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- PDB-1cov: COXSACKIEVIRUS B3 COAT PROTEIN -

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基本情報

登録情報
データベース: PDB / ID: 1cov
タイトルCOXSACKIEVIRUS B3 COAT PROTEIN
要素(COXSACKIEVIRUS COAT ...) x 4
キーワードVIRUS / COXSACKIEVIRUS B3 / Icosahedral virus
機能・相同性
機能・相同性情報


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
類似検索 - 分子機能
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A ...Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Few Secondary Structures / Irregular / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
類似検索 - ドメイン・相同性
MYRISTIC ACID / PALMITIC ACID / Genome polyprotein
類似検索 - 構成要素
生物種Human coxsackievirus B3 (コクサッキーウイルス)
手法X線回折 / 解像度: 3.5 Å
データ登録者Muckelbauer, J.K. / Rossmann, M.G.
引用
ジャーナル: Acta Crystallogr.,Sect.D / 年: 1995
タイトル: Structure determination of coxsackievirus B3 to 3.5 A resolution.
著者: Muckelbauer, J.K. / Kremer, M. / Minor, I. / Tong, L. / Zlotnick, A. / Johnson, J.E. / Rossmann, M.G.
#1: ジャーナル: Structure / 年: 1995
タイトル: The Structure of Coxsackievirus B3 at 3.5 Angstroms Resolution
著者: Muckelbauer, J.K. / Kremer, M. / Minor, I. / Diana, G. / Dutko, F.J. / Groarke, J. / Pevear, D.C. / Rossmann, M.G.
履歴
登録1994年10月19日処理サイト: BNL
改定 1.01996年3月8日Provider: repository / タイプ: Initial release
改定 1.12008年3月24日Group: Version format compliance
改定 1.22011年7月13日Group: Version format compliance
改定 1.32011年8月10日Group: Advisory
改定 2.02023年4月19日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
カテゴリ: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_ref_seq_dif / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_database_status.process_site / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
詳細: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / タイプ: Remediation

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
1: COXSACKIEVIRUS COAT PROTEIN
2: COXSACKIEVIRUS COAT PROTEIN
3: COXSACKIEVIRUS COAT PROTEIN
4: COXSACKIEVIRUS COAT PROTEIN
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,3206
ポリマ－93,8354
非ポリマー4852
水00
1
1: COXSACKIEVIRUS COAT PROTEIN
2: COXSACKIEVIRUS COAT PROTEIN
3: COXSACKIEVIRUS COAT PROTEIN
4: COXSACKIEVIRUS COAT PROTEIN
ヘテロ分子
x 60


分子量 (理論値)分子数
合計 (水以外)5,659,212360
ポリマ－5,630,125240
非ポリマー29,088120
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
point symmetry operation59
2


  • 登録構造と同一
  • icosahedral asymmetric unit
タイプ名称対称操作数
identity operation1_555x,y,z1
3
1: COXSACKIEVIRUS COAT PROTEIN
2: COXSACKIEVIRUS COAT PROTEIN
3: COXSACKIEVIRUS COAT PROTEIN
4: COXSACKIEVIRUS COAT PROTEIN
ヘテロ分子
x 5


  • icosahedral pentamer
  • 472 kDa, 20 ポリマー
分子量 (理論値)分子数
合計 (水以外)471,60130
ポリマ－469,17720
非ポリマー2,42410
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
point symmetry operation4
4
1: COXSACKIEVIRUS COAT PROTEIN
2: COXSACKIEVIRUS COAT PROTEIN
3: COXSACKIEVIRUS COAT PROTEIN
4: COXSACKIEVIRUS COAT PROTEIN
ヘテロ分子
x 6


  • icosahedral 23 hexamer
  • 566 kDa, 24 ポリマー
分子量 (理論値)分子数
合計 (水以外)565,92136
ポリマ－563,01224
非ポリマー2,90912
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
point symmetry operation5
5


  • 登録構造と同一（異なる座標系）
  • icosahedral asymmetric unit, std point frame
タイプ名称対称操作数
transform to point frame1
6
1: COXSACKIEVIRUS COAT PROTEIN
2: COXSACKIEVIRUS COAT PROTEIN
3: COXSACKIEVIRUS COAT PROTEIN
4: COXSACKIEVIRUS COAT PROTEIN
ヘテロ分子
x 120


  • crystal asymmetric unit
  • 11.3 MDa, 480 ポリマー
分子量 (理論値)分子数
合計 (水以外)11,318,424720
ポリマ－11,260,249480
非ポリマー58,175240
水0
タイプ名称対称操作数
identity operation1_555x,y,z2
transform to crystal frame1
point symmetry operation59
単位格子
Length a, b, c (Å)574.620, 302.070, 521.610
Angle α, β, γ (deg.)90.00, 107.70, 90.00
Int Tables number4
Space group name H-MP1211
対称性点対称性: (ヘルマン・モーガン記号: 532 / シェーンフリース記号: I (正20面体型対称))
非結晶学的対称性 (NCS)NCS oper:
IDCodeMatrixベクター
1given(1), (1), (1)
2generate(0.80122195, -0.36352299, 0.47528059), (-0.25875514, 0.5056995, 0.82299516), (-0.53952347, -0.7823803, 0.31111254)-67.12188, -112.73127, 63.41869
3generate(0.47959502, -0.84694618, 0.22949333), (-0.78219784, -0.29409977, 0.54925105), (-0.39768565, -0.44292845, -0.80352922)-49.77931, -100.17801, 207.56159
4generate(0.47959669, -0.78219513, -0.39769215), (-0.8469481, -0.2941024, -0.44292725), (0.22949843, 0.54924462, -0.80352826)28.06085, 20.3116, 233.22812
5generate(0.80122465, -0.25875361, -0.53952682), (-0.36352324, 0.50569523, -0.78238307), (0.47528167, 0.82298947, 0.31111409)58.82616, 82.22501, 104.948
6generate(0.18614395, -0.49152027, -0.8507427), (-0.49152075, -0.79632117, 0.35253537), (-0.85073666, 0.35253252, -0.38982277)72.89507, -64.72146, 139.0267
7generate(0.73532168, 0.34937518, -0.58072492), (-0.37796613, -0.49983685, -0.77930057), (-0.56252996, 0.79252752, -0.23548482)61.85746, 80.39797, 131.66626
8generate(0.81206797, 0.36372025, 0.4563474), (0.24695154, 0.49434155, -0.83345345), (-0.52873232, 0.78951203, 0.31162446)-63.71303, 112.69279, 65.14755
9generate(0.31032207, -0.46830946, 0.82727555), (0.51961729, 0.81229327, 0.26491416), (-0.79605095, 0.34765336, 0.49541865)-130.28225, -12.46734, 31.39717
10generate(-0.07652026, -0.99687716, 0.01944943), (0.06321631, 0.01461984, 0.99789556), (-0.99506058, 0.07758517, 0.06190042)-45.8538, -122.11537, 77.057
11generate(-0.74179673, -0.35819657, 0.56695251), (-0.35819667, -0.50308599, -0.78651407), (0.56694834, -0.78650806, 0.24488271)-139.51178, 82.07164, 115.38917
12generate(-0.80754281, -0.35505214, -0.47096959), (0.26752386, 0.49115552, -0.82897565), (0.52564448, -0.79542691, -0.30164669)-13.38566, 112.9483, 181.52872
13generate(-0.30105031, 0.48248803, -0.82254016), (0.5345088, 0.79970025, 0.27346279), (0.78972417, -0.35732842, -0.49864995)50.97534, -12.94954, 216.78593
14generate(0.07772536, 0.99697188, -0.00190061), (0.07379404, -0.00385013, 0.9972688), (0.99423825, -0.0776498, -0.07387523)-35.37351, -121.63535, 172.43652
15generate(-0.19467091, 0.47740023, 0.85685308), (-0.47792828, -0.8090163, 0.34216707), (0.85655522, -0.34289742, 0.38565322)-153.10102, -62.90903, 109.76988
16generate(-0.44434722, 0.84971683, 0.28379019), (0.84971743, 0.29940715, 0.4339787), (0.28378832, 0.43397554, -0.85505994)-91.58057, -20.82514, 241.66609
17generate(-0.72900082, 0.36919995, 0.57641392), (0.36919741, -0.49701817, 0.78528106), (0.57640895, 0.78527968, 0.22601898)-139.5472, -84.08995, 119.46829
18generate(-0.99061268, 0.00073789, 0.13669943), (0.0007375, -0.99994203, 0.01073961), (0.1366938, 0.01074484, 0.9905547)-95.68027, -3.04019, 6.58689
19generate(-0.86764411, 0.2535327, -0.42768279), (0.25353677, -0.51434074, -0.8192557), (-0.42768573, -0.81924818, 0.38198485)-20.60237, 110.31613, 59.02015
20generate(-0.53003349, 0.77823054, -0.3367757), (0.77823521, 0.28870122, -0.55767955), (-0.33677631, -0.55767722, -0.75866774)-18.06862, 99.32443, 204.30708
21generate(-0.31860356, -0.50527421, 0.80199181), (-0.4726733, 0.81807081, 0.32763231), (-0.8216258, -0.27469899, -0.49946725)-152.05224, -59.48508, 153.23128
22generate(-0.55722328, -0.76715979, -0.3177546), (-0.76716158, 0.32919255, 0.55054639), (-0.31775055, 0.55053808, -0.77196926)-22.8455, -99.20251, 207.67195
23generate(-0.07651692, 0.06321609, -0.99506365), (-0.99687965, 0.01461673, 0.07758875), (0.01945228, 0.99789, 0.06190019)80.88769, -49.90455, 117.97983
24generate(0.45919567, 0.8383022, -0.29391724), (-0.84436497, 0.30907645, -0.43762922), (-0.27602017, 0.44913164, 0.84976185)15.79158, 20.2807, 8.10638
25generate(0.30957791, 0.48695587, 0.81672411), (-0.52038763, 0.80563837, -0.2830938), (-0.79583502, -0.33737161, 0.5028177)-128.17321, 14.35961, 29.89297
26generate(-0.49323721, 0.84168885, -0.21971205), (-0.76881287, -0.30361755, 0.56280373), (0.40699469, 0.44651591, 0.79685476)-31.07651, -101.33773, 41.67844
27generate(-0.49444398, 0.77684308, 0.3899246), (-0.84107297, -0.31438464, -0.44018232), (-0.21936706, -0.54559253, 0.80882862)-106.78801, 20.1859, 14.55937
28generate(-0.80754498, 0.26752159, 0.52564889), (-0.3550488, 0.49115519, -0.79542893), (-0.47096886, -0.82897247, -0.30164419)-136.446, 84.16549, 142.08389
29generate(-0.99984528, 0.01758937, -0.00010552), (0.01759077, 0.99977326, -0.01199737), (-0.00010558, -0.01200248, -0.99992798)-79.06415, 2.18343, 248.01745
30generate(-0.80559238, 0.37244424, -0.46076392), (-0.23812949, 0.5085767, 0.82743657), (0.54250574, 0.7762927, -0.32101829)-13.94223, -112.46387, 185.96347
31generate(0.87201455, -0.26245396, 0.41316613), (0.24334786, -0.49993546, -0.83117603), (0.42470346, 0.82533578, -0.37207909)-56.53081, 111.40405, 187.67966
32generate(0.54367568, -0.77297321, 0.32699442), (0.7727755, 0.3090161, -0.55437523), (0.32746727, 0.55408976, 0.76534219)-59.27284, 98.71635, 42.53484
33generate(0.45919451, -0.84436478, -0.27602265), (0.83830364, 0.30907989, 0.44913087), (-0.29391969, -0.43762763, 0.84975958)12.11044, -23.14732, 6.62838
34generate(0.73532114, -0.37796793, -0.56253599), (0.34937462, -0.49983226, 0.79253095), (-0.58072176, -0.77929667, -0.23548888)58.96976, -85.77551, 129.58178
35generate(0.99045795, -0.01832726, -0.13659391), (-0.01832827, -0.99983123, 0.00125776), (-0.13658822, 0.00125764, -0.99062672)16.54714, -2.61819, 241.47762
36generate(-0.06017378, -0.07396069, -0.99544588), (0.99813832, -0.0145178, -0.05926001), (-0.01007236, -0.99715269, 0.07469158)81.46228, 45.94379, 113.49258
37generate(0.50799158, 0.76328993, -0.39916442), (0.83545904, -0.32382402, 0.44401116), (0.20965033, -0.55903531, -0.80220155)30.70907, -23.1747, 231.31579
38generate(0.42486739, 0.51362709, 0.7454374), (0.51362481, -0.81485181, 0.26870931), (0.74543628, 0.2687101, -0.61001558)-114.74941, -14.58858, 229.38986
39generate(-0.19467154, -0.47792364, 0.85655876), (0.47739958, -0.80901745, -0.34290436), (0.85684751, 0.34216751, 0.38565501)-153.89448, 59.83643, 110.37636
40generate(-0.49444348, -0.84107286, -0.21936628), (0.77684539, -0.31438384, -0.54560054), (0.38991751, -0.44017873, 0.80882731)-32.62898, 97.24749, 38.7479
41generate(-0.31859932, -0.47267426, -0.82163024), (-0.505276, 0.81806922, -0.2746953), (0.80199096, 0.32762625, -0.4994699)49.33865, 13.92647, 217.96781
42generate(0.31032694, 0.51961436, -0.79605217), (-0.46831327, 0.81229283, 0.34765798), (0.82727353, 0.26491368, 0.49541421)71.90209, -61.80125, 95.52722
43generate(0.54367671, 0.77277329, 0.32747066), (-0.77297745, 0.30901797, 0.55409361), (0.32699433, -0.55436856, 0.7653393)-57.98901, -99.88998, 41.55354
44generate(0.05896855, -0.06305452, 0.99626789), (-0.99823301, 0.00375338, 0.05932458), (-0.00747777, -0.99800027, -0.06272193)-160.82956, -47.70238, 130.63655
45generate(-0.47394734, -0.83278343, 0.28608447), (-0.8327844, 0.31836435, -0.45289514), (0.28608629, -0.45289749, -0.84441701)-94.49742, 22.64006, 239.66657
46generate(0.87201486, 0.24334716, 0.42470183), (-0.2624587, -0.49993147, 0.82534068), (0.41316802, -0.83116991, -0.37208339)-57.52205, -114.04227, 185.7849
47generate(0.4065735, -0.52621526, 0.74685534), (-0.52621851, -0.80313562, -0.27940886), (0.74685649, -0.27940757, -0.60343788)-116.55212, 12.27438, 228.15409
48generate(0.05897053, -0.99823053, -0.00748006), (-0.06305471, 0.00375124, -0.99800578), (0.99626487, 0.05932213, -0.06272178)-37.1566, 120.41391, 171.25241
49generate(0.30958142, -0.52038957, -0.79583848), (0.48695607, 0.8056389, -0.33737353), (0.81671924, -0.28309374, 0.50281365)70.94261, 60.93116, 93.71605
50generate(0.81207045, 0.24694763, -0.52873538), (0.36371764, 0.49434586, 0.78951655), (0.45634558, -0.83344809, 0.31161766)58.35607, -83.97073, 102.69762
51generate(-0.06017562, 0.9981358, -0.01006877), (-0.07395564, -0.01452096, -0.99715858), (-0.99544254, -0.05925749, 0.07469659)-39.81337, 119.86185, 75.33603
52generate(-0.30105446, 0.53450961, 0.7897281), (0.48249296, 0.79969857, -0.3573289), (-0.8225378, 0.27345864, -0.49864411)-148.93394, 63.22436, 153.56933
53generate(-0.8055954, -0.23812625, 0.54250779), (0.37244517, 0.50857697, 0.77629809), (-0.46076396, 0.82742863, -0.32101555)-138.89902, -81.97384, 146.32892
54generate(-0.87654002, -0.25201527, -0.41007963), (-0.2520167, -0.4855656, 0.83708841), (-0.41008018, 0.83708479, 0.36210562)-23.57654, -115.07377, 63.62079
55generate(-0.41584526, 0.51203669, -0.75159072), (-0.52790758, -0.8088579, -0.25896808), (-0.74052972, 0.28908263, 0.60666918)37.66176, 9.66754, 19.74477
56generate(-0.49323991, -0.7688087, 0.40699719), (0.84169034, -0.30361678, 0.44651319), (-0.21971644, 0.56280116, 0.7968567)-110.20051, -23.22101, 16.99322
57generate(-0.41584598, -0.5279087, -0.74053127), (0.51203882, -0.80885577, 0.28907979), (-0.75159222, -0.25896474, 0.60666778)35.38669, -17.17246, 18.83132
58generate(0.20294816, 0.46358349, -0.86249839), (0.46358699, -0.82134618, -0.33238592), (-0.86249524, -0.33238219, -0.38160197)75.84735, 57.97494, 136.9471
59generate(0.50799005, 0.83545936, 0.20965022), (0.76329363, -0.32382669, -0.55903946), (-0.39916129, 0.44400921, -0.80219734)-44.73379, 98.37003, 208.10857
60generate(0.07772215, 0.07379911, 0.99424164), (0.99697434, -0.00385232, -0.07765333), (-0.00190215, 0.99726295, -0.07386984)-159.71768, 48.18817, 133.973
61generate(0.99973361, -0.00041514, -0.02320947), (0.00041031, 0.99999739, -0.00048809), (0.02319826, 0.00048554, 0.99973175)210.61915, 0.10145, 249.81899
62generate(0.81363798, -0.34547746, 0.46759156), (-0.25816237, 0.5059309, 0.82303617), (-0.52091743, -0.79035799, 0.32245436)142.09004, -112.68802, 311.60882
63generate(0.48902205, -0.83631833, 0.24785366), (-0.78180491, -0.29423032, 0.54973598), (-0.38683299, -0.46260011, -0.79772315)156.07729, -100.19804, 456.12147
64generate(0.474494, -0.79461234, -0.37875286), (-0.84686112, -0.29469066, -0.44269707), (0.24015145, 0.53080892, -0.81275354)233.251, 20.31067, 483.64536
65generate(0.79013109, -0.27799577, -0.54627909), (-0.36342552, 0.50518605, -0.78275426), (0.49356469, 0.8170116, 0.29813468)266.95972, 82.29916, 356.14342
66generate(0.20604355, -0.49924083, -0.84161484), (-0.49102785, -0.79669283, 0.35237565), (-0.84642889, 0.34064889, -0.40928278)280.29494, -64.65779, 390.46801
67generate(0.74833872, 0.33109547, -0.57478122), (-0.37738887, -0.50007902, -0.77942187), (-0.54550439, 0.80017714, -0.24927184)269.37085, 80.46032, 382.92394
68generate(0.82402071, 0.34509398, 0.4493392), (0.24754217, 0.49410414, -0.83341613), (-0.50963202, 0.79797794, 0.32172267)145.36427, 112.736, 313.52574
69generate(0.3284996, -0.47659077, 0.81544679), (0.52013181, 0.81192931, 0.26501109), (-0.78838618, 0.33709054, 0.51460573)79.64807, -12.43464, 278.17936
70generate(-0.05343129, -0.99841837, 0.01759331), (0.06367043, 0.01417291, 0.99787072), (-0.9965381, 0.05444564, 0.06281952)163.03981, -122.07003, 325.7323
71generate(-0.75460899, -0.33963786, 0.5614444), (-0.35877683, -0.50284775, -0.78639892), (0.54941395, -0.79485088, 0.25758745)68.43234, 82.05931, 361.98062
72generate(-0.81963867, -0.33670001, -0.46349893), (0.26693525, 0.4913968, -0.8290195), (0.50689978, -0.80321166, -0.31289395)192.97699, 112.95536, 431.04333
73generate(-0.31952108, 0.49032092, -0.81086117), (0.53399842, 0.80007054, 0.27336797), (0.78278801, -0.3456514, -0.51746491)256.5548, -12.93295, 467.72301
74generate(0.05459827, 0.99851011, -0.0005995), (0.07334046, -0.00340314, 0.99730147), (0.99581047, -0.05450283, -0.0734153)171.3034, -121.63226, 421.32959
75generate(-0.21430083, 0.48556737, 0.84753197), (-0.47842499, -0.80865094, 0.34232952), (0.85157737, -0.33212339, 0.40559341)55.03733, -62.92381, 355.97719
76generate(-0.45116817, 0.83929384, 0.30337992), (0.84939437, 0.2995432, 0.43451136), (0.27381668, 0.45371645, -0.84803642)113.46269, -20.87917, 489.28563
77generate(-0.74233803, 0.351082, 0.57068859), (0.36861599, -0.49724867, 0.7854052), (0.55952204, 0.79339251, 0.23971143)68.37124, -84.10386, 365.97715
78generate(-0.99352168, 0.00090343, 0.11366831), (0.00026432, -0.99994436, 0.01031218), (0.113677, 0.01027356, 0.99346539)114.81276, -2.98121, 254.18302
79generate(-0.85759187, 0.272693, -0.43609442), (0.25338885, -0.5138355, -0.81961549), (-0.44757574, -0.81339663, 0.37156311)188.60665, 110.38003, 308.39893
80generate(-0.52239897, 0.79084676, -0.31884619), (0.77818008, 0.28929198, -0.55744598), (-0.34860397, -0.53933385, -0.76654761)187.77226, 99.31849, 453.70033
81generate(-0.29925296, -0.4991036, 0.81323452), (-0.47240176, 0.81799543, 0.3282043), (-0.82902595, -0.28594958, -0.48056937)55.07569, -59.52065, 399.45293
82generate(-0.54938154, -0.77986978, -0.29998151), (-0.76723311, 0.3286082, 0.55079137), (-0.33096441, 0.53275346, -0.77886623)183.00096, -99.21154, 456.85709
83generate(-0.07653417, 0.04003269, -0.99626745), (-0.99691794, 0.01415557, 0.07715005), (0.01718798, 0.99909592, 0.03883751)288.76776, -49.82737, 369.61939
84generate(0.46583016, 0.82752647, -0.31337979), (-0.84403963, 0.30920039, -0.43816344), (-0.26570356, 0.46860838, 0.84250305)226.20997, 20.38462, 258.29937
85generate(0.32818238, 0.49432191, 0.80495393), (-0.5198708, 0.80600074, -0.28300337), (-0.78869254, -0.32559341, 0.52149195)81.78033, 14.39384, 276.73751
86generate(-0.50223278, 0.83122727, -0.23838174), (-0.7692119, -0.30348935, 0.56232317), (0.39506999, 0.46577443, 0.79181733)178.62566, -101.26911, 290.71612
87generate(-0.48887171, 0.78942956, 0.37123098), (-0.84116658, -0.31379877, -0.44041596), (-0.23118682, -0.52757741, 0.8174435)103.5133, 20.23638, 261.90696
88generate(-0.79625152, 0.28648644, 0.53284008), (-0.35514934, 0.49166829, -0.79506394), (-0.48974855, -0.82230559, -0.28975534)70.87687, 84.14139, 388.74032
89generate(-0.99958377, 0.01744821, 0.02310729), (0.01718053, 0.99978373, -0.01150932), (-0.02329168, -0.01110579, -0.99966803)125.8188, 2.13137, 495.93681
90generate(-0.81787019, 0.35411656, -0.45353401), (-0.23872421, 0.50834928, 0.82740204), (0.52355625, 0.78497145, -0.33121935)192.41122, -112.45861, 435.35453
91generate(0.86182408, -0.2813321, 0.42203687), (0.24349772, -0.50044468, -0.83082272), (0.44493691, 0.81878317, -0.36279811)149.70121, 111.3904, 436.19097
92generate(0.5356097, -0.78575571, 0.30937427), (0.77283673, 0.30842769, -0.55461318), (0.34036697, 0.53615953, 0.77245342)150.33391, 98.77246, 291.01532
93generate(0.46554588, -0.83411105, -0.29585804), (0.83863333, 0.30894623, 0.44860168), (-0.28278131, -0.45694796, 0.84334646)222.58214, -23.04408, 256.71529
94generate(0.74845846, -0.35957268, -0.55724958), (0.34995887, -0.49960567, 0.792413), (-0.56333818, -0.78809851, -0.24809077)266.60129, -85.71289, 380.69235
95generate(0.99337185, -0.01793649, -0.11356612), (-0.01785516, -0.99983676, 0.00168523), (-0.11358358, 0.00034669, -0.99352911)221.5584, -2.62781, 491.61443
96generate(-0.06033834, -0.05079157, -0.99688965), (0.99811594, -0.0140614, -0.05970475), (-0.01098095, -0.99860801, 0.05155015)289.40656, 46.02315, 365.19321
97generate(0.50264355, 0.77619594, -0.38062374), (0.83556296, -0.32323712, 0.44423777), (0.22178426, -0.54133558, -0.81103069)235.96095, -23.1735, 481.77387
98generate(0.40723981, 0.50759192, 0.7592854), (0.51343395, -0.81477009, 0.26931222), (0.75534188, 0.28015764, -0.59242863)90.58235, -14.64614, 476.47824
99generate(-0.21470485, -0.485402, 0.84752208), (0.47690023, -0.80937845, -0.34274024), (0.85233342, 0.33059592, 0.40525574)54.17906, 59.8207, 356.6247
100generate(-0.50368404, -0.83050197, -0.23785379), (0.77645017, -0.31451327, -0.54608391), (0.37871987, -0.45972472, 0.80325651)177.05917, 97.31639, 287.84677
101generate(-0.33691847, -0.48049199, -0.8097049), (-0.50579685, 0.81771322, -0.27478792), (0.79413955, 0.31697034, -0.51852968)254.87996, 13.94174, 468.87966
102generate(0.29123811, 0.51299022, -0.80748274), (-0.4685885, 0.81237461, 0.34708863), (0.83402328, 0.27729116, 0.47698309)280.31061, -61.71677, 346.95858
103generate(0.53626341, 0.78530574, 0.30939028), (-0.77291196, 0.30960482, 0.55385297), (0.33914366, -0.53614282, 0.77299978)151.72263, -99.83234, 289.96763
104generate(0.0595408, -0.03987622, 0.99743361), (-0.99820255, 0.00421462, 0.05976382), (-0.00659248, -0.99919349, -0.03956462)46.82023, -47.73056, 376.66637
105generate(-0.48011527, -0.82218224, 0.30579475), (-0.83311633, 0.31824288, -0.45236441), (0.27461045, -0.47194055, -0.83777373)110.57497, 22.58569, 487.24008
106generate(0.8623021, 0.26278089, 0.43288191), (-0.26230188, -0.49942462, 0.8256944), (0.43315898, -0.82554446, -0.3617305)148.8478, -114.05481, 434.16426
107generate(0.38934951, -0.51925677, 0.76077784), (-0.52641485, -0.80321306, -0.27880716), (0.75583245, -0.29192985, -0.58608592)88.79765, 12.21662, 475.21402
108generate(0.03585822, -0.999343, -0.00560801), (-0.06351662, 0.00331269, -0.99797563), (0.99733502, 0.03615082, -0.06336304)169.44779, 120.41622, 420.22195
109generate(0.29034118, -0.51401494, -0.80715646), (0.48668319, 0.80556145, -0.33794462), (0.82391834, -0.29469876, 0.4840529)279.34247, 61.01582, 345.18523
110generate(0.80111159, 0.26602051, -0.53615477), (0.36382715, 0.4948527, 0.78914544), (0.47523838, -0.82725574, 0.29965167)266.61098, -83.89524, 353.80205
111generate(-0.0370252, 0.99925126, -0.01138579), (-0.07349426, -0.01408246, -0.99719656), (-0.99660739, -0.03609363, 0.07395882)169.01812, 119.90987, 324.2694
112generate(-0.2820839, 0.5276884, 0.80123933), (0.48276965, 0.79978232, -0.35676055), (-0.82906683, 0.28617326, -0.48036352)58.13438, 63.18958, 399.92281
113generate(-0.79484132, -0.25747812, 0.5494916), (0.37233855, 0.50807407, 0.77667534), (-0.47914794, 0.82192949, -0.30796728)68.39495, -82.00059, 392.84663
114generate(-0.86668415, -0.27117485, -0.41872218), (-0.25217554, -0.48607631, 0.83674122), (-0.43042674, 0.83077817, 0.35290179)185.62006, -115.01275, 312.8199
115generate(-0.39832802, 0.50552662, -0.76536347), (-0.52771538, -0.80878679, -0.2595719), (-0.75023428, 0.30049071, 0.5889451)247.8086, 9.77478, 270.43684
116generate(-0.48835844, -0.78154016, 0.38820878), (0.841593, -0.30420614, 0.44629008), (-0.23069114, 0.54466775, 0.80630137)100.06324, -23.17301, 264.23992
117generate(-0.39850372, -0.52142185, -0.75453444), (0.5122337, -0.80894387, 0.28847907), (-0.7607889, -0.27153456, 0.58946636)245.56648, -17.06563, 269.45783
118generate(0.2227197, 0.47151538, -0.85327386), (0.46409003, -0.82099159, -0.33255269), (-0.85733074, -0.32193749, -0.40166946)283.24376, 58.04051, 388.51703
119generate(0.51680217, 0.82506602, 0.22844503), (0.7636949, -0.32369976, -0.55856043), (-0.38689912, 0.46311408, -0.79739007)161.02636, 98.35129, 456.88175
120generate(0.07733171, 0.05063511, 0.99572349), (0.99700456, -0.00430879, -0.07720912), (0.00038545, 0.99870558, -0.05082305)47.81457, 48.15857, 380.07427

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要素

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COXSACKIEVIRUS COAT ... , 4種, 4分子 1234

#1: タンパク質 COXSACKIEVIRUS COAT PROTEIN


分子量: 31380.068 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: ISOLATED FROM HUMAN HELA CELLS
由来: (天然) Human coxsackievirus B3 (コクサッキーウイルス)
属: Enterovirus / 生物種: Human enterovirus B / 株: GAUNTT / 参照: UniProt: Q66282
#2: タンパク質 COXSACKIEVIRUS COAT PROTEIN


分子量: 28877.592 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: ISOLATED FROM HUMAN HELA CELLS
由来: (天然) Human coxsackievirus B3 (コクサッキーウイルス)
属: Enterovirus / 生物種: Human enterovirus B / 株: GAUNTT / 参照: UniProt: Q66282
#3: タンパク質 COXSACKIEVIRUS COAT PROTEIN


分子量: 26198.684 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: ISOLATED FROM HUMAN HELA CELLS
由来: (天然) Human coxsackievirus B3 (コクサッキーウイルス)
属: Enterovirus / 生物種: Human enterovirus B / 株: GAUNTT / 参照: UniProt: Q66282
#4: タンパク質 COXSACKIEVIRUS COAT PROTEIN


分子量: 7379.065 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: ISOLATED FROM HUMAN HELA CELLS
由来: (天然) Human coxsackievirus B3 (コクサッキーウイルス)
属: Enterovirus / 生物種: Human enterovirus B / 株: GAUNTT / 参照: UniProt: Q66282

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非ポリマー , 2種, 2分子

#5: 化合物 ChemComp-PLM / PALMITIC ACID / パルミチン酸


分子量: 256.424 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C16H32O2
#6: 化合物 ChemComp-MYR / MYRISTIC ACID / ミリスチン酸


分子量: 228.371 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C14H28O2

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実験情報

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実験

実験手法: X線回折

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試料調製

結晶
*PLUS
溶媒含有率: 49 %
結晶化
*PLUS
手法: 蒸気拡散法, シッティングドロップ法 / pH: 6
溶液の組成
*PLUS
ID濃度一般名Crystal-IDSol-ID化学式
15 mg/mlvirus1drop
250 mMMES1drop
30.75 M1dropNaCl
42 Mammonium sulfate1reservoir

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データ収集

放射散乱光タイプ: x-ray
放射波長相対比: 1
反射解像度: 3→30 Å / Num. obs: 185662 / % possible obs: 55 % / Observed criterion σ(F): 3
反射
*PLUS
Num. all: 3345935 / Num. obs: 1856628 / Num. measured all: 3113647 / Rmerge(I) obs: 0.128
反射 シェル
*PLUS
最高解像度: 3 Å / 最低解像度: 3.5 Å / % possible obs: 44 %

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解析

ソフトウェア
名称分類
X-PLORモデル構築
X-PLOR精密化
X-PLOR位相決定
精密化解像度: 3.5→10 Å / σ(F): 3 /
Rfactor反射数%反射
Rwork0.264 --
obs0.264 125208 55 %
原子変位パラメータBiso mean: 18 Å2
精密化ステップサイクル: LAST / 解像度: 3.5→10 Å
タンパク質核酸リガンド溶媒全体
原子数6376 0 33 0 6409
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
精密化
*PLUS
Num. reflection obs: 1252081
溶媒の処理
*PLUS
原子変位パラメータ
*PLUS

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万見について

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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

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