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- PDB-1nov: NODAMURA VIRUS -

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Basic information

Entry
Database: PDB / ID: 1nov
TitleNODAMURA VIRUS
Components(NODAMURA VIRUS COAT PROTEINS) x 2
KeywordsVIRUS / INSECT VIRUS / NODAMURA VIRUS / COAT PROTEIN / Icosahedral virus
Function / homology
Function and homology information


nodavirus endopeptidase / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / T=3 icosahedral viral capsid / aspartic-type endopeptidase activity
Similarity search - Function
Peptidase A6, nodavirus coat protein / Peptidase A6 family / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Capsid protein alpha
Similarity search - Component
Biological speciesNodamura virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsNatarajan, P. / Johnson, J.E.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Resolution of space-group ambiguity and structure determination of nodamura virus to 3.3 A resolution from pseudo-R32 (monoclinic) crystals.
Authors: Zlotnick, A. / Natarajan, P. / Munshi, S. / Johnson, J.E.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: The Refined Three-Dimensional Structure of an Insect Virus at 2.8 A Resolution
Authors: Wery, J.P. / Reddy, V.S. / Hosur, M.V. / Johnson, J.E.
#2: Journal: Nature / Year: 1993
Title: Ordered Duplex RNA Controls Capsid Architecture in an Icosahedral Animal Virus
Authors: Fisher, A.J. / Johnson, J.E.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: A Monoclinic Crystal with R32 Pseudo-Symmetry: A Preliminary Report of Nodamura Virus Structure Determination
Authors: Zlotnick, A. / Mckinney, B.R. / Munshi, S. / Bibler, J. / Rossmann, M.G. / Johnson, J.E.
#4: Journal: J.Mol.Biol. / Year: 1990
Title: Structural Homology Among Four Nodaviruses as Deduced by Sequencing and X-Ray Crystallography
Authors: Kaesberg, P. / Dasgupta, R. / Sgro, J.Y. / Wery, J.P. / Selling, B.H. / Hosur, M.V. / Johnson, J.E.
History
DepositionSep 16, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 30, 2011Group: Advisory
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: 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
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
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


Theoretical massNumber of molelcules
Total (without water)129,3816
Polymers129,3816
Non-polymers00
Water0
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


Theoretical massNumber of molelcules
Total (without water)7,762,876360
Polymers7,762,876360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
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 polymers
Theoretical massNumber of molelcules
Total (without water)646,90630
Polymers646,90630
Non-polymers00
Water0
TypeNameSymmetry operationNumber
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 polymers
Theoretical massNumber of molelcules
Total (without water)776,28836
Polymers776,28836
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
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 polymers
Theoretical massNumber of molelcules
Total (without water)15,525,753720
Polymers15,525,753720
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
transform to crystal frame1
point symmetry operation59
Unit cell
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
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
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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Components

#1: Protein NODAMURA VIRUS COAT PROTEINS


Mass: 38508.711 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: 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
Source: (gene. exp.) Nodamura virus / Genus: Alphanodavirus / Description: GROWN IN WAX MOTH LARVAE / Production host: Galleria mellonella (greater wax moth) / References: UniProt: P12871
#2: Protein/peptide NODAMURA VIRUS COAT PROTEINS


Mass: 4618.380 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: GROWN IN WAX MOTH LARVAE / Source: (natural) Nodamura virus / Genus: Alphanodavirus / References: UniProt: P12871
Compound detailsNODAMURA 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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 39

-
Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 65 %
Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD.
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: 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 ...Details: 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
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
30.24-0.28 Msodium citrate1reservoir
2phosphate1drop

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FILM / Detector: IMAGE PLATE / Date: Sep 1, 1992 / Details: COLLIMATOR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 1708846 / % possible obs: 49.9 % / Observed criterion σ(I): 2 / Redundancy: 1.2 % / Rmerge(I) obs: 0.141 / Rsym value: 0.105 / Net I/σ(I): 11.7
Reflection shellResolution: 3.3→3.7 Å / Mean I/σ(I) obs: 8.5 / % possible all: 39
Reflection shell
*PLUS
% possible obs: 39 %

-
Processing

Software
NameVersionClassification
OSCPROGRAM (PURDUE)data collection
OSCPROGRAM (PURDUE)data reduction
X-PLOR3.8model building
X-PLOR3.8refinement
PURDUE(OSC)data reduction
OSCPROGRAM (PURDUE)data scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FLOCK HOUSE VIRUS

Resolution: 3.5→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 4
Details: 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 ...Details: 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.
RfactorNum. reflection% reflection
Rwork0.296 --
obs0.296 1377412 48.1 %
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 3.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7451 0 0 0 7451
Refine LS restraints
Refine-IDTypeDev 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
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev 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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