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- PDB-2izw: Crystal structure of Ryegrass Mottle Virus -

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Basic information

Entry
Database: PDB / ID: 2izw
TitleCrystal structure of Ryegrass Mottle Virus
ComponentsRYEGRASS MOTTLE VIRUS COAT PROTEIN
KeywordsVIRUS / RNA / ASSEMBLY / CAPSID PROTEIN
Function / homology
Function and homology information


viral capsid / structural molecule activity
Similarity search - Function
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 speciesRYEGRASS MOTTLE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPlevka, P. / Tars, K. / Zeltins, A. / Balke, I. / Truve, E. / Liljas, L.
CitationJournal: Virology / Year: 2007
Title: The Three-Dimensional Structure of Ryegrass Mottle Virus at 2.9 A Resolution.
Authors: Plevka, P. / Tars, K. / Zeltins, A. / Balke, I. / Truve, E. / Liljas, L.
History
DepositionJul 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RYEGRASS MOTTLE VIRUS COAT PROTEIN
B: RYEGRASS MOTTLE VIRUS COAT PROTEIN
C: RYEGRASS MOTTLE VIRUS COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)76,5723
Polymers76,5723
Non-polymers00
Water00
1
A: RYEGRASS MOTTLE VIRUS COAT PROTEIN
B: RYEGRASS MOTTLE VIRUS COAT PROTEIN
C: RYEGRASS MOTTLE VIRUS COAT PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)4,594,299180
Polymers4,594,299180
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: RYEGRASS MOTTLE VIRUS COAT PROTEIN
B: RYEGRASS MOTTLE VIRUS COAT PROTEIN
C: RYEGRASS MOTTLE VIRUS COAT PROTEIN
x 5


  • icosahedral pentamer
  • 383 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)382,85815
Polymers382,85815
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: RYEGRASS MOTTLE VIRUS COAT PROTEIN
B: RYEGRASS MOTTLE VIRUS COAT PROTEIN
C: RYEGRASS MOTTLE VIRUS COAT PROTEIN
x 6


  • icosahedral 23 hexamer
  • 459 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)459,43018
Polymers459,43018
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: RYEGRASS MOTTLE VIRUS COAT PROTEIN
B: RYEGRASS MOTTLE VIRUS COAT PROTEIN
C: RYEGRASS MOTTLE VIRUS COAT PROTEIN
x 60


  • crystal asymmetric unit, crystal frame
  • 4.59 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)4,594,299180
Polymers4,594,299180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)277.641, 298.719, 392.485
Angle α, β, γ (deg.)90.00, 92.74, 90.00
Int Tables number4
Space group name H-MP1211
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.806549, 0.213728, -0.55118), (0.396439, 0.496092, 0.772482), (0.438537, -0.841554, 0.315393)66.5407, -101.36774, 38.71558
3generate(0.493539, 0.742258, -0.453291), (0.85518, -0.319248, 0.408348), (0.158388, -0.589181, -0.792325)77.20472, -95.36905, 165.41315
4generate(0.493539, 0.85518, 0.158388), (0.742258, -0.319248, -0.589181), (-0.453291, 0.408348, -0.792325)17.25474, 9.70608, 205.00097
5generate(0.806549, 0.396439, 0.438537), (0.213728, 0.496092, -0.841554), (-0.55118, 0.772482, 0.315393)-30.4604, 68.64739, 102.77003
6generate(-0.560858, 0.752061, -0.346182), (0.752061, 0.287957, -0.592861), (-0.346182, -0.592861, -0.727099)134.94772, 9.43232, 191.67619
7generate(-0.306027, 0.544552, 0.780904), (0.46074, 0.802514, -0.379063), (-0.833106, 0.243791, -0.496488)7.99044, 7.33247, 200.58791
8generate(0.311511, -0.452431, 0.835624), (0.523525, 0.815596, 0.246423), (-0.793021, 0.360706, 0.490926)-37.33963, -58.03425, 101.21812
9generate(0.438339, -0.861091, -0.257644), (0.853649, 0.309124, 0.419197), (-0.281323, -0.403688, 0.870571)61.60213, -96.33325, 30.89249
10generate(-0.100815, -0.116674, -0.98804), (0.994892, -0.016975, -0.099509), (-0.005162, -0.993025, 0.117789)168.08157, -54.63662, 86.79865
11generate(0.464962, -0.52845, 0.710317), (-0.52845, -0.809374, -0.25623), (0.710317, -0.25623, -0.655588)-34.98981, 59.31418, 116.29078
12generate(0.477016, -0.760555, -0.440467), (-0.859455, -0.298837, -0.414769), (0.183827, 0.576413, -0.796213)77.01725, 96.27503, 164.14779
13generate(-0.109938, 0.095323, -0.989357), (-0.993555, 0.01711, 0.112053), (0.027609, 0.995299, 0.092828)168.80107, 53.32071, 87.12418
14generate(-0.48475, 0.856389, -0.177805), (-0.745428, -0.29816, 0.596185), (0.457552, 0.421542, 0.78291)113.51953, -10.18737, -8.33605
15generate(-0.129442, 0.470876, 0.872651), (-0.457978, -0.808956, 0.368574), (0.879489, -0.351946, 0.320364)-12.43016, -6.4832, 9.6899
16generate(-0.904104, -0.223611, -0.364135), (-0.223611, -0.478583, 0.849091), (-0.364135, 0.849091, 0.382687)158.92213, -68.7465, 84.06902
17generate(-0.977539, 0.002275, 0.210743), (0.002275, -0.999769, 0.02135), (0.210743, 0.02135, 0.977308)107.33165, -2.23975, -11.41529
18generate(-0.695113, -0.38515, 0.607024), (-0.38515, -0.513459, -0.766825), (0.607024, -0.766825, 0.208571)50.21389, 100.0826, 38.28054
19generate(-0.447129, -0.850478, 0.277062), (-0.850478, 0.308284, -0.426202), (0.277062, -0.426202, -0.861156)66.50366, 96.81455, 164.47857
20generate(-0.576292, -0.750642, -0.323148), (-0.750642, 0.329838, 0.572489), (-0.323148, 0.572489, -0.753546)133.68904, -7.52757, 192.77741
21generate(0.69105, -0.405939, -0.598049), (0.379946, -0.499858, 0.77832), (-0.614891, -0.765085, -0.191192)78.60945, -100.87252, 156.54326
22generate(0.134169, 0.449604, -0.883094), (0.449604, -0.821769, -0.350074), (-0.883094, -0.350074, -0.3124)142.58774, 5.21198, 185.78084
23generate(-0.100815, 0.994892, -0.005162), (-0.116674, -0.016975, -0.993025), (-0.98804, -0.099509, 0.117789)71.75061, 104.87654, 150.41057
24generate(0.310839, 0.476355, 0.822475), (-0.536311, 0.802327, -0.261997), (-0.784697, -0.359663, 0.504869)-36.00743, 60.38813, 99.31297
25generate(0.800238, -0.389406, 0.45605), (-0.229383, 0.503888, 0.832755), (-0.554078, -0.771012, 0.313908)-31.76844, -66.77179, 103.10318
26generate(-0.485838, 0.757379, 0.436278), (-0.858461, -0.319631, -0.4011), (-0.164337, -0.569397, 0.805469)53.40434, 94.87102, 29.70169
27generate(0.099726, -0.095258, 0.990445), (-0.995002, -0.004496, 0.099753), (-0.00505, -0.995442, -0.09523)-38.80675, 54.61989, 107.66925
28generate(0.477016, -0.859455, 0.183827), (-0.760555, -0.298837, 0.576413), (-0.440467, -0.414769, -0.796213)15.83085, -7.27055, 204.5521
29generate(0.12463, -0.479117, -0.868858), (-0.479117, -0.795885, 0.370153), (-0.868858, 0.370153, -0.328745)141.80983, -5.26981, 186.46143
30generate(-0.470447, 0.520141, -0.712835), (-0.539626, -0.808737, -0.233984), (-0.6982, 0.274587, 0.661149)165.03152, 57.85716, 78.39793
31generate(0.111026, 0.116609, 0.986953), (0.993665, 0.00436, -0.112296), (-0.017398, 0.993168, -0.115386)-39.19584, -53.30397, 110.44391
32generate(0.568591, -0.748996, 0.340161), (0.753922, 0.30904, -0.579737), (0.329097, 0.586088, 0.740402)-5.41805, 8.02561, 4.14375
33generate(0.310839, -0.536311, -0.784697), (0.476355, 0.802327, -0.359663), (0.822475, -0.261997, 0.504869)121.50994, 4.42054, -4.70326
34generate(-0.306027, 0.46074, -0.833106), (0.544552, 0.802514, 0.243791), (0.780904, -0.379063, -0.496488)166.17796, -59.13708, 96.12916
35generate(-0.429518, 0.864267, 0.261834), (0.864267, 0.309344, 0.396672), (0.261834, 0.396672, -0.879826)66.85633, -94.81279, 167.29402
36generate(-0.316238, -0.468049, -0.825181), (-0.515151, 0.815129, -0.264924), (0.796626, 0.341314, -0.498891)166.0621, 59.30547, 95.34713
37generate(-0.802487, 0.39465, -0.447511), (-0.208524, 0.517225, 0.830058), (0.559046, 0.759428, -0.332772)160.51711, -67.85747, 94.44215
38generate(-0.687041, 0.400874, 0.606032), (0.400874, -0.486515, 0.776275), (0.606032, 0.776275, 0.173555)49.78866, -102.02653, 41.77658
39generate(-0.129442, -0.457978, 0.879489), (0.470876, -0.808956, -0.351946), (0.872651, 0.368574, 0.320364)-13.10031, 4.01877, 10.13243
40generate(0.099726, -0.995002, -0.00505), (-0.095258, -0.004496, -0.995442), (0.990445, 0.099753, -0.09523)58.76063, 103.72743, 43.24086
41generate(0.69105, 0.379946, -0.614891), (-0.405939, -0.499858, -0.765085), (-0.598049, 0.77832, -0.191192)80.26005, 101.25761, 155.45329
42generate(0.438339, 0.853649, -0.281323), (-0.861091, 0.309124, -0.403688), (-0.257644, 0.419197, 0.870571)63.92288, 95.29491, 29.35998
43generate(0.568591, 0.753922, 0.329097), (-0.748996, 0.30904, 0.586088), (0.340161, -0.579737, 0.740402)-4.33372, -8.96693, 3.42771
44generate(0.901802, 0.218586, 0.37279), (-0.224565, -0.499994, 0.836407), (0.369219, -0.83799, -0.401809)-30.18145, -67.4416, 113.494
45generate(0.977486, -0.012544, -0.210626), (-0.012544, -0.99992, 0.001336), (-0.210626, 0.001336, -0.977566)22.10037, 0.68092, 207.45097
46generate(0.111026, 0.993665, -0.017398), (0.116609, 0.00436, 0.993168), (0.986953, -0.112296, -0.115386)59.23958, -104.88637, 45.44231
47generate(0.475846, 0.53132, 0.700906), (0.53132, -0.808719, 0.252334), (0.700906, 0.252334, -0.667127)-34.77184, -59.11803, 118.03082
48generate(0.901802, -0.224565, 0.369219), (0.218586, -0.499994, -0.83799), (0.37279, 0.836407, -0.401809)-29.83148, 67.98366, 113.26289
49generate(0.800238, -0.229383, -0.554078), (-0.389406, 0.503888, -0.771012), (0.45605, 0.832755, 0.313908)67.23325, 100.76848, 37.72765
50generate(0.311511, 0.523525, -0.793021), (-0.452431, 0.815596, 0.360706), (0.835624, 0.246423, 0.490926)122.28219, -6.07108, -4.18778
51generate(-0.316238, -0.515151, 0.796626), (-0.468049, 0.815129, 0.341314), (-0.825181, -0.264924, -0.498891)7.11043, -3.15966, 200.31049
52generate(-0.109938, -0.993555, 0.027609), (0.095323, 0.01711, 0.995299), (-0.989357, 0.112053, 0.092828)69.12923, -103.71759, 152.94225
53generate(-0.470447, -0.539626, -0.6982), (0.520141, -0.808737, 0.274587), (-0.712835, -0.233984, 0.661149)163.59722, -60.57557, 79.34508
54generate(-0.899554, 0.219321, -0.377758), (0.219321, -0.521119, -0.824823), (-0.377758, -0.824823, 0.420673)159.96284, 66.6456, 81.22776
55generate(-0.804248, 0.234448, 0.546095), (-0.391414, 0.482485, -0.783584), (-0.447192, -0.843945, -0.296271)63.24869, 102.13058, 155.9885
56generate(-0.485838, -0.858461, -0.164337), (0.757379, -0.319631, -0.569397), (0.436278, -0.4011, 0.805469)112.26999, 6.78843, -9.17011
57generate(-0.804248, -0.391414, -0.447192), (0.234448, 0.482485, -0.843945), (0.546095, -0.783584, -0.296271)160.59978, 67.54071, 91.70294
58generate(-0.999947, 0.010269, -0.000116), (0.010269, 0.99969, -0.022686), (-0.000116, -0.022686, -0.999743)129.44803, 1.55885, 196.00031
59generate(-0.802487, -0.208524, 0.559046), (0.39465, 0.517225, 0.759428), (-0.447511, 0.830058, -0.332772)61.8654, -99.97247, 159.58658
60generate(-0.48475, -0.745428, 0.457552), (0.856389, -0.298161, 0.421542), (-0.177805, 0.596185, 0.78291)51.24879, -96.74041, 32.78429

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Components

#1: Protein RYEGRASS MOTTLE VIRUS COAT PROTEIN / COAT PROTEIN


Mass: 25523.885 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-235 / Source method: isolated from a natural source / Source: (natural) RYEGRASS MOTTLE VIRUS / References: UniProt: Q9E962

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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

CrystalDescription: NONE
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.3M LITHIUM SULPHATE, 0.05 M NATRIUM CITRATE, PH 3.0, 1% PEG 8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.9→34.9 Å / Num. obs: 569869 / % possible obs: 40.5 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 5
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 1 % / Mean I/σ(I) obs: 1.06 / % possible all: 22.9

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Processing

Software
NameVersionClassification
CCP4Imodel building
SCALEPACKdata scaling
AVEphasing
CNSphasing
GLRFphasing
CCP4Iphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NG0

1ng0


Resolution: 2.9→34.9 Å / Data cutoff high absF: 10376268.11 / Isotropic thermal model: RESTRAINED / σ(F): 0 / Stereochemistry target values: RESIDUAL
RfactorNum. reflection% reflectionSelection details
Rwork0.294 ---
obs0.294 569869 40.5 %-
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.
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.1609 Å2 / ksol: 0.318571 e/Å3
Displacement parametersBiso mean: 46 Å2
Baniso -1Baniso -2Baniso -3
1--13.04 Å20 Å2-2 Å2
2--19.91 Å20 Å2
3----6.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.56 Å
Luzzati d res low-5 Å
Luzzati sigma a0.95 Å0.94 Å
Refinement stepCycle: LAST / Resolution: 2.9→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4324 0 0 0 4324
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.9→3.08 Å / Total num. of bins used: 6 /
RfactorNum. reflection
Rwork0.41 53405
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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