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- PDB-1vb2: T=1 capsid structure of Sesbania mosaic virus coat protein deleti... -

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Basic information

Entry
Database: PDB / ID: 1vb2
TitleT=1 capsid structure of Sesbania mosaic virus coat protein deletion mutant CP-N(delta)65-D146N-D149N
Componentscoat protein
KeywordsVIRUS / T=1 capsids / Calcium mutant / Icosahedral virus
Function / homology
Function and homology information


viral capsid / 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 speciesSesbania mosaic virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSangita, V. / Lokesh, G.L. / Satheshkumar, P.S. / Vijay, C.S. / Saravanan, V. / Savithri, H.S. / Murthy, M.R.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: T=1 capsid structures of Sesbania mosaic virus coat protein mutants: determinants of T=3 and T=1 capsid assembly
Authors: Sangita, V. / Lokesh, G.L. / Satheshkumar, P.S. / Vijay, C.S. / Saravanan, V. / Savithri, H.S. / Murthy, M.R.
History
DepositionFeb 21, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: coat protein


Theoretical massNumber of molelcules
Total (without water)21,4691
Polymers21,4691
Non-polymers00
Water52229
1
A: coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)1,288,15560
Polymers1,288,15560
Non-polymers00
Water1,08160
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
x 5


  • icosahedral pentamer
  • 107 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)107,3465
Polymers107,3465
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: coat protein
x 6


  • icosahedral 23 hexamer
  • 129 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)128,8156
Polymers128,8156
Non-polymers00
Water1086
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
x 60


  • crystal asymmetric unit, crystal frame
  • 1.29 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,288,15560
Polymers1,288,15560
Non-polymers00
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)188.484, 187.569, 188.826
Angle α, β, γ (deg.)119.76, 61.82, 88.96
Int Tables number1
Space group name H-MP1
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.46592662, -0.50495877, 0.72658725), (0.84612477, 0.49446489, -0.19894055), (-0.25881511, 0.70747516, 0.65764248)
3generate(-0.39822227, 0.02908432, 0.91682775), (0.86409987, -0.32350809, 0.38558259), (0.3078156, 0.94577831, 0.10369637)
4generate(-0.39822227, 0.86409987, 0.3078156), (0.02908432, -0.32350809, 0.94577831), (0.91682775, 0.38558259, 0.10369637)
5generate(0.46592662, 0.84612477, -0.25881511), (-0.50495877, 0.49446489, 0.70747516), (0.72658725, -0.19894055, 0.65764248)
6generate(-0.39552376, -0.00982282, 0.91840322), (-0.00982282, -0.99984038, -0.01492418), (0.91840322, -0.01492418, 0.39536414)
7generate(-0.43029301, 0.84461362, 0.3185526), (-0.84670382, -0.49998433, 0.18195689), (0.31295457, -0.19142493, 0.93027734)
8generate(0.43171731, 0.86028007, -0.27117959), (-0.86464416, 0.3090558, -0.39607446), (-0.25692534, 0.40546605, 0.87726088)
9generate(0.99923824, 0.01552603, -0.03580351), (-0.03885091, 0.30921405, -0.95019855), (-0.00368186, 0.95086572, 0.3095817)
10generate(0.48797514, -0.52222713, 0.69939909), (0.48945774, -0.49972827, -0.71463471), (0.72271114, 0.69105027, 0.01175314)
11generate(-0.99942997, 0.03375981, -1.41E-5), (0.03375981, 0.99942963, -0.00083511), (-1.41E-5, -0.00083511, -0.99999965)
12generate(-0.43709236, 0.521354, -0.73289854), (0.8615879, 0.47654473, -0.17484683), (0.25810184, -0.70788073, -0.65748636)
13generate(0.42716278, -0.04000265, -0.9032894), (0.84990604, -0.32313152, 0.416228), (-0.3085315, -0.94550823, -0.10403127)
14generate(0.39896423, -0.87453432, -0.2757123), (0.01485817, -0.29447372, 0.95554407), (-0.9168461, -0.38532448, -0.10449051)
15generate(-0.48271859, -0.82894661, 0.28254254), (-0.48954794, 0.52291402, 0.69778489), (-0.72617187, 0.19851562, -0.65822942)
16generate(0.39495374, -0.02393699, -0.91838912), (-0.02393699, -0.99958925, 0.01575929), (-0.91838911, 0.01575929, -0.39536449)
17generate(0.40145876, -0.86100885, -0.31224131), (-0.86100885, -0.47102529, 0.1918305), (-0.31224131, 0.1918305, -0.93043346)
18generate(-0.46065782, -0.84936174, 0.25764124), (-0.84936174, 0.33758381, -0.40573613), (0.25764124, -0.40573613, -0.87692598)
19generate(-0.99998019, -0.00509158, 0.00370021), (-0.00509158, 0.30876776, -0.95112383), (0.00370021, -0.95112383, -0.30878757)
20generate(-0.47118317, 0.50504897, -0.72312652), (0.50504897, -0.51765064, -0.69062534), (-0.72312652, -0.69062534, -0.0111662)
21generate(0.4825146, 0.54198055, 0.6880674), (0.82700228, -0.0231333, -0.56172242), (-0.28852535, 0.84007258, -0.4593813)
22generate(0.50531732, 0.51113097, 0.6952694), (0.51113097, -0.82644532, 0.23607894), (0.6952694, 0.23607894, -0.678872)
23generate(0.48797514, 0.48945774, 0.72271114), (-0.52222713, -0.49972827, 0.69105027), (0.69939909, -0.71463471, 0.01175314)
24generate(0.45445436, 0.50691253, 0.73246906), (-0.84500624, 0.50550599, 0.17443666), (-0.28184337, -0.69821443, 0.65807365)
25generate(0.45107956, 0.53937341, 0.71105805), (-0.01113661, 0.80005788, -0.59981944), (-0.89241426, 0.26264752, 0.36689655)
26generate(0.43575354, -0.55690253, 0.70709153), (-0.84275949, 0.02338936, 0.5377819), (-0.31603052, -0.83024846, -0.4591429)
27generate(-0.45118582, 0.00484337, 0.89241688), (-0.51205985, 0.81759135, -0.26332317), (-0.7309077, -0.57577854, -0.36640553)
28generate(-0.43709236, 0.8615879, 0.25810184), (0.521354, 0.47654473, -0.70788073), (-0.73289854, -0.17484683, -0.65748636)
29generate(0.45855724, 0.82933924, -0.31925177), (0.82933924, -0.52843567, -0.18152734), (-0.31925177, -0.18152734, -0.93012157)
30generate(0.99800567, -0.04733606, -0.04176089), (-0.01372927, -0.80850109, 0.5883345), (-0.06161316, -0.58658783, -0.80753857)
31generate(-0.4639521, 0.55738641, -0.68852657), (-0.82730393, 0.00526844, 0.56172988), (0.31672806, 0.83023649, 0.45868366)
32generate(0.4336519, 0.02276924, -0.90079276), (-0.52638934, 0.81776937, -0.23273916), (0.73134143, 0.57509549, 0.36661272)
33generate(0.45445436, -0.84500624, -0.28184337), (0.50691253, 0.50550599, -0.69821443), (0.73246906, 0.17443666, 0.65807365)
34generate(-0.43029301, -0.84670382, 0.31295457), (0.84461362, -0.49998433, -0.19142493), (0.3185526, 0.18195689, 0.93027734)
35generate(-0.99789941, 0.0200225, 0.06161053), (0.0200225, -0.80914814, 0.58726348), (0.06161053, 0.58726348, 0.80704755)
36generate(-0.45431605, -0.54246443, -0.70663235), (0.84306114, -0.00552449, -0.53778936), (0.28782781, -0.84006061, 0.45984054)
37generate(-0.4877834, -0.53874358, -0.68689352), (0.52731822, -0.8089154, 0.25998339), (-0.69570313, -0.23539589, 0.67866481)
38generate(-0.50533713, -0.50603939, -0.69896961), (-0.50603939, -0.48232244, 0.71504489), (-0.69896961, 0.71504489, -0.01234043)
39generate(-0.48271859, -0.48954794, -0.72617187), (-0.82894661, 0.52291402, 0.19851562), (0.28254254, 0.69778489, -0.65822942)
40generate(-0.45118582, -0.51205985, -0.7309077), (0.00484337, 0.81759135, -0.57577854), (0.89241688, -0.26332317, -0.36640553)
41generate(0.4825146, 0.82700228, -0.28852535), (0.54198055, -0.0231333, 0.84007258), (0.6880674, -0.56172242, -0.4593813)
42generate(0.99923824, -0.03885091, -0.00368186), (0.01552603, 0.30921405, 0.95086572), (-0.03580351, -0.95019855, 0.3095817)
43generate(0.4336519, -0.52638934, 0.73134143), (0.02276924, 0.81776937, 0.57509549), (-0.90079276, -0.23273916, 0.36661272)
44generate(-0.43262332, 0.03814852, 0.90076732), (0.55370031, 0.79972649, 0.23206357), (-0.7115146, 0.59915126, -0.36710318)
45generate(-0.4024245, 0.87459055, 0.27045498), (0.87459055, 0.28002006, 0.39582842), (0.27045498, 0.39582842, -0.87759556)
46generate(-0.4639521, -0.82730393, 0.31672806), (0.55738641, 0.00526844, 0.83023649), (-0.68852657, 0.56172988, 0.45868366)
47generate(-0.99814398, 0.04928117, 0.03577644), (0.04928117, 0.3085196, 0.94994054), (0.03577644, 0.94994054, -0.31037562)
48generate(-0.43262332, 0.55370031, -0.7115146), (0.03814852, 0.79972649, 0.59915126), (0.90076732, 0.23206357, -0.36710318)
49generate(0.45107956, -0.01113661, -0.89241426), (0.53937341, 0.80005788, 0.26264752), (0.71105805, -0.59981944, 0.36689655)
50generate(0.43171731, -0.86464417, -0.25692534), (0.86028007, 0.3090558, 0.40546605), (-0.27117959, -0.39607446, 0.87726088)
51generate(-0.45431605, 0.84306114, 0.28782781), (-0.54246443, -0.00552449, -0.84006061), (-0.70663235, -0.53778936, 0.45984054)
52generate(0.42716278, 0.84990604, -0.3085315), (-0.04000265, -0.32313152, -0.94550823), (-0.9032894, 0.416228, -0.10403127)
53generate(0.99800567, -0.01372927, -0.06161316), (-0.04733606, -0.80850109, -0.58658783), (-0.04176089, 0.5883345, -0.80753857)
54generate(0.46932715, -0.55433014, 0.68735007), (-0.55433014, -0.79086897, -0.2593152), (0.68735007, -0.2593152, -0.67845818)
55generate(-0.42825704, -0.02480455, 0.90331647), (-0.8603363, -0.29460214, -0.41596999), (0.27643691, -0.95529802, 0.10482518)
56generate(0.43575354, -0.84275949, -0.31603052), (-0.55690253, 0.02338936, -0.83024846), (0.70709153, 0.5377819, -0.4591429)
57generate(-0.42825704, -0.8603363, 0.27643691), (-0.02480455, -0.29460214, -0.95529802), (0.90331647, -0.41596999, 0.10482518)
58generate(-0.99903425, -0.0135817, 0.04178633), (-0.0135817, -0.80899477, -0.58765892), (0.04178633, -0.58765892, 0.80802902)
59generate(-0.4877834, 0.52731822, -0.69570313), (-0.53874358, -0.8089154, -0.23539589), (-0.68689352, 0.25998339, 0.67866481)
60generate(0.39896423, 0.01485817, -0.9168461), (-0.87453432, -0.29447372, -0.38532448), (-0.2757123, 0.95554407, -0.10449051)

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Components

#1: Protein coat protein


Mass: 21469.244 Da / Num. of mol.: 1 / Fragment: residues 66-268 / Mutation: D146N/D149N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sesbania mosaic virus / Genus: Sobemovirus / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EB06
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, Magnesium Chloride, Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 20, 2003 / Details: MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→16 Å / Num. all: 282321 / Num. obs: 266680 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.107 / Rsym value: 0.091 / Net I/σ(I): 6.7
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.329 / % possible all: 94.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→15.96 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 248573.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 11552 5 %RANDOM
Rwork0.261 ---
obs0.261 232314 91.3 %-
all-266680 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.233376 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.85 Å2-3.59 Å2-9.52 Å2
2---1.49 Å21.83 Å2
3----2.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 3.4→15.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 0 29 1427
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.762
X-RAY DIFFRACTIONc_scbond_it1.692
X-RAY DIFFRACTIONc_scangle_it2.842.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 1846 5.1 %
Rwork0.35 34489 -
obs--85.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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