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- PDB-1ng0: The three-dimensional structure of Cocksfoot mottle virus at 2.7A... -

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Basic information

Entry
Database: PDB / ID: 1ng0
TitleThe three-dimensional structure of Cocksfoot mottle virus at 2.7A resolution
Componentscoat protein
KeywordsVIRUS / sobemovirus / virus assembly / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / peptidase activity / RNA-dependent RNA polymerase activity / structural molecule activity / metal ion binding
Similarity search - Function
Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCocksfoot mottle virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTars, K. / Zeltins, A. / Liljas, L.
CitationJournal: Virology / Year: 2003
Title: The three-dimensional structure of cocksfoot mottle virus at 2.7 A resolution.
Authors: Tars, K. / Zeltins, A. / Liljas, L.
History
DepositionDec 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2017Group: Database references / Category: pdbx_database_related
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: coat protein
B: coat protein
C: coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6656
Polymers82,5453
Non-polymers1203
Water4,612256
1
A: coat protein
B: coat protein
C: coat protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,959,929360
Polymers4,952,715180
Non-polymers7,214180
Water3,243180
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: coat protein
B: coat protein
C: coat protein
hetero molecules
x 5


  • icosahedral pentamer
  • 413 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)413,32730
Polymers412,72615
Non-polymers60115
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: coat protein
B: coat protein
C: coat protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 496 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)495,99336
Polymers495,27118
Non-polymers72118
Water32418
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: coat protein
B: coat protein
C: coat protein
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 4.96 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)4,959,929360
Polymers4,952,715180
Non-polymers7,214180
Water3,243180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)291.069, 537.250, 555.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.53694885, -0.52364965, 0.66142043), (-0.10180224, 0.73808172, 0.66698701), (-0.83744984, -0.42547199, 0.34300342)5.3195, -57.59, 218.39951
3generate(-0.21228366, -0.94908518, 0.23275089), (-0.68836914, 0.31428905, 0.65373566), (-0.69360188, -0.02144113, -0.72003938)182.78668, 45.03198, 313.35941
4generate(-0.21228366, -0.68836914, -0.69360188), (-0.94908518, 0.31428905, -0.02144113), (0.23275089, 0.65373566, -0.72003938)287.14792, 166.04585, 153.64834
5generate(0.53694885, -0.10180224, -0.83744984), (-0.52364965, 0.73808172, -0.42547199), (0.66142043, 0.66698701, 0.34300342)174.17955, 138.21455, -40.01843
6generate(-0.99120386, -0.13038535, -0.02268414), (-0.13038535, 0.93270433, 0.33624736), (-0.02268414, 0.33624736, -0.94150047)157.54969, -32.93113, 250.37613
7generate(-0.49995542, 0.43245997, -0.75034855), (-0.44655196, 0.61362443, 0.65119614), (0.74204847, 0.66063865, -0.11366901)154.83167, -13.9029, 25.26774
8generate(0.3159034, 0.90024457, -0.29960766), (-0.84758801, 0.40967604, 0.33728344), (0.42637966, 0.14739488, 0.89245456)-36.60897, 90.60396, -33.65637
9generate(0.32888343, 0.62650603, 0.70662994), (-0.7792753, 0.6027089, -0.17167405), (-0.53344699, -0.49419851, 0.68644165)-152.20777, 136.16451, 155.03492
10generate(-0.47895328, -0.01045829, 0.87777809), (-0.33601969, 0.92595817, -0.17231438), (-0.81098368, -0.37748126, -0.44700489)-32.21112, 59.81563, 330.57666
11generate(0.941058, 0.18069528, -0.28593539), (0.18069528, -0.98317887, -0.02661805), (-0.28593539, -0.02661805, -0.95787913)21.86443, 275.87497, 322.76321
12generate(0.72636137, -0.23775931, 0.64487958), (0.21940522, -0.80896214, -0.54538207), (0.65135283, 0.53763441, -0.53543322)-45.98401, 327.64408, 113.57478
13generate(-0.12583097, -0.83022288, 0.54304378), (0.65689367, -0.47992684, -0.58151606), (0.74340922, 0.28354929, 0.60575781)112.41381, 256.28815, -30.86107
14generate(-0.43781817, -0.77793091, -0.45070917), (0.88856646, -0.45078858, -0.08508408), (-0.13698501, -0.43773641, 0.88860674)278.15748, 160.41866, 89.0611
15generate(0.22155548, -0.15314912, -0.96304648), (0.59425967, -0.76181543, 0.25786175), (-0.77315497, -0.62943037, -0.07777404)222.19488, 172.52398, 307.61293
16generate(-0.94985415, -0.05030993, 0.30861953), (-0.05030993, -0.94952546, -0.30962932), (0.30861953, -0.30962932, 0.8993796)92.58593, 330.05612, 38.76067
17generate(-0.7633548, 0.32894899, -0.55595145), (0.32894899, -0.54274401, -0.77280108), (-0.55595145, -0.77280108, 0.30609881)157.83288, 316.84878, 254.65799
18generate(0.02221123, 0.87906348, -0.476187), (0.87906348, -0.24403824, -0.40950304), (-0.476187, -0.40950304, -0.77817299)13.40852, 181.07587, 363.05805
19generate(0.32121839, 0.83979402, 0.43768111), (0.83979402, -0.46620938, 0.27819926), (0.43768111, 0.27819926, -0.85500901)-141.0976, 110.37094, 214.15565
20generate(-0.27955105, 0.26540966, 0.92271822), (0.26540966, -0.90222445, 0.33992462), (0.92271822, 0.33992462, 0.1817755)-92.16327, 202.44581, 13.72885
21generate(0.23182809, -0.30607961, 0.92334772), (-0.96445214, 0.05144472, 0.25920167), (-0.12683771, -0.95061491, -0.2832728)-45.16752, 161.81191, 341.1092
22generate(-0.61761799, -0.74016705, 0.26589614), (-0.74016705, 0.43272238, -0.51468833), (0.26589614, -0.51468833, -0.81510439)175.3515, 210.32833, 333.31376
23generate(-0.47895328, -0.33601969, -0.81098368), (-0.01045829, 0.92595817, -0.37748126), (0.87777809, -0.17231438, -0.44700489)272.76389, 69.06285, 186.35069
24generate(0.4561923, 0.34784457, -0.81908042), (0.21624143, 0.84951698, 0.48120738), (0.8632081, -0.39664223, 0.3123247)112.44903, -66.76043, 103.31797
25generate(0.89547935, 0.36634855, 0.25279533), (-0.37335919, 0.30903795, 0.87469907), (0.24232139, -0.87765841, 0.4135167)-84.04339, -9.43836, 198.96399
26generate(-0.21082594, -0.00523552, -0.9775096), (0.94338128, 0.26088902, -0.20486258), (0.25609408, -0.9653546, -0.05006308)232.6207, 73.06656, 281.50604
27generate(0.7059455, 0.52243764, -0.47822575), (0.65155054, -0.21428057, 0.72771267), (0.27771001, -0.82531373, -0.49166493)18.31311, 18.31839, 327.52935
28generate(0.72636137, 0.21940522, 0.65135283), (-0.23775931, -0.80896214, 0.53763441), (0.64487958, -0.54538207, -0.53543322)-112.46307, 193.05682, 269.15706
29generate(-0.17779237, -0.49555228, 0.85018693), (-0.49555228, -0.70132598, -0.51241566), (0.85018693, -0.51241566, -0.12088166)21.0204, 355.79928, 187.05769
30generate(-0.75700598, -0.6343879, -0.15650541), (0.23443275, -0.04012159, -0.97130404), (0.60990428, -0.77197296, 0.17909359)234.2939, 281.64122, 194.68978
31generate(-0.10116126, 0.31824353, -0.94259613), (-0.97242452, -0.23175075, 0.02611777), (-0.21013555, 0.91924569, 0.33291201)173.48424, 238.57779, -15.34493
32generate(0.70266065, 0.68891104, -0.17795952), (-0.5204218, 0.32704639, -0.7887977), (-0.48521043, 0.64687112, 0.58832695)-51.24406, 252.45562, 3.30572
33generate(0.4561923, 0.21624143, 0.8632081), (0.34784457, 0.84951698, -0.39664223), (-0.81908042, 0.48120738, 0.3123247)-126.04692, 58.5796, 91.96166
34generate(-0.49995542, -0.44655196, 0.74204846), (0.43245997, 0.61362443, 0.66063865), (-0.75034855, 0.65119613, -0.11366901)52.45068, -75.12019, 128.10339
35generate(-0.84441886, -0.3835112, -0.37399992), (-0.3835112, -0.05463578, 0.9219187), (-0.37399992, 0.9219187, -0.10094535)237.57112, 36.12481, 61.78427
36generate(0.08015911, -0.0069284, 0.996758), (0.99349538, -0.08058298, -0.08045686), (0.08087917, 0.99672382, 0.00042387)-88.93738, 99.54369, 4.6297
37generate(-0.79098816, -0.47118163, 0.39028913), (0.60903831, -0.5454882, 0.57577336), (-0.05839572, 0.69313094, 0.71844237)129.5795, 91.89763, -52.24881
38generate(-0.7036004, -0.09962696, -0.70357725), (-0.09962696, -0.966513, 0.23648907), (-0.70357725, 0.23648907, 0.67011341)237.74614, 252.30069, 64.43061
39generate(0.22155548, 0.59425967, -0.77315497), (-0.15314912, -0.76181543, -0.62943037), (-0.96304648, 0.25786175, -0.07777404)86.07993, 359.0813, 193.42096
40generate(0.7059455, 0.65155054, 0.27771001), (0.52243764, -0.21428057, -0.82531373), (-0.47822575, 0.72771267, -0.49166493)-115.82159, 264.67228, 156.46197
41generate(0.23182809, -0.96445214, -0.12683771), (-0.30607961, 0.05144472, -0.95061491), (0.92334772, 0.25920167, -0.2832728)209.79646, 302.11427, 96.39037
42generate(0.32888343, -0.7792753, -0.53344699), (0.62650603, 0.6027089, -0.49419851), (0.70662995, -0.17167405, 0.68644165)238.87117, 89.90955, 24.50805
43generate(0.70266065, -0.5204218, -0.48521043), (0.68891104, 0.32704639, 0.64687112), (-0.17795952, -0.7887977, 0.58832695)168.99456, -49.40047, 188.0722
44generate(0.83661233, -0.54561838, -0.04878931), (-0.20510618, -0.39458661, 0.89567453), (-0.50794809, -0.73932537, -0.44202572)96.73374, 76.70593, 361.04272
45generate(0.5456218, -0.82004422, 0.17269721), (-0.82004422, -0.56491781, -0.09162613), (0.17269721, -0.09162613, -0.98070399)121.95069, 293.95398, 304.38023
46generate(-0.10116126, -0.97242452, -0.21013555), (0.31824353, -0.23175075, 0.91924569), (-0.94259613, 0.02611777, 0.33291201)246.32427, 14.18611, 162.40296
47generate(0.22065456, -0.57534892, -0.78758186), (-0.57534892, -0.7288124, 0.37122245), (-0.78758186, 0.37122245, -0.49184216)255.89456, 229.98834, 228.59252
48generate(0.83661233, -0.20510618, -0.50794809), (-0.54561838, -0.39458661, -0.73932537), (-0.04878931, 0.89567453, -0.44202572)118.19518, 349.97487, 95.6062
49generate(0.89547935, -0.37335919, 0.24232139), (0.36634855, 0.30903795, -0.87765841), (0.25279533, 0.87469907, 0.4135167)23.52199, 208.3284, -52.77343
50generate(0.3159034, -0.84758801, 0.42637966), (0.90024457, 0.40967604, 0.14739488), (-0.29960766, 0.33728344, 0.89245456)102.71012, 0.79953, -11.49076
51generate(0.08015911, 0.99349538, 0.08087917), (-0.0069284, -0.08058298, 0.99672382), (0.996758, -0.08045686, 0.00042387)-92.1415, 2.7908, 96.65605
52generate(-0.12583097, 0.65689367, 0.74340922), (-0.83022288, -0.47992684, 0.28354929), (0.54304378, -0.58151606, 0.60575781)-131.26652, 225.07872, 106.68439
53generate(-0.75700598, 0.23443275, 0.60990428), (-0.6343879, -0.04012159, -0.77197296), (-0.15650541, -0.97130404, 0.17909359)-7.40617, 310.22836, 275.35983
54generate(-0.94110351, 0.30993926, -0.13513636), (0.30993926, 0.63103686, -0.71114706), (-0.13513636, -0.71114706, -0.68993335)108.26875, 140.56582, 369.57864
55generate(-0.42370703, 0.77906576, -0.46209186), (0.69773055, 0.60603034, 0.38196767), (0.57761962, -0.16057322, -0.8003573)55.89943, -49.44104, 259.13364
56generate(-0.21082594, 0.94338128, 0.25609408), (-0.00523552, 0.26088902, -0.9653546), (-0.9775096, -0.20486258, -0.05006308)-91.97918, 253.90878, 256.45063
57generate(-0.42370703, 0.69773055, 0.57761962), (0.77906576, 0.60603034, -0.16057322), (-0.46209186, 0.38196767, -0.8003573)-91.49916, 28.02336, 252.11505
58generate(-0.782267, 0.49109523, 0.38325424), (0.49109524, 0.10766181, 0.86442721), (0.38325424, 0.86442721, -0.32539481)-7.78353, -37.8028, 52.86179
59generate(-0.79098816, 0.60903831, -0.05839572), (-0.47118163, -0.5454882, 0.69313094), (0.39028913, 0.57577336, 0.71844237)43.47557, 147.39982, -65.94791
60generate(-0.43781817, 0.88856646, -0.13698501), (-0.77793091, -0.45078858, -0.43773641), (-0.45070917, -0.08508408, 0.88860674)-8.5602, 327.68749, 59.87691

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Components

#1: Protein coat protein


Mass: 27515.082 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Cocksfoot mottle virus / Genus: Sobemovirus / Strain: Russian isolate / References: GenBank: 11557855, UniProt: Q9E958*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 3.3
Details: 0.25 M sodium succinate, 0.5 % PEG 8000, pH 3.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.25 Msodium succinate1reservoirpH3.3
30.5 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 14, 2002
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 2353839 / Num. obs: 1859533 / % possible obs: 79 % / Observed criterion σ(F): 1.3 / Observed criterion σ(I): 1.3 / Rmerge(I) obs: 0.19
Reflection shellResolution: 2.7→2.82 Å / % possible all: 70
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 1653761 / % possible obs: 79 %
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.75 Å / % possible obs: 70 % / Num. unique obs: 153029 / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
TFmodel building
RAVEmodel building
CNS1refinement
TFphasing
RAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: rice yellow mottle virus (1F2N)

1f2n


Resolution: 2.7→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rwork0.281 ---
obs0.281 1859533 100 %-
all-1859533 --
Rfree---Due to high non-crystallographic symmetry, R-free for viruses is always very similar to R-observed. Therefore, no reflections were selected for R-free determination.
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4634 0 3 256 4893
Refinement
*PLUS
Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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