890.4058-0.0426-0.00590.42750.05580.452752.0206-12.2002-43.365
142.2154-0.34420.42561.0998-0.51042.6106-0.15390.4508-0.0387-0.35260.0556-0.27440.2397-0.13770.12490.3494-0.01450.02860.3682-0.06030.436547.7818-19.1963-41.4996
150.52960.1035-0.84110.09260.12581.8107-0.06130.2011-0.07580.02180.0198-0.04310.006-0.03430.03030.3951-0.0308-0.03890.3103-0.00670.410234.4539-13.6263-25.0606
165.88560.044-0.01250.282-0.02063.0295-0.025-0.25670.21420.53070.08450.0211-0.4102-0.1239-0.02960.508-0.03990.00360.3239-0.04970.414131.2817-5.5969-5.9878
172.8730.7781-0.3053.0259-0.9623.7080.13760.31190.28920.0491-0.0975-0.3107-0.1484-0.3342-0.04330.49190.0211-0.04360.3208-0.0360.39425.7088-6.6981-15.6586
182.26510.37880.15220.6937-1.56223.94770.0355-0.068-0.1223-0.2834-0.02220.1105-0.0132-0.2495-0.01870.450.0482-0.01430.2375-0.06280.349427.5021-9.3877-4.3179
192.0274-0.18790.74371.60360.82723.80440.0046-0.20340.08990.29760.09040.0437-0.0418-0.0969-0.02580.43670.0522-0.00710.36590.0570.39546.9019-54.1044-16.6447
202.84220.77280.40091.25570.70972.65040.05410.2147-0.00040.34810.07980.01010.44980.5092-0.11150.46750.1251-0.03580.3888-0.00860.349218.5028-58.5754-19.6712
210.58670.4388-0.46151.70970.92842.3847-0.03080.80590.0793-0.16720.0892-0.34550.06980.5858-0.02810.2628-0.00220.02080.66910.11940.466221.1698-44.993-35.9009
220.5276-0.67530.9062.7448-0.28022.0481-0.22550.95430.3037-0.63890.1518-0.2386-0.0067-0.23110.0590.4229-0.04870.01210.70450.22660.514710.8872-41.8378-45.6708
231.71110.14610.6321.099-0.56951.86840.33080.05210.0743-0.4062-0.1447-0.09830.32870.61230.01790.38530.06840.02180.6610.07950.433421.0757-50.582-41.3872
241.64150.13250.441.0831-0.09681.25820.06740.45170.0206-0.1666-0.0441-0.06510.29490.75620.03990.35360.07250.04250.64990.07680.37220.2841-51.0117-39.2136
250.9582-0.40720.76790.6816-0.09511.62040.08040.1907-0.25740.04210.0684-0.14840.76630.1503-0.14240.60030.0635-0.03130.3685-0.00760.404911.7219-65.2554-25.7656
262.09240.01770.24892.1143-0.00163.3307-0.0025-0.01980.0810.1920.0910.00950.33210.1843-0.11270.50030.0901-0.02740.27650.07770.395411.4515-57.9081-10.1129
271.785-1.04240.45481.033-0.67032.68850.09230.15520.1250.07090.1670.10920.78730.3194-0.14950.77530.0329-0.07880.35910.02860.410210.6503-66.6514-13.943
282.65350.2116-0.73110.91380.24540.3102-0.0531-0.6498-0.15620.29840.1519-0.28950.65380.3644-0.01590.73350.0587-0.07560.28920.09510.255413.7738-64.294-3.3212
291.6645-0.770.59691.00430.7133.6547-0.0887-0.19340.15090.1945-0.0085-0.30670.10750.33470.12730.3389-0.0239-0.0870.28410.04020.49668.9575-38.0758-18.2797
301.4249-0.09381.23130.5576-0.49042.6774-0.0209-0.1730.06490.06610.01070.13570.1673-0.42490.04510.2593-0.01980.02940.34380.02620.3719-6.8492-43.7744-27.0879
312.0378-1.01610.66541.65660.3592.03250.05380.4070.0939-0.07250.012-0.42990.26640.3214-0.06510.3436-0.02340.00910.42880.0190.3534-1.0472-55.9388-43.3754
321.9029-0.71710.75831.58380.44471.92490.08840.146-0.1071-0.0924-0.2030.1744-0.021-0.33170.11540.3846-0.02020.00110.41790.0850.4176-10.7535-45.4918-37.9538
331.51260.00861.01750.4750.12292.2996-0.22870.02670.27720.01520.01160.0859-0.1418-0.10740.18530.3167-0.02140.00810.31650.05880.4431-4.2959-37.8918-32.305
343.20670.52450.853.13170.72164.63670.0389-0.3493-0.02960.4002-0.1392-0.08150.27480.25960.24870.50250.0266-0.04740.4344-0.02620.44971.9418-40.1042-8.1721
352.80420.2992-0.02951.62760.18882.5985-0.3922-0.26420.62190.2608-0.0565-0.155-0.558-0.14490.34710.50760.0514-0.19730.321-0.03420.59667.871-25.6181-11.1993
361.3203-0.97480.91542.88790.14762.11520.19991.44390.0046-0.96950.0841-0.16310.2210.0489-0.23230.757-0.1299-0.05340.566-0.06210.554867.398814.1669-61.1897
373.2982-0.41341.16292.0776-0.00492.0496-0.33160.1557-0.3482-0.180.29820.7524-0.1412-0.3588-0.11490.5146-0.1335-0.03450.40930.10140.48160.683622.3769-56.4031
384.1949-0.19860.63370.11030.51763.31380.27850.383-0.54230.13640.30190.1821-0.3182-0.0109-0.4040.5313-0.0754-0.08990.41010.13080.688261.925511.1861-45.7355
392.511-1.29030.425.7483-1.3192.012-0.1901-0.0270.48820.51210.1711-0.2372-0.6399-0.31420.27160.4645-0.0639-0.05620.42190.07940.585366.237527.2585-51.2079
401.8505-0.48931.1263.7090.34353.5831-0.11130.51410.3074-0.25040.030.10420.10340.65870.02130.562-0.2089-0.09670.51580.09970.453667.790525.1317-57.4282
417.0530.53870.91843.5973-2.23766.97010.152-0.5928-0.3880.3483-0.2269-0.72830.99790.64240.08240.54150.01630.03880.54460.04180.809779.612613.3814-54.2543
422.53980.2089-0.29321.7484-0.29841.5941-0.23220.19390.3804-0.44150.3188-0.10960.3428-0.4386-0.06740.4762-0.0763-0.07350.49840.08510.573359.750316.6923-50.6723
431.8522.0348-1.92512.4162-2.1252.5318-0.85030.2537-0.964-0.34150.55660.00910.76990.09920.30080.7032-0.1349-0.09860.5832-0.11490.590568.72310.8064-57.6567
445.1859-1.82190.1643.90450.37520.0824-0.25410.00990.3894-0.02690.3356-0.11780.4338-0.6294-0.15210.4758-0.1840.06870.84940.03750.313228.1323-20.813-62.7935
456.2665-2.34280.04171.4588-0.53920.4644-0.414-0.1104-0.8341-0.29150.53720.05870.1271-0.053-0.09520.4947-0.17720.14560.625-0.12430.490736.9711-29.1066-62.9324
465.7986-0.84441.93582.7576-1.88682.92-0.4383-0.70540.49950.33320.4767-0.3573-0.2416-0.1982-0.0250.3506-0.11250.01460.4102-0.13010.323535.1228-30.8508-54.4107
473.10331.20821.64890.59340.47891.0599-0.1452-0.3964-0.26850.07460.0299-0.25880.50370.20130.0180.4689-0.08610.05310.5817-0.03790.329732.263-24.4989-48.4326
481.32190.82561.7425.64040.14983.26130.1117-0.5536-0.5791-0.69770.9591-0.32690.67040.068-0.4090.4712-0.25550.05210.7422-0.01540.444827.3941-36.9299-56.403
492.0226-0.11551.58652.661-0.61672.6478-0.40550.5668-0.728-0.13680.38520.17720.4286-0.2821-0.16580.4992-0.18670.17480.6513-0.09370.477132.2363-32.9404-63.1701
501.055-0.26660.68450.78050.0950.54130.0622-0.0232-0.18670.5659-0.07450.3559-0.163-1.0704-0.03880.4721-0.04850.08671.11330.12490.436117.2439-20.9954-56.5333
514.1443-1.63292.3921.4637-1.57331.86120.1360.6539-0.9192-0.64380.42120.14480.19530.21010.11440.3528-0.11590.1180.5231-0.06960.364932.5277-22.4668-54.5904
520.9732-0.52250.64730.5727-0.88692.3241-0.15350.44910.16460.05440.2151-0.0697-0.1461-0.2148-0.10780.3799-0.10280.06330.61340.00420.394530.0967-20.5904-57.0888
534.76980.32871.29660.0352-0.13833.91650.73760.6538-0.6803-0.2354-0.11190.0399-0.21070.2350.12860.92170.5302-0.07241.4284-0.10890.413922.9826-64.4222-63.6365
542.3730.0216-0.06482.48922.22971.9989-0.0199-0.04190.0656-0.6150.2942-0.2141-1.0971-0.3187-0.97090.82940.28440.4551.1950.22680.361832.555-55.2621-61.5128
551.2473-0.1439-0.4691.9057-0.79830.75540.47790.5187-0.2901-0.0631-0.2946-0.1934-0.05430.49710.07810.56560.3364-0.0881.0743-0.17530.560125.5054-64.0235-50.7773
563.69373.3704-1.32675.2912-2.64261.76020.1251-0.1258-1.1462-0.4068-0.55930.0331-0.20290.40010.54530.61110.29270.12281.1933-0.12410.807637.8577-67.6645-57.7879
572.09770.6509-1.62033.16381.03062.76360.44110.6401-0.541-0.7955-0.5037-0.34390.08980.09980.05290.62610.2683-0.04131.099-0.18920.557725.0486-65.4909-56.5297
584.54292.8343-4.64624.3253-3.80786.65040.4884-0.1526-0.6202-0.5858-0.11210.16550.67950.2924-0.1830.6068-0.0233-0.2290.5367-0.00130.6318-16.6891-42.3536-60.2645
595.628-0.6028-1.66629.52712.21316.18840.10560.2544-0.0774-0.1219-0.27670.4692-0.87240.31460.09570.52560.0051-0.08780.46080.04880.3688-13.2579-23.0049-64.3019
603.41171.7826-0.36093.34192.13173.01850.09820.008-1.17990.2543-0.1356-0.44670.0547-0.6894-0.06950.4374-0.0425-0.18910.49530.01530.7035-23.7714-40.7091-59.0176
615.33170.9416-0.51395.3721-1.11495.55460.5092-1.0735-0.67011.3839-0.3036-0.291-0.1978-0.2806-0.14570.41250.0126-0.05340.53150.09330.3514-23.5996-36.7413-51.3475
622.75472.8729-1.1224.0338-2.3143.2931-0.0054-0.02070.4159-0.9022-0.1649-0.5480.02750.25870.32960.43510.0652-0.08810.27650.01060.4117-11.9085-35.8163-45.9049
634.80120.35572.40435.46110.27825.2432-0.0032-1.0709-0.9220.25720.16761.05180.2425-1.66760.29510.36730.0905-0.0120.7173-0.04140.6031-28.6035-32.4192-51.7507
643.67023.5733-1.13993.5576-0.87331.35680.21120.59320.55110.2628-0.03560.5238-0.301-0.50410.06910.46550.16610.01020.4585-0.12150.4947-25.3285-22.7848-53.8558
652.8766-0.1988-1.1364.4647-0.77963.01490.12690.1581-0.0646-0.4609-0.15080.91950.2782-0.37-0.04880.35020.0629-0.11850.4932-0.02380.5369-27.0878-34.8156-59.907
664.4506-0.83154.38727.0286-0.02917.3559-0.5555-0.44790.22870.6074-0.06990.3053-0.7434-0.47330.4940.60370.0503-0.13430.4544-0.0360.4662-14.359-19.7454-57.4514
671.45462.3773-1.14055.235-0.99752.0179-0.16730.52660.4141-0.26720.42290.7161-0.0853-0.1773-0.11790.36010.0077-0.04940.51040.05270.3855-15.3187-34.6032-53.3986
682.5504-3.4622.28744.7809-3.61115.0011-0.29880.31680.0780.61890.03020.4020.3940.28420.10240.5136-0.1861-0.01520.51290.03930.5487-21.1681-44.2955-45.7695
691.5560.51910.17094.4644-0.50231.5467-0.22760.0264-0.3072-0.5467-0.2672-0.94830.05910.01860.38030.33640.0445-0.05090.38150.02460.3575-11.3227-29.6751-59.7883
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 228 through 250 )
2X-RAY DIFFRACTION2chain 'A' and (resid 251 through 332 )
3X-RAY DIFFRACTION3chain 'A' and (resid 333 through 349 )
4X-RAY DIFFRACTION4chain 'A' and (resid 350 through 372 )
5X-RAY DIFFRACTION5chain 'A' and (resid 373 through 399 )
6X-RAY DIFFRACTION6chain 'A' and (resid 400 through 419 )
7X-RAY DIFFRACTION7chain 'A' and (resid 420 through 464 )
8X-RAY DIFFRACTION8chain 'A' and (resid 465 through 492 )
9X-RAY DIFFRACTION9chain 'A' and (resid 493 through 512 )
10X-RAY DIFFRACTION10chain 'A' and (resid 513 through 530 )
11X-RAY DIFFRACTION11chain 'B' and (resid 228 through 250 )
12X-RAY DIFFRACTION12chain 'B' and (resid 251 through 332 )
13X-RAY DIFFRACTION13chain 'B' and (resid 333 through 360 )
14X-RAY DIFFRACTION14chain 'B' and (resid 361 through 399 )
15X-RAY DIFFRACTION15chain 'B' and (resid 400 through 464 )
16X-RAY DIFFRACTION16chain 'B' and (resid 465 through 492 )
17X-RAY DIFFRACTION17chain 'B' and (resid 493 through 512 )
18X-RAY DIFFRACTION18chain 'B' and (resid 513 through 530 )
19X-RAY DIFFRACTION19chain 'C' and (resid 228 through 250 )
20X-RAY DIFFRACTION20chain 'C' and (resid 251 through 282 )
21X-RAY DIFFRACTION21chain 'C' and (resid 283 through 332 )
22X-RAY DIFFRACTION22chain 'C' and (resid 333 through 349 )
23X-RAY DIFFRACTION23chain 'C' and (resid 350 through 372 )
24X-RAY DIFFRACTION24chain 'C' and (resid 373 through 419 )
25X-RAY DIFFRACTION25chain 'C' and (resid 420 through 446 )
26X-RAY DIFFRACTION26chain 'C' and (resid 447 through 492 )
27X-RAY DIFFRACTION27chain 'C' and (resid 493 through 512 )
28X-RAY DIFFRACTION28chain 'C' and (resid 513 through 530 )
29X-RAY DIFFRACTION29chain 'D' and (resid 228 through 250 )
30X-RAY DIFFRACTION30chain 'D' and (resid 251 through 332 )
31X-RAY DIFFRACTION31chain 'D' and (resid 333 through 349 )
32X-RAY DIFFRACTION32chain 'D' and (resid 350 through 372 )
33X-RAY DIFFRACTION33chain 'D' and (resid 373 through 454 )
34X-RAY DIFFRACTION34chain 'D' and (resid 455 through 471 )
35X-RAY DIFFRACTION35chain 'D' and (resid 472 through 530 )
36X-RAY DIFFRACTION36chain 'E' and (resid 2 through 17 )
37X-RAY DIFFRACTION37chain 'E' and (resid 18 through 37 )
38X-RAY DIFFRACTION38chain 'E' and (resid 38 through 44 )
39X-RAY DIFFRACTION39chain 'E' and (resid 45 through 56 )
40X-RAY DIFFRACTION40chain 'E' and (resid 57 through 77 )
41X-RAY DIFFRACTION41chain 'E' and (resid 78 through 85 )
42X-RAY DIFFRACTION42chain 'E' and (resid 86 through 98 )
43X-RAY DIFFRACTION43chain 'E' and (resid 99 through 110 )
44X-RAY DIFFRACTION44chain 'F' and (resid 2 through 17 )
45X-RAY DIFFRACTION45chain 'F' and (resid 18 through 28 )
46X-RAY DIFFRACTION46chain 'F' and (resid 29 through 37 )
47X-RAY DIFFRACTION47chain 'F' and (resid 38 through 49 )
48X-RAY DIFFRACTION48chain 'F' and (resid 50 through 61 )
49X-RAY DIFFRACTION49chain 'F' and (resid 62 through 77 )
50X-RAY DIFFRACTION50chain 'F' and (resid 78 through 85 )
51X-RAY DIFFRACTION51chain 'F' and (resid 86 through 92 )
52X-RAY DIFFRACTION52chain 'F' and (resid 93 through 112 )
53X-RAY DIFFRACTION53chain 'G' and (resid 2 through 22 )
54X-RAY DIFFRACTION54chain 'G' and (resid 23 through 32 )
55X-RAY DIFFRACTION55chain 'G' and (resid 33 through 49 )
56X-RAY DIFFRACTION56chain 'G' and (resid 50 through 61 )
57X-RAY DIFFRACTION57chain 'G' and (resid 62 through 106 )
58X-RAY DIFFRACTION58chain 'H' and (resid 2 through 8 )
59X-RAY DIFFRACTION59chain 'H' and (resid 9 through 17 )
60X-RAY DIFFRACTION60chain 'H' and (resid 18 through 28 )
61X-RAY DIFFRACTION61chain 'H' and (resid 29 through 37 )
62X-RAY DIFFRACTION62chain 'H' and (resid 38 through 44 )
63X-RAY DIFFRACTION63chain 'H' and (resid 45 through 56 )
64X-RAY DIFFRACTION64chain 'H' and (resid 57 through 61 )
65X-RAY DIFFRACTION65chain 'H' and (resid 62 through 77 )
66X-RAY DIFFRACTION66chain 'H' and (resid 78 through 85 )
67X-RAY DIFFRACTION67chain 'H' and (resid 86 through 92 )
68X-RAY DIFFRACTION68chain 'H' and (resid 93 through 98 )
69X-RAY DIFFRACTION69chain 'H' and (resid 99 through 111 )

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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