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- PDB-3s4g: Low Resolution Structure of STNV complexed with RNA -

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Basic information

Entry
Database: PDB / ID: 3s4g
TitleLow Resolution Structure of STNV complexed with RNA
Components
  • Capsid protein
  • RNA (5'-R(P*AP*AP*A)-3')
  • RNA (5'-R(P*UP*UP*UP*U)-3')
KeywordsVIRUS / Protein-RNA complex / Low resolution structure / jelly-roll -sandwich / Virus Capsid Protein
Function / homology
Function and homology information


viral capsid / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
Satellite tobacco necrosis virus coat protein-like / Satellite tobacco necrosis virus coat protein / Satellite virus coat / Satellite virus coat domain superfamily / Viral coat protein subunit
Similarity search - Domain/homology
RNA / Capsid protein
Similarity search - Component
Biological speciesSatellite tobacco necrosis virus 1
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 6 Å
AuthorsLane, S.W. / Dennis, C.A. / Lane, C.L. / Trinh, C.H. / Rizkallah, P.J. / Stockley, P.G. / Phillips, S.E.V.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Construction and crystal structure of recombinant STNV capsids.
Authors: Lane, S.W. / Dennis, C.A. / Lane, C.L. / Trinh, C.H. / Rizkallah, P.J. / Stockley, P.G. / Phillips, S.E.
History
DepositionMay 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_oper_list / struct_ref / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _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: Capsid protein
B: RNA (5'-R(P*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)23,8623
Polymers23,8623
Non-polymers00
Water00
1
A: Capsid protein
B: RNA (5'-R(P*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*U)-3')
x 60


Theoretical massNumber of molelcules
Total (without water)1,431,721180
Polymers1,431,721180
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: Capsid protein
B: RNA (5'-R(P*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*U)-3')
x 5


  • icosahedral pentamer
  • 119 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)119,31015
Polymers119,31015
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: RNA (5'-R(P*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*U)-3')
x 6


  • icosahedral 23 hexamer
  • 143 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)143,17218
Polymers143,17218
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: Capsid protein
B: RNA (5'-R(P*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*U)-3')
x 60


  • crystal asymmetric unit, crystal frame
  • 1.43 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)1,431,721180
Polymers1,431,721180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)313.146, 302.121, 183.385
Angle α, β, γ (deg.)90.00, 93.82, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-0.9732, -0.22321, -0.05534), (-0.22037, 0.83644, 0.50181), (-0.06572, 0.50055, -0.86321)148.87123, -6.96992, 90.41208
3generate(-0.40356, -0.24593, -0.88128), (-0.91082, 0.01656, 0.41246), (-0.08684, 0.96915, -0.23068)144.47185, 48.53883, 62.77232
4generate(0.32817, 0.55577, 0.76382), (0.87728, 0.12052, -0.46461), (-0.35027, 0.82255, -0.44801)15.03239, -43.88661, 92.34768
5generate(-0.03926, -0.97833, 0.20329), (-0.42887, -0.16726, -0.88775), (0.90251, -0.12204, -0.41301)67.63017, 72.38328, -2.43241
6generate(-0.49578, -0.62054, -0.60756), (0.48057, 0.38669, -0.7871), (0.72337, -0.6822, 0.1065)138.85167, 0.57686, -13.04252
7generate(-0.94304, 0.02515, 0.33173), (0.02594, -0.98854, 0.14868), (0.33166, 0.14882, 0.93158)129.27132, -8.92447, -21.51191
8generate(-0.26687, -0.89301, 0.36237), (0.66047, -0.44329, -0.60603), (0.70183, 0.07761, 0.70811)77.38263, -21.30423, -38.88194
9generate(-0.998, 0.04261, 0.04664), (0.03794, -0.186, 0.98182), (0.05051, 0.98162, 0.18402)146.2128, -47.58636, 33.56308
10generate(-0.30706, -0.50537, -0.80642), (-0.48688, 0.81149, -0.32316), (0.81772, 0.2934, -0.49523)133.89391, 50.45002, 7.32154
11generate(0.46554, 0.31715, -0.82625), (-0.75726, 0.62594, -0.18641), (0.45806, 0.71247, 0.53157)77.29893, 64.62584, -12.68185
12generate(0.71807, -0.38904, 0.57708), (0.36318, -0.49786, -0.78755), (0.59369, 0.7751, -0.21621)-5.35738, 9.07461, 11.34176
13generate(-0.67534, 0.40453, -0.61666), (0.54414, 0.83771, -0.04637), (0.49783, -0.36686, -0.78586)152.51253, -38.39476, 45.04448
14generate(-0.30612, 0.82832, 0.46923), (-0.04738, -0.50554, 0.8615), (0.95081, 0.2415, 0.194)75.68676, -35.65438, -33.93148
15generate(-0.30082, -0.044, 0.95267), (0.82975, -0.50452, 0.23871), (0.47013, 0.86228, 0.18828)52.77769, -72.45176, 2.30129
16generate(-0.46898, 0.60685, -0.64171), (-0.25928, 0.59995, 0.75685), (0.8443, 0.52133, -0.12402)138.46211, -15.02369, -11.39559
17generate(0.33008, 0.87681, -0.34963), (0.55679, 0.11825, 0.82219), (0.76226, -0.46606, -0.44917)65.67338, -78.99164, 9.88116
18generate(0.60142, -0.71495, -0.35657), (0.17885, 0.55547, -0.81208), (0.77866, 0.42462, 0.46194)45.95425, 23.69934, -33.37909
19generate(0.06404, 0.96411, -0.25767), (0.96479, -0.12582, -0.23098), (-0.25511, -0.2338, -0.93822)81.62112, -61.47903, 107.48206
20generate(0.95757, -0.05914, -0.28207), (0.28553, 0.3276, 0.90064), (0.03914, -0.94296, 0.33058)16.19232, -62.50926, 27.73519
21generate(0.35945, 0.29196, 0.88632), (0.06903, 0.93887, -0.33727), (-0.93061, 0.18242, 0.31732)7.13055, 10.03797, 100.45338
22generate(0.60307, 0.17515, 0.77823), (-0.71294, 0.55596, 0.42735), (-0.35782, -0.81254, 0.46015)-6.02246, 33.24167, 51.33627
23generate(0.07936, 0.99639, 0.03015), (0.1051, 0.02171, -0.99422), (-0.99129, 0.08207, -0.103)67.15411, 37.52291, 124.15989
24generate(0.3441, -0.83743, -0.42462), (0.93236, 0.35819, 0.04913), (0.11095, -0.4128, 0.90404)68.3544, -71.56564, -3.43945
25generate(-0.48908, -0.85309, 0.18178), (0.77402, -0.3284, 0.54133), (-0.40211, 0.40546, 0.82092)102.04567, -82.42929, 38.228
26generate(0.89113, 0.18891, -0.41255), (0.39923, -0.75852, 0.51504), (-0.21564, -0.62367, -0.75136)26.93027, -53.23392, 96.04679
27generate(0.54968, 0.59829, 0.58301), (0.59779, -0.76921, 0.22576), (0.58353, 0.22443, -0.78047)6.83574, -54.73974, 38.08333
28generate(0.95898, 0.28137, 0.0344), (-0.06199, 0.32657, -0.94314), (-0.27661, 0.90232, 0.33062)1.67641, 47.87468, 51.01036
29generate(-0.55627, 0.75636, 0.34421), (0.75729, 0.29086, 0.58473), (0.34215, 0.58593, -0.73458)99.89864, -83.12364, 54.37728
30generate(0.35103, 0.92935, 0.11442), (-0.8348, 0.36596, -0.41132), (-0.42413, 0.04887, 0.90428)42.91896, 80.62047, 35.93227
31generate(0.89041, 0.40068, -0.21594), (0.19001, -0.75832, -0.62358), (-0.41361, 0.51421, -0.75134)18.10781, 14.21761, 110.87966
32generate(0.71865, 0.36533, 0.59168), (-0.38479, -0.49982, 0.77596), (0.57921, -0.78531, -0.21862)-6.05806, -7.04824, 12.63749
33generate(-0.04061, -0.15298, 0.98739), (-0.15036, -0.97602, -0.15741), (0.9878, -0.15486, 0.01664)32.23494, 18.24876, -28.53622
34generate(-0.48904, 0.77489, -0.40049), (-0.8524, -0.32711, 0.40794), (0.1851, 0.54087, 0.82048)128.72354, 44.43108, -5.66446
35generate(0.658, -0.51112, -0.55299), (-0.7105, -0.17811, -0.68079), (0.24947, 0.84085, -0.48035)50.65151, 83.70034, 49.14962
36generate(-0.47573, -0.25685, 0.84126), (0.60538, 0.59825, 0.52499), (-0.63813, 0.75903, -0.12912)71.49503, -69.25034, 99.24734
37generate(0.50147, 0.85699, -0.11869), (-0.55767, 0.42506, 0.71297), (0.66146, -0.29135, 0.69108)42.45128, 8.84365, -35.04607
38generate(0.24839, 0.50805, -0.82473), (-0.70542, -0.48862, -0.51345), (-0.66384, 0.70932, 0.23702)93.51123, 75.68497, 84.43878
39generate(0.81416, -0.48188, 0.32394), (-0.48234, -0.87188, -0.08469), (0.32325, -0.0873, -0.94228)-0.88127, 39.67362, 64.86946
40generate(-0.26917, 0.66237, 0.69915), (-0.8936, -0.44251, 0.0752), (0.35919, -0.60452, 0.71101)62.43854, 62.8532, -13.55944
41generate(-0.88221, -0.24975, 0.39915), (-0.25245, -0.46469, -0.84873), (0.39745, -0.84952, 0.3469)121.32668, 57.44682, 0.36035
42generate(0.36097, 0.06466, -0.93033), (0.29185, 0.93965, 0.17855), (0.88573, -0.33596, 0.32031)90.00611, -29.4693, -34.81621
43generate(-0.64798, -0.19202, -0.73705), (-0.19545, -0.89337, 0.40458), (-0.73615, 0.40622, 0.54136)156.03133, -4.08331, 75.66092
44generate(-0.12273, -0.98971, -0.07362), (-0.98943, 0.11625, 0.08664), (-0.07719, 0.08348, -0.99352)86.47758, 69.42669, 97.08543
45generate(0.43996, -0.50703, -0.74118), (-0.50717, -0.82142, 0.26087), (-0.74109, 0.26113, -0.61854)75.34903, 25.76724, 129.1093
46generate(-0.03723, -0.4255, 0.90419), (-0.98003, -0.16131, -0.11627), (0.19532, -0.89047, -0.41099)35.3843, 77.83802, 50.34671
47generate(-0.40452, -0.91038, -0.08706), (-0.24782, 0.01748, 0.96865), (-0.88031, 0.41341, -0.23268)108.42786, -26.00991, 121.76114
48generate(-0.70325, 0.67046, -0.23647), (-0.42339, -0.66216, -0.61829), (-0.57112, -0.3347, 0.74953)137.15263, 59.57811, 53.9915
49generate(-0.81593, 0.44158, -0.37317), (0.4415, 0.05918, -0.89531), (-0.37327, -0.89527, -0.24325)151.87914, 7.81284, 84.71953
50generate(0.25009, -0.7079, -0.66056), (0.51061, -0.48323, 0.71118), (-0.82264, -0.51514, 0.24061)85.77174, -70.96624, 95.70348
51generate(-0.30953, -0.49057, 0.81457), (-0.5094, 0.8089, 0.29359), (-0.80293, -0.32407, -0.50028)60.02832, 24.44744, 128.33191
52generate(0.65682, -0.71177, 0.24892), (-0.51131, -0.17779, 0.84081), (-0.55421, -0.67954, -0.48071)14.19488, -0.47872, 108.91917
53generate(-0.49368, 0.48458, 0.72212), (-0.61792, 0.38883, -0.68336), (-0.61193, -0.78358, 0.10748)77.82272, 77.13026, 86.27694
54generate(0.50125, -0.55672, 0.66243), (0.85703, 0.42503, -0.2913), (-0.11938, 0.71373, 0.69017)6.74827, -50.33623, 23.11616
55generate(0.01297, 0.37741, -0.92595), (0.37686, -0.85959, -0.34508), (-0.92618, -0.34447, -0.15338)115.52331, -12.34954, 121.61179
56generate(0.46145, -0.76201, 0.45431), (0.31809, 0.62016, 0.71709), (-0.82818, -0.18639, 0.52856)19.55496, -56.69216, 83.16889
57generate(-0.67318, 0.54353, 0.5014), (0.40257, 0.83813, -0.36806), (-0.62029, -0.04592, -0.78302)101.40125, -13.19423, 127.5778
58generate(-0.90132, -0.40445, 0.15504), (-0.40566, 0.66272, -0.62948), (0.15184, -0.63025, -0.7614)134.00621, 58.76748, 69.37045
59generate(0.086, 0.10815, -0.99041), (0.99597, 0.01599, 0.08823), (0.02538, -0.99401, -0.10634)112.75107, -78.36338, 49.22248
60generate(-0.70632, -0.42074, -0.56929), (0.6667, -0.66571, -0.33517), (-0.23796, -0.61628, 0.75071)152.70837, -34.14207, 29.126
DetailsThe biological assembly is 60 capsid subunits generated from a monomer using the matrices provided.

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Components

#1: Protein Capsid protein / Coat protein


Mass: 21739.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Satellite tobacco necrosis virus 1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P03606
#2: RNA chain RNA (5'-R(P*AP*AP*A)-3')


Mass: 942.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Arbitrary modelled RNA structure / Source: (synth.) Synthetic construct (others)
#3: RNA chain RNA (5'-R(P*UP*UP*UP*U)-3')


Mass: 1179.706 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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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: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.4 % PEG 6000, pH 6.2-7.0, 1 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 1, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 6→140 Å / Num. obs: 24647 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 11.8
Reflection shellResolution: 6→6.32 Å / % possible all: 97

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
FFTmodel building
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 6→95.85 Å / Stereochemistry target values: NR
RfactorNum. reflectionSelection details
Rfree0.43 -NR
obs0.38 24647 -
Refinement stepCycle: LAST / Resolution: 6→95.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 147 0 0 1574

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