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- PDB-1nov: NODAMURA VIRUS -

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基本情報

登録情報
データベース: PDB / ID: 1nov
タイトルNODAMURA VIRUS
要素(NODAMURA VIRUS COAT PROTEINS) x 2
キーワードVIRUS / INSECT VIRUS / NODAMURA VIRUS / COAT PROTEIN / Icosahedral virus
機能・相同性
機能・相同性情報


nodavirus endopeptidase / symbiont entry into host cell via permeabilization of host membrane / T=3 icosahedral viral capsid / aspartic-type endopeptidase activity / proteolysis / metal ion binding
類似検索 - 分子機能
Peptidase A6, nodavirus coat protein / Peptidase A6 family / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Capsid protein alpha
類似検索 - 構成要素
生物種Nodamura virus (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.5 Å
データ登録者Natarajan, P. / Johnson, J.E.
引用
ジャーナル: Acta Crystallogr.,Sect.D / 年: 1997
タイトル: Resolution of space-group ambiguity and structure determination of nodamura virus to 3.3 A resolution from pseudo-R32 (monoclinic) crystals.
著者: Zlotnick, A. / Natarajan, P. / Munshi, S. / Johnson, J.E.
#1: ジャーナル: J.Mol.Biol. / 年: 1994
タイトル: The Refined Three-Dimensional Structure of an Insect Virus at 2.8 A Resolution
著者: Wery, J.P. / Reddy, V.S. / Hosur, M.V. / Johnson, J.E.
#2: ジャーナル: Nature / 年: 1993
タイトル: Ordered Duplex RNA Controls Capsid Architecture in an Icosahedral Animal Virus
著者: Fisher, A.J. / Johnson, J.E.
#3: ジャーナル: Acta Crystallogr.,Sect.D / 年: 1993
タイトル: A Monoclinic Crystal with R32 Pseudo-Symmetry: A Preliminary Report of Nodamura Virus Structure Determination
著者: Zlotnick, A. / Mckinney, B.R. / Munshi, S. / Bibler, J. / Rossmann, M.G. / Johnson, J.E.
#4: ジャーナル: J.Mol.Biol. / 年: 1990
タイトル: Structural Homology Among Four Nodaviruses as Deduced by Sequencing and X-Ray Crystallography
著者: Kaesberg, P. / Dasgupta, R. / Sgro, J.Y. / Wery, J.P. / Selling, B.H. / Hosur, M.V. / Johnson, J.E.
履歴
登録1997年9月16日処理サイト: BNL
改定 1.01998年1月14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11月30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_torsion / struct_ncs_oper
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_torsion.phi / _pdbx_validate_torsion.psi
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
改定 2.12024年4月3日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 2.22024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: NODAMURA VIRUS COAT PROTEINS
D: NODAMURA VIRUS COAT PROTEINS
B: NODAMURA VIRUS COAT PROTEINS
E: NODAMURA VIRUS COAT PROTEINS
C: NODAMURA VIRUS COAT PROTEINS
F: NODAMURA VIRUS COAT PROTEINS


分子量 (理論値)分子数
合計 (水以外)129,3816
ポリマ－129,3816
非ポリマー00
水00
1
A: NODAMURA VIRUS COAT PROTEINS
D: NODAMURA VIRUS COAT PROTEINS
B: NODAMURA VIRUS COAT PROTEINS
E: NODAMURA VIRUS COAT PROTEINS
C: NODAMURA VIRUS COAT PROTEINS
F: NODAMURA VIRUS COAT PROTEINS
x 60


分子量 (理論値)分子数
合計 (水以外)7,762,876360
ポリマ－7,762,876360
非ポリマー00
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
A: NODAMURA VIRUS COAT PROTEINS
D: NODAMURA VIRUS COAT PROTEINS
B: NODAMURA VIRUS COAT PROTEINS
E: NODAMURA VIRUS COAT PROTEINS
C: NODAMURA VIRUS COAT PROTEINS
F: NODAMURA VIRUS COAT PROTEINS
x 5


  • icosahedral pentamer
  • 647 kDa, 30 ポリマー
分子量 (理論値)分子数
合計 (水以外)646,90630
ポリマ－646,90630
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
point symmetry operation4
4
A: NODAMURA VIRUS COAT PROTEINS
D: NODAMURA VIRUS COAT PROTEINS
B: NODAMURA VIRUS COAT PROTEINS
E: NODAMURA VIRUS COAT PROTEINS
C: NODAMURA VIRUS COAT PROTEINS
F: NODAMURA VIRUS COAT PROTEINS
x 6


  • icosahedral 23 hexamer
  • 776 kDa, 36 ポリマー
分子量 (理論値)分子数
合計 (水以外)776,28836
ポリマ－776,28836
非ポリマー00
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
A: NODAMURA VIRUS COAT PROTEINS
D: NODAMURA VIRUS COAT PROTEINS
B: NODAMURA VIRUS COAT PROTEINS
E: NODAMURA VIRUS COAT PROTEINS
C: NODAMURA VIRUS COAT PROTEINS
F: NODAMURA VIRUS COAT PROTEINS
x 120


  • crystal asymmetric unit, crystal frame
  • 720-MERIC
  • 15.5 MDa, 720 ポリマー
分子量 (理論値)分子数
合計 (水以外)15,525,753720
ポリマ－15,525,753720
非ポリマー00
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)562.090, 354.130, 612.770
Angle α, β, γ (deg.)90.00, 110.89, 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(0.5238201, -0.78411975, 0.33282045), (0.79468963, 0.30914847, -0.52239253), (0.30673452, 0.538133, 0.7850654)66.81918, -111.38984, -43.04407
3generate(-0.24665681, -0.47404544, 0.84524217), (0.50171567, -0.80867572, -0.3071202), (0.8291291, 0.348316, 0.43729856)174.83743, -70.23942, -116.28329
4generate(-0.24665784, 0.50171075, 0.82911576), (-0.47404183, -0.80867755, 0.34831796), (0.84525217, -0.30713036, 0.43730141)174.7772, 66.58277, -118.50353
5generate(0.52381843, 0.79468695, 0.30672737), (-0.78411917, 0.30914552, 0.53812868), (0.3328222, -0.52240148, 0.78507003)66.72173, 109.99312, -46.63651
6generate(0.38229875, -0.48973967, 0.78358056), (-0.4897363, -0.82648953, -0.27761571), (0.78358806, -0.27762028, -0.55580921)86.50705, 69.02873, -109.46224
7generate(0.05141594, -0.02949972, 0.99823518), (-0.99849071, -0.02089025, 0.05081122), (0.01935135, -0.99935204, -0.0305257)132.87547, 140.3172, -2.25516
8generate(0.30968278, 0.48774724, 0.81620262), (-0.52404522, 0.80382129, -0.28151509), (-0.79340137, -0.34054882, 0.5045299)96.62889, 73.73871, 111.66949
9generate(0.80018327, 0.34718349, 0.48904568), (0.27793264, 0.50792177, -0.81533097), (-0.53147346, 0.78834573, 0.30992893)27.85887, -38.69753, 74.87172
10generate(0.84506241, -0.25693664, 0.46888414), (0.29913672, -0.49966573, -0.81292102), (0.4431596, 0.8272377, -0.34539668)21.60323, -41.60846, -61.79521
11generate(-0.83797029, -0.28614994, -0.46467205), (-0.28615209, -0.49464572, 0.82063274), (-0.46467908, 0.82063897, 0.33261602)258.39405, 39.98567, 65.4776
12generate(-0.80887703, 0.31855088, -0.49420901), (-0.29126565, 0.5130681, 0.80741234), (0.51076986, 0.79705498, -0.32222504)254.27713, 40.64036, -71.29986
13generate(-0.32214794, 0.4667858, -0.82360582), (0.50282034, 0.82149659, 0.26890939), (0.80212531, -0.32749633, -0.49934865)186.01807, -70.72667, -112.08458
14generate(-0.05042607, -0.04630079, -0.99764729), (0.99870602, 0.00440207, -0.05068334), (0.00674395, -0.99892328, 0.046024)147.94856, -140.20995, -0.51346
15generate(-0.36922181, -0.51164067, -0.77581401), (0.51109425, -0.8090186, 0.29030044), (-0.77618422, -0.28933664, 0.56020644)192.67938, -71.78596, 109.226
16generate(-0.54432845, 0.77588961, -0.31890851), (0.77588839, 0.32113526, -0.54301703), (-0.31890898, -0.54301869, -0.77680681)217.01518, -108.74157, 45.51836
17generate(0.23364099, 0.49506859, -0.83684662), (0.49506673, -0.80132632, -0.33583102), (-0.83685573, -0.33583594, -0.43231467)107.9445, -69.29488, 118.13281
18generate(0.25912197, -0.4804876, -0.83783897), (-0.48049079, -0.81664217, 0.3197259), (-0.83785304, 0.31972915, -0.4424798)104.43188, 67.50022, 118.2321
19generate(-0.50309936, -0.80259346, -0.32051416), (-0.80259683, 0.2963537, 0.51769636), (-0.32052266, 0.51770791, -0.79325434)211.33164, 112.59755, 45.679
20generate(-0.99965903, -0.02610965, 0.0002025), (-0.0261118, 0.99953881, -0.0155081), (0.00020241, -0.01549958, -0.99987978)280.91194, 3.67414, 0.73944
21generate(0.02433438, 0.04596778, 0.99863977), (0.99945758, 0.02110044, -0.02532335), (-0.02223287, 0.9987256, -0.04543482)136.67456, -140.32639, 3.45598
22generate(0.35559425, 0.53253081, 0.76808329), (0.53253673, -0.79079859, 0.30173672), (0.76809443, 0.30173775, -0.56479566)90.19469, -74.80381, -107.32178
23generate(0.84506181, 0.29913358, 0.44315454), (-0.25693293, -0.49967226, 0.82722946), (0.46888884, -0.81293143, -0.34538955)21.57525, 35.87881, -65.29775
24generate(0.81630951, -0.33167689, 0.472894), (-0.27793117, 0.49215273, 0.82494176), (-0.50635769, -0.80484702, 0.30957173)25.64597, 38.76184, 71.45229
25generate(0.30907207, -0.48814195, 0.81620275), (0.49856087, 0.81400797, 0.29803514), (-0.8098876, 0.31481859, 0.49495394)96.78125, -70.13896, 113.94443
26generate(0.76931311, -0.32715205, -0.54874662), (0.35191465, -0.49988305, 0.79137267), (-0.53321396, -0.80193431, -0.26943006)32.6394, -49.63777, 75.44684
27generate(-0.0253222, -0.99967082, -0.00385706), (0.02982941, -0.00461757, 0.99953887), (-0.99924058, 0.02519762, 0.02993977)144.10598, -4.50514, 140.74262
28generate(-0.80887541, -0.29126668, 0.51076478), (0.3185488, 0.51306751, 0.79704341), (-0.49421446, 0.80742566, -0.32222607)253.93316, -45.02184, 69.87869
29generate(-0.49850262, 0.81906993, 0.28392902), (0.81907243, 0.33774899, 0.46372813), (0.28393548, 0.46373725, -0.83924637)210.34352, -115.19517, -39.2134
30generate(0.47687152, 0.79689155, -0.37088504), (0.83969366, -0.28828887, 0.46022342), (0.25983246, -0.53090192, -0.80661663)73.57645, -118.04797, -35.7721
31generate(-0.49759227, 0.78982166, 0.35857874), (-0.83178647, -0.3172133, -0.45552724), (-0.24604433, -0.524939, 0.81480557)210.18901, 117.1131, 34.67089
32generate(0.47700273, 0.82730714, -0.29669805), (-0.82751853, 0.30901995, -0.46874437), (-0.29611755, 0.46911789, 0.83201129)73.5275, 116.4759, 41.63073
33generate(0.8163085, -0.27792954, -0.50635019), (-0.33167597, 0.49215986, -0.80483979), (0.47289739, 0.82495143, 0.30956563)26.01792, 46.93677, -66.22372
34generate(0.05141599, -0.99848886, 0.01935447), (-0.02949635, -0.0208867, -0.99934107), (0.99824798, 0.05081177, -0.03052929)133.31689, 4.59643, -139.84128
35generate(-0.76061934, -0.33858233, 0.55390994), (-0.33858164, -0.52110682, -0.78345403), (0.55391757, -0.78346639, 0.28172617)247.14088, 47.96779, -77.48498
36generate(-0.29605522, -0.50863739, -0.8084719), (-0.51958577, 0.7959959, -0.31052208), (0.80149116, 0.32814771, -0.49994068)182.41332, 73.1239, -112.03999
37generate(-0.80727478, -0.36016713, -0.46752817), (0.26515238, 0.48639621, -0.83253122), (0.5272637, -0.79605326, -0.2971554)254.08811, -36.89411, -73.51785
38generate(-0.85249489, 0.27006264, -0.44756913), (0.2700601, -0.5055551, -0.81943308), (-0.44757177, -0.81944566, 0.35804999)260.38995, -37.5209, 63.1765
39generate(-0.36922288, 0.51109582, -0.77617749), (-0.51164491, -0.80901503, -0.28932882), (-0.77582577, 0.29029801, 0.56020393)192.6099, 72.10973, 109.13611
40generate(-0.02532425, 0.02983273, -0.99922766), (-0.9996729, -0.00461227, 0.02519547), (-0.00386243, 0.99954972, 0.02993652)144.4177, 140.49198, 0.84636
41generate(0.02433239, 0.99945564, -0.0222358), (0.04597319, 0.02109699, 0.99871432), (0.998653, -0.02532536, -0.04542938)137.00123, -6.77444, -139.88727
42generate(0.80018234, 0.27793486, -0.5314664), (0.3471874, 0.50791475, 0.78833597), (0.48905395, -0.81533989, 0.30993689)28.25502, -49.04127, -68.38164
43generate(0.47700446, -0.82751525, -0.29610994), (0.82730819, 0.30901417, 0.46911549), (-0.29669752, -0.46875068, 0.83201536)73.63991, -116.35223, 41.77618
44generate(-0.49858041, -0.78920023, 0.35857897), (0.82282494, -0.30073091, 0.48220474), (-0.2727196, 0.53546775, 0.79931133)210.43552, -115.68585, 38.35182
45generate(-0.77834715, 0.33992988, 0.52784249), (0.33993335, -0.4786735, 0.80951481), (0.52785105, 0.80951966, 0.25702066)249.59498, -47.96305, -73.92236
46generate(-0.49759117, -0.83178305, -0.24603934), (0.78982414, -0.31721468, -0.52492778), (0.35858862, -0.45553673, 0.81480586)210.53129, -110.66264, -50.27212
47generate(-0.99712639, 0.00062472, 0.07575177), (0.00062507, -0.99986411, 0.01647757), (0.0757547, 0.01646901, 0.99699051)280.52537, 0.04228, -10.64192
48generate(-0.49858271, 0.82282415, -0.27272031), (-0.78919998, -0.30072947, 0.53546555), (0.35858101, 0.4822041, 0.79931219)210.56795, 110.74949, -50.32907
49generate(0.30906945, 0.49856359, -0.80987901), (-0.48813963, 0.81400892, 0.31481242), (0.81621119, 0.29803847, 0.49495561)97.33781, 68.46538, -114.48727
50generate(0.30968226, -0.5240399, -0.79338925), (0.48775094, 0.8038205, -0.3405467), (0.8162159, -0.28151723, 0.50453123)97.31515, -68.37484, -114.45207
51generate(-0.29605363, -0.51958673, 0.80148346), (-0.50864276, 0.79599312, 0.32813881), (-0.80848456, -0.31051853, -0.4999395)181.79654, 71.34176, 114.17146
52generate(-0.32214639, 0.50281675, 0.80211246), (0.46678168, 0.82149922, -0.32749715), (-0.82361503, 0.26891844, -0.49935284)185.39204, -65.43531, 116.25723
53generate(0.4768721, 0.83968956, 0.25982613), (0.79689186, -0.28828453, -0.53089726), (-0.37088817, 0.4602303, -0.80662155)73.33162, -111.65519, 52.76335
54generate(0.99678543, 0.02548493, -0.07595427), (0.02548673, -0.9996747, -0.00096947), (-0.07595711, -0.00096944, -0.99711072)0.47896, -3.44358, 11.4362
55generate(0.51909106, -0.81459401, 0.25880837), (-0.78137805, -0.32955426, 0.52994401), (-0.34640655, -0.47731841, -0.80757078)67.51397, 109.65475, 49.38851
56generate(0.76931242, 0.35191415, -0.53320832), (-0.32715457, -0.49987543, -0.80192535), (-0.54875706, 0.79138062, -0.26943699)32.58722, 46.36816, 77.52164
57generate(0.51909044, -0.78137633, -0.34639782), (-0.81459415, -0.32954986, -0.47731638), (0.25880637, 0.52995243, -0.80757455)67.74385, 114.70714, -35.69995
58generate(-0.45529384, -0.83499846, 0.30900412), (-0.83500007, 0.27999983, -0.47368379), (0.30900468, -0.47368372, -0.82470599)204.3768, 117.53077, -42.67673
59generate(-0.80727446, 0.26515171, 0.52725432), (-0.36017203, 0.4863967, -0.79604769), (-0.46753448, -0.83253678, -0.29715622)253.66398, 50.93689, 66.23297
60generate(-0.05042617, 0.99870404, 0.0067384), (-0.04630624, 0.00440727, -0.99891212), (-0.9976604, -0.05068403, 0.0460189)147.49219, 6.95598, 140.51965
61generate(0.35953616, -0.50749282, 0.78305998), (0.49809492, 0.8140022, 0.29884142), (-0.78908192, 0.28258618, 0.54543296)261.48291, -70.08274, 396.76519
62generate(0.02522452, -0.01741963, 0.99952474), (0.99945623, 0.0218979, -0.02484244), (-0.02146555, 0.99961128, 0.01795703)308.33027, -140.33537, 289.0845
63generate(0.30595867, 0.51271295, 0.80218742), (0.53331727, -0.7902922, 0.30169723), (0.78864468, 0.33552314, -0.5152362)268.93251, -74.92241, 175.53071
64generate(0.81377355, 0.35027971, 0.46376147), (-0.25613376, -0.500149, 0.82719371), (0.52170397, -0.79193101, -0.31729182)197.73599, 35.75766, 213.0313
65generate(0.84688627, -0.28024212, 0.45194006), (-0.27790238, 0.49135947, 0.82542871), (-0.4533847, -0.82464785, 0.33823777)193.13188, 38.74874, 349.76173
66generate(0.99958432, 0.02596505, -0.01261842), (0.02594321, -0.99966558, -0.00178111), (-0.01266299, 0.00146695, -0.99991628)171.83824, -3.51633, 288.30629
67generate(0.54036602, -0.78255715, 0.30921187), (-0.78138064, -0.33034614, 0.52945398), (-0.3121762, -0.52770514, -0.78998051)236.28055, 109.64643, 330.33723
68generate(-0.24398951, -0.49924091, 0.83139842), (-0.50942373, 0.79548664, 0.32816691), (-0.82520028, -0.34347029, -0.44841577)346.24654, 71.44256, 402.26284
69generate(-0.26952959, 0.48438035, 0.83229716), (0.46597872, 0.82197013, -0.32747044), (-0.84275337, 0.2995652, -0.44725292)349.76695, -65.33148, 404.68438
70generate(0.49904131, 0.80897549, 0.31066607), (0.79685369, -0.28749495, -0.53138953), (-0.34057772, 0.51274814, -0.78809898)241.97669, -111.65862, 334.25536
71generate(-0.51993208, 0.79075743, -0.32307334), (-0.78918254, -0.29993163, 0.53594551), (0.3269133, 0.53361924, 0.77998353)385.36536, 110.73787, 239.88417
72generate(0.25695811, 0.47829404, -0.83976351), (-0.48734924, 0.81450018, 0.31477823), (0.83455331, 0.32836327, 0.44238281)276.44798, 68.3454, 168.71482
73generate(0.25711068, -0.50552651, -0.8236056), (0.48854487, 0.80333421, -0.3405671), (0.83379678, -0.31481594, 0.45352133)276.48746, -68.49526, 168.86069
74generate(-0.51968521, -0.80109766, -0.2969293), (0.78984731, -0.31799854, -0.52442552), (0.32568919, -0.5070666, 0.79800603)385.42924, -110.67496, 240.1202
75generate(-0.99992405, 4.986E-5, 0.01241665), (0.00016835, -0.99985432, 0.01728907), (0.01241797, 0.01729518, 0.99977076)452.71949, 0.0972, 284.01512
76generate(-0.83918841, -0.30922966, -0.44736822), (0.26514441, 0.48559501, -0.83300582), (0.47483161, -0.81767237, -0.3255002)430.33689, -36.90168, 219.62079
77generate(-0.82254864, 0.32168273, -0.46897311), (0.26927365, -0.50605193, -0.81938977), (-0.50091156, -0.80026941, 0.32964066)427.9646, -37.41934, 356.43989
78generate(-0.31907983, 0.49205446, -0.80998023), (-0.51243841, -0.80852865, -0.28929704), (-0.79724118, 0.3227631, 0.51013064)357.3569, 72.21223, 397.92219
79generate(-0.02455875, -0.0335624, -0.99912934), (-0.99969227, -0.0038226, 0.02470225), (-0.00463978, 0.99943241, -0.0334613)316.09123, 140.48591, 286.74056
80generate(-0.34600353, -0.52878323, -0.77502278), (-0.51911966, 0.7959898, -0.31132825), (0.78154444, 0.29460453, -0.54990956)361.19534, 73.04981, 176.54423
81generate(-0.51587812, 0.7878808, 0.33632034), (0.8190374, 0.3385327, 0.46322633), (0.25110455, 0.51442821, -0.81994627)384.54323, -115.19904, 251.14848
82generate(0.45905443, 0.82906745, -0.31924437), (0.84014419, -0.28828917, 0.45940841), (0.28883855, -0.47910148, -0.82887218)247.83417, -118.11988, 245.91883
83generate(0.80138998, -0.27544464, -0.53094365), (0.35190043, -0.50067498, 0.79088293), (-0.48368126, -0.82064097, -0.30430846)199.8997, -49.64446, 354.26386
84generate(0.03803243, -0.9992573, -0.00621629), (0.0290424, -0.00511479, 0.99956337), (-0.99885876, -0.0381943, 0.02881566)306.98363, -4.40348, 426.45442
85generate(-0.77608403, -0.34208604, 0.52978233), (0.31774892, 0.51354409, 0.79706045), (-0.54473616, 0.78692383, -0.28986603)421.09961, -44.91844, 362.72561
86generate(-0.31953678, -0.4918986, -0.8098901), (0.51030385, -0.80950986, 0.29033433), (-0.79843732, -0.32051168, 0.50968098)357.48817, -71.68384, 398.13428
87generate(-0.80670776, -0.33734318, -0.48520092), (-0.28694612, -0.49415958, 0.82065291), (-0.51660808, 0.80126093, 0.30182954)425.79046, 40.08825, 358.54635
88generate(-0.83948075, 0.26716373, -0.47317774), (-0.29128906, 0.51385185, 0.80690995), (0.4587256, 0.81521563, -0.35355452)430.34853, 40.63485, 221.78272
89generate(-0.37256459, 0.48621415, -0.79043618), (0.50327682, 0.82148689, 0.26809775), (0.77968573, -0.2979325, -0.55075273)364.86329, -70.79941, 176.84608
90generate(-0.05122154, 0.01708783, -0.99853586), (0.99868848, 0.00360438, -0.05116353), (0.00271632, -0.99985057, -0.01724384)319.83311, -140.21618, 285.83734
91generate(0.05055578, 0.03389421, 0.99814046), (-0.99845244, -0.02167968, 0.05130372), (0.02338902, -0.99919312, 0.03274811)304.76879, 140.30276, 282.91404
92generate(0.35958164, 0.50796887, 0.78272546), (-0.52450145, 0.80381227, -0.28070331), (-0.77175181, -0.30961598, 0.55546477)261.40739, 73.79356, 394.36722
93generate(0.83212262, 0.29629313, 0.46880766), (0.27793547, 0.50871357, -0.8148408), (-0.4799275, 0.80834245, 0.34096248)195.16007, -38.7071, 353.37801
94generate(0.81514313, -0.30860435, 0.49021079), (0.29991778, -0.49915939, -0.81294889), (0.49557066, 0.80970163, -0.31432391)197.57839, -41.72713, 216.5921
95generate(0.33210826, -0.47077579, 0.81735644), (-0.48893333, -0.82696045, -0.27764213), (0.80663738, -0.30741679, -0.50481087)265.3203, 68.90704, 173.04297
96generate(0.78485913, -0.32987641, -0.5245707), (-0.33088881, 0.49265684, -0.80486439), (0.52394376, 0.80527659, 0.27751719)202.22321, 46.81724, 212.37964
97generate(-0.01192831, -0.99969314, 0.02171983), (-0.02869662, -0.02136352, -0.999358), (0.99952134, -0.01254347, -0.02842214)313.99139, 4.4752, 145.74404
98generate(-0.79403184, -0.28801222, 0.53531373), (-0.33854684, -0.52189044, -0.78295208), (0.50488316, -0.80291711, 0.31690051)423.6151, 47.95383, 215.15185
99generate(-0.48061097, 0.8216475, 0.30644169), (-0.832237, -0.31721271, -0.45471224), (-0.27639763, -0.47357484, 0.83626099)379.59809, 117.16715, 324.68385
100generate(0.49519732, 0.79577401, -0.34860291), (-0.82750408, 0.30981198, -0.46825478), (-0.26461754, 0.52034353, 0.81192074)242.77038, 116.46469, 322.97053
101generate(0.7674225, 0.3288026, -0.55040885), (0.34798099, 0.50742851, 0.78830394), (0.5384894, -0.79650395, 0.27499005)204.63767, -49.16164, 210.44651
102generate(0.49445795, -0.79629548, -0.34845706), (0.82732765, 0.30822434, 0.46960847), (-0.26655291, -0.52049694, 0.81119318)242.98278, -116.36403, 323.31368
103generate(-0.48068456, -0.82140403, 0.30698294), (0.82235869, -0.30072505, 0.48301083), (-0.30443834, 0.48462839, 0.82002916)379.72029, -115.62959, 328.56384
104generate(-0.81039124, 0.28817611, 0.51011537), (0.33994103, -0.47787232, 0.80998942), (0.47718949, 0.82982299, 0.28928696)425.88361, -47.9733, 218.94145
105generate(-0.03901866, 0.9990429, -0.0197819), (0.04675948, 0.02159406, 0.99867092), (0.99814749, 0.03803967, -0.04756573)317.67659, -6.89384, 145.94092
106generate(-0.29893571, -0.49478449, 0.8159789), (0.50223209, -0.80865361, -0.30634558), (0.81141964, 0.31823974, 0.49022983)353.97094, -70.3212, 171.94696
107generate(-0.29949975, 0.52054469, 0.79957661), (-0.47351614, -0.80865879, 0.3490864), (0.82831016, -0.27405799, 0.48867347)353.98721, 66.4997, 169.61519
108generate(0.50204524, 0.82604782, 0.25611164), (-0.78359319, 0.30915264, 0.53889712), (0.3659875, -0.47124765, 0.80248504)241.57446, 109.91001, 234.45497
109generate(0.99799131, -0.00047004, -0.06336591), (0.00051689, 1.00000329, 0.00077461), (0.06336585, -0.00081984, 0.99798763)172.08329, -0.08184, 276.85993
110generate(0.50295787, -0.8167893, 0.28265109), (0.79520062, 0.30916103, -0.5216141), (0.33865806, 0.48711021, 0.80500329)241.54813, -111.47085, 238.22785
111generate(-0.48140133, -0.83392565, -0.26984841), (-0.80310781, 0.29634085, 0.51691793), (-0.35109897, 0.46556611, -0.8123921)380.04301, 112.6607, 335.74591
112generate(-0.99765159, -0.02554488, 0.06356767), (-0.02662844, 0.99951661, -0.01628257), (-0.06312084, -0.0179423, -0.99784211)452.38239, 3.73808, 295.39509
113generate(-0.52339181, 0.80858902, -0.26878962), (0.77536256, 0.32111674, -0.54378539), (-0.35339516, -0.49302431, -0.79500631)385.82935, -108.67633, 336.12719
114generate(0.28596711, 0.51573136, -0.8076138), (0.49454088, -0.80133321, -0.33659957), (-0.82077268, -0.30313271, -0.48419687)272.35794, -69.22964, 401.65183
115generate(0.31191866, -0.49939853, -0.80826817), (-0.48100745, -0.81664555, 0.31895114), (-0.81935356, 0.28930874, -0.49494187)268.78179, 67.56417, 401.41618
116generate(0.01291454, 0.99990754, 0.00427836), (-0.04710526, 0.00488425, -0.99887629), (-0.99881007, 0.01269809, 0.04717221)310.37178, 7.05925, 426.43707
117generate(0.80269338, 0.30129567, -0.51468722), (-0.32718307, -0.49908216, -0.80241231), (-0.49863641, 0.81249723, -0.30202453)199.67103, 46.36336, 356.25247
118generate(0.50203114, -0.81323281, -0.29430497), (-0.81412806, -0.32954433, -0.47812257), (0.291846, 0.47964356, -0.82750789)241.8993, 114.63304, 245.43043
119generate(-0.47356718, -0.80343743, 0.36086434), (-0.8349988, 0.27920224, -0.47416446), (0.28021733, -0.52587044, -0.80307772)378.69856, 117.5219, 247.12323
120generate(-0.77585787, 0.31714493, 0.54539898), (-0.36095265, 0.48589046, -0.79600796), (-0.51745198, -0.81445861, -0.26249568)421.01689, 51.03764, 358.99149

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要素

#1: タンパク質 NODAMURA VIRUS COAT PROTEINS


分子量: 38508.711 Da / 分子数: 3 / 由来タイプ: 組換発現
詳細: THE COAT PROTEIN PRECURSOR IS ENZYMATICALLY CLEAVED INTO COAT PROTEINS BETA AND GAMMA. CHAINS A, B, AND C ARE THE BETA PROTEIN, CHAINS D, E, AND F ARE THE GAMMA PROTEIN
由来: (組換発現) Nodamura virus (ウイルス) / 属: Alphanodavirus / 解説: GROWN IN WAX MOTH LARVAE
発現宿主: Galleria mellonella (ハチノスツヅリガ)
参照: UniProt: P12871
#2: タンパク質・ペプチド NODAMURA VIRUS COAT PROTEINS


分子量: 4618.380 Da / 分子数: 3 / 由来タイプ: 天然 / 詳細: GROWN IN WAX MOTH LARVAE / 由来: (天然) Nodamura virus (ウイルス) / 属: Alphanodavirus / 参照: UniProt: P12871
構成要素の詳細NODAMURA VIRUS (NOV) IS THE TYPE MEMBER OF NON-ENVELOPED RNA NODAVIRUS FAMILY. NOV HAS A WIDE HOST ...NODAMURA VIRUS (NOV) IS THE TYPE MEMBER OF NON-ENVELOPED RNA NODAVIRUS FAMILY. NOV HAS A WIDE HOST RANGE, EXTENDING FROM INSECTS TO MAMMALS. THE COAT PROTEIN ASSEMBLES INTO A T=3 (180 SUBUNITS) CLOSED SHELL, SPECIFICALLY ENCAPSIDATING GENOMIC RNA. THE RNA ACTS AS A MOLECULAR SWITCH CONTROLLING THE PARTICLE ARCHITECTURE. THE COAT PROTEIN UNDERGOES A POST-ASSEMBLY MATURATION CLEAVAGE FORMING BETA PROTEIN AND 44 RESIDUE LONG GAMMA PEPTIDE. THE CLEAVAGE IS REQUIRED FOR VIRUS INFECTIVITY. THE OTHER MEMBERS OF NODAVIRUS FAMILY WHOSE CRYSTAL STRUCTURES ARE AVAILABLE ARE BLACK BEETLE VIRUS (BBV) AND FLOCK HOUSE VIRUS (FHV). THE NUMBERING SCHEME FOR NODAMURA VIRUS (NOV) IS SAME AS THAT FOR BBV. TOTAL NUMBER OF RESIDUES IN NOV : 399 (IN BBV : 407). SUBUNIT CHAIN-ID RESIDUES TYPE A A 1 - 363 BETA A D 364 - 407 GAMMA B B 1 - 363 BETA B E 364 - 407 GAMMA C C 1 - 363 BETA C F 364 - 407 GAMMA THE FOLLOWING RESIDUES ARE ORDERED AND CLEARLY VISIBLE IN THE ELECTRON DENSITY MAP: CHAIN RESIDUES A 55 - 363 D 364 - 383 B 55 - 363 E 364 - 380 C 13 - 29, 57 - 363 F 364 - 380 FIT OF RESIDUES TO THE ELECTRON DENSITY IS UNAMBIGUOUS. RESIDUES 55, 56, 58, 379 - 383 OF A SUBUNIT, RESIDUES 55 - 58, 379, 380 OF B SUBUNIT, AND 57, 58, 380 OF C SUBUNIT WERE MODELED AS ALANINES, AS THE SIDE CHAIN DENSITY WAS NOT CLEAR FOR THESE RESIDUES. ALSO, FOR SEVERAL RESIDUES IN THE N-TERMINAL STRETCH OF THE C-SUBUNIT (13 - 29) THE SIDE CHAIN DENSITY WAS NOT OBSERVED. THE ENDS OF ALL THE CHAINS MIGHT HAVE POOR OR UNACCEPTABLE STEREOCHEMISTRY. THESE RESIDUES ARE 55, 56, 363, 364, 380 - 383 OF A SUBUNIT; 56, 56, 363, 364, 380 OF B SUBUNIT; 13 - 17, 29, 363, 364, 380 OF C SUBUNIT.
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: 39

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試料調製

結晶マシュー密度: 3.5 Å3/Da / 溶媒含有率: 65 % / 解説: DATA WERE COLLECTED USING THE OSCILLATION METHOD.
結晶化手法: 蒸気拡散法, シッティングドロップ法 / pH: 6
詳細: 10 - 15 MICRO LITRES OF 7MG/ML OF VIRUS IN PHOSPHATE BUFFER MIXED WITH ONE VOLUME OF CITRATE BUFFER AND EQUILIBRATED VERSES 20 ML OF CITRATE BUFFER (0.24 - 0.28 M SODIUM CITRATE, PH ADJUSTED ...詳細: 10 - 15 MICRO LITRES OF 7MG/ML OF VIRUS IN PHOSPHATE BUFFER MIXED WITH ONE VOLUME OF CITRATE BUFFER AND EQUILIBRATED VERSES 20 ML OF CITRATE BUFFER (0.24 - 0.28 M SODIUM CITRATE, PH ADJUSTED TO 6.0 WITH ACETIC ACID, OR 0.24 M POTASSIUM CITRATE PH 6.0, BOTH WITH 0.1% BETA-OCTYL GLUCOPYRANOSIDE. CRYSTALS GROWN FROM VAPOR DIFFUSION USING SITTING DROP METHOD., vapor diffusion - sitting drop
結晶化
*PLUS
手法: 蒸気拡散法, シッティングドロップ法
溶液の組成
*PLUS
ID濃度一般名Crystal-IDSol-ID
17 mg/mlprotein1drop
30.24-0.28 Msodium citrate1reservoir
2phosphate1drop

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データ収集

回折平均測定温度: 295 K
放射光源由来: シンクロトロン / サイト: CHESS / ビームライン: F1 / 波長: 0.918
検出器タイプ: FILM / 検出器: IMAGE PLATE / 日付: 1992年9月1日 / 詳細: COLLIMATOR
放射モノクロメーター: SI(111) / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.918 Å / 相対比: 1
反射解像度: 3.3→20 Å / Num. obs: 1708846 / % possible obs: 49.9 % / Observed criterion σ(I): 2 / 冗長度: 1.2 % / Rmerge(I) obs: 0.141 / Rsym value: 0.105 / Net I/σ(I): 11.7
反射 シェル解像度: 3.3→3.7 Å / Mean I/σ(I) obs: 8.5 / % possible all: 39
反射 シェル
*PLUS
% possible obs: 39 %

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解析

ソフトウェア
名称バージョン分類
OSCPROGRAM (PURDUE)データ収集
OSCPROGRAM (PURDUE)データ削減
X-PLOR3.8モデル構築
X-PLOR3.8精密化
PURDUE(OSC)データ削減
OSCPROGRAM (PURDUE)データスケーリング
X-PLOR3.8位相決定
精密化構造決定の手法: 分子置換
開始モデル: FLOCK HOUSE VIRUS

解像度: 3.5→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 4
詳細: REFINEMENT WAS CARRIED OUT PRIMARILY TO OBTAIN REASONABLE GEOMETRY AND TO AVOID NON-BONDED ATOMIC CONTACTS. ICOSAHEDRAL SYMMETRY WAS RETAINED BY CONSTRAINING THE RELATED SUBUNITS DURING ...詳細: REFINEMENT WAS CARRIED OUT PRIMARILY TO OBTAIN REASONABLE GEOMETRY AND TO AVOID NON-BONDED ATOMIC CONTACTS. ICOSAHEDRAL SYMMETRY WAS RETAINED BY CONSTRAINING THE RELATED SUBUNITS DURING CONJUGATE ENERGY MINIMIZATION.
Rfactor反射数%反射
Rwork0.296 --
obs0.296 1377412 48.1 %
原子変位パラメータBiso mean: 20 Å2
精密化ステップサイクル: LAST / 解像度: 3.5→8 Å
タンパク質核酸リガンド溶媒全体
原子数7451 0 0 0 7451
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg3.12
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d4.2
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
ソフトウェア
*PLUS
名称: X-PLOR / バージョン: 3.8 / 分類: refinement
精密化
*PLUS
溶媒の処理
*PLUS
原子変位パラメータ
*PLUS
拘束条件
*PLUS
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg4.2

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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://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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