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- PDB-3cji: Structure of Seneca Valley Virus-001 -

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Basic information

Entry
Database: PDB / ID: 3cji
TitleStructure of Seneca Valley Virus-001
Components(Polyprotein) x 4
KeywordsVIRUS / virus capsid protein structure / ATP-binding / Cytoplasm / Cytoplasmic vesicle / Helicase / Hydrolase / Membrane / Nucleotide-binding / Nucleotidyltransferase / Phosphoprotein / Protease / RNA replication / RNA-binding / RNA-directed RNA polymerase / Thiol protease / Transferase / Virion / icosahedral virus
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / host cell nucleolus / adhesion receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / host cell nucleolus / adhesion receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / entry receptor-mediated virion attachment to host cell / RNA helicase activity / RNA helicase / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein ...Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesSeneca valley virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVenkataraman, S. / Reddy, V.S.
CitationJournal: Structure / Year: 2008
Title: Structure of Seneca Valley Virus-001: an oncolytic picornavirus representing a new genus
Authors: Venkataraman, S. / Reddy, S.P. / Loo, J. / Idamakanti, N. / Hallenbeck, P.L. / Reddy, V.S.
History
DepositionMar 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Polyprotein
B: Polyprotein
C: Polyprotein
D: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7515
Polymers94,7114
Non-polymers401
Water4,810267
1
A: Polyprotein
B: Polyprotein
C: Polyprotein
D: Polyprotein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,685,057300
Polymers5,682,653240
Non-polymers2,40560
Water4,324240
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: Polyprotein
B: Polyprotein
C: Polyprotein
D: Polyprotein
hetero molecules
x 5


  • icosahedral pentamer
  • 474 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)473,75525
Polymers473,55420
Non-polymers2005
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Polyprotein
B: Polyprotein
C: Polyprotein
D: Polyprotein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 569 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)568,50630
Polymers568,26524
Non-polymers2406
Water43224
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: Polyprotein
B: Polyprotein
C: Polyprotein
D: Polyprotein
hetero molecules
x 20
A: Polyprotein
B: Polyprotein
C: Polyprotein
D: Polyprotein
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 3.79 MDa, 160 polymers
Theoretical massNumber of molelcules
Total (without water)3,790,038200
Polymers3,788,435160
Non-polymers1,60340
Water2,882160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z3
point symmetry operation38
transform to crystal frame1
Unit cell
Length a, b, c (Å)311.510, 311.510, 1526.401
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.792592, 0.476001, -0.381082), (0.119087, 0.492103, 0.862365), (0.598021, -0.728868, 0.333345)
3generate(0.456987, 0.889276, -0.018587), (0.668695, -0.329701, 0.666453), (0.586534, -0.316982, -0.745325)
4generate(0.456986, 0.668683, 0.58653), (0.889293, -0.329701, -0.316989), (-0.018584, 0.666445, -0.745324)
5generate(0.79259, 0.119086, 0.598018), (0.476011, 0.492104, -0.72888), (-0.381082, 0.862352, 0.333346)
6generate(-0.036013, 0.923704, 0.381404), (0.346634, 0.369502, -0.862167), (-0.937315, 0.101161, -0.333489)
7generate(0.309538, 0.15942, 0.937431), (-0.196851, 0.975238, -0.100848), (-0.930288, -0.153313, 0.333263)
8generate(0.824924, -0.45747, 0.332008), (-0.100199, 0.459716, 0.882406), (-0.556297, -0.761165, 0.3334)
9generate(0.797891, -0.074442, -0.598191), (0.503028, -0.464623, 0.728774), (-0.33218, -0.882373, -0.333269)
10generate(0.265803, 0.779165, -0.567663), (0.77918, -0.520376, -0.349432), (-0.567658, -0.349422, -0.745427)
11generate(-0.450634, -0.8927, -0.000326), (-0.892717, 0.450634, 0.000529), (-0.000325, 0.000528, -1)
12generate(-0.463673, -0.653566, -0.598213), (-0.653579, -0.203562, 0.728986), (-0.598216, 0.728973, -0.332765)
13generate(-0.803069, -0.10631, -0.586324), (-0.106313, -0.942614, 0.316525), (-0.58633, 0.316519, 0.745683)
14generate(-0.9998, -0.007224, 0.018909), (-0.007223, -0.745167, -0.666846), (0.018905, -0.666836, 0.744966)
15generate(-0.78198, -0.493246, 0.381076), (-0.493254, 0.115905, -0.862143), (0.381076, -0.862131, -0.333925)
16generate(-0.292907, -0.74614, 0.597892), (0.187858, -0.658043, -0.729184), (0.937509, -0.101266, 0.33291)
17generate(0.036544, -0.942386, -0.332519), (-0.36553, 0.297077, -0.882129), (0.930083, 0.153776, -0.333621)
18generate(-0.28211, -0.20399, -0.937447), (-0.781871, 0.615152, 0.101429), (0.555976, 0.761556, -0.333041)
19generate(-0.808502, 0.448602, -0.380903), (-0.485786, -0.143386, 0.862249), (0.332186, 0.882151, 0.333848)
20generate(-0.815169, 0.113536, 0.567989), (0.113537, -0.930258, 0.348902), (0.567983, 0.348894, 0.745427)
21generate(-0.450193, -0.892922, -0.000404), (0.892928, -0.450199, -0.000696), (0.000438, -0.00067, 1.000002)179.67, 253.383
22generate(-0.463396, -0.653408, -0.598598), (0.653699, 0.203997, -0.728746), (0.59829, -0.728991, 0.332601)179.67, 253.383
23generate(-0.803061, -0.10582, -0.586422), (0.106603, 0.942711, -0.316115), (0.586288, -0.316373, -0.745781)179.67, 253.383
24generate(-0.999794, -0.006908, 0.019296), (0.007709, 0.745053, 0.666955), (-0.01898, 0.66696, -0.744857)179.67, 253.383
25generate(-0.781706, -0.49337, 0.381475), (0.493691, -0.115809, 0.861896), (-0.381055, 0.862076, 0.334097)179.67, 253.383
26generate(-0.292927, -0.745822, 0.598277), (-0.187559, 0.658382, 0.728944), (-0.937564, 0.101318, -0.332745)179.67, 253.383
27generate(0.036797, -0.94252, -0.332109), (0.365665, -0.296594, 0.882228), (-0.930022, -0.153896, 0.333742)179.67, 253.383
28generate(-0.281681, -0.204234, -0.937522), (0.782094, -0.614921, -0.10103), (-0.55587, -0.761675, 0.332955)179.67, 253.383
29generate(-0.808236, 0.448741, -0.381302), (0.486228, 0.143315, -0.862003), (-0.332168, -0.882096, -0.334019)179.67, 253.383
30generate(-0.815181, 0.114022, 0.567874), (-0.113048, 0.930254, -0.34905), (-0.568065, -0.348733, -0.745444)179.67, 253.383
31generate(0.999999, -0.000494, 7.8E-5), (-0.000483, -0.999992, 0.000166), (7.5E-5, -0.000165, -1.000002)179.67, 253.383
32generate(0.792579, 0.475701, -0.381482), (-0.119369, -0.492451, -0.862118), (-0.597982, 0.728825, -0.333516)179.67, 253.383
33generate(0.456702, 0.889414, -0.018974), (-0.668813, 0.329216, -0.666563), (-0.586611, 0.317105, 0.745216)179.67, 253.383
34generate(0.456545, 0.668897, 0.586628), (-0.88951, 0.329486, 0.316579), (0.018472, -0.666341, 0.745423)179.67, 253.383
35generate(0.792325, 0.11891, 0.598403), (-0.476454, -0.492014, 0.728641), (0.381064, -0.862426, -0.333182)179.67, 253.383
36generate(-0.036257, 0.923529, 0.381803), (-0.34677, -0.369928, 0.86192), (0.937257, -0.101152, 0.333661)179.67, 253.383
37generate(0.309563, 0.158927, 0.937505), (0.196545, -0.975333, 0.10045), (0.930346, 0.153164, -0.333177)179.67, 253.383
38generate(0.82493, -0.457755, 0.331598), (0.099707, -0.459618, -0.882504), (0.556377, 0.761056, -0.333521)179.67, 253.383
39generate(0.797616, -0.074281, -0.598576), (-0.503465, 0.464508, -0.728535), (0.332158, 0.882446, 0.333104)179.67, 253.383
40generate(0.265375, 0.779394, -0.567548), (-0.779397, 0.519937, 0.349579), (0.567551, 0.349567, 0.745444)179.67, 253.383

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Polyprotein


Mass: 29092.826 Da / Num. of mol.: 1 / Fragment: sequence database residues 674-936 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus / References: UniProt: Q155Z9
#2: Protein Polyprotein


Mass: 26492.084 Da / Num. of mol.: 1 / Fragment: sequence database residues 151-434 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus / References: UniProt: Q155Z9
#3: Protein Polyprotein


Mass: 31732.090 Da / Num. of mol.: 1 / Fragment: sequence database residues 435-673 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus / References: UniProt: Q155Z9
#4: Protein Polyprotein


Mass: 7393.875 Da / Num. of mol.: 1 / Fragment: sequence database residues 80-150 / Source method: isolated from a natural source / Source: (natural) Seneca valley virus / References: UniProt: Q155Z9

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Non-polymers , 2 types, 268 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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

CrystalDensity Matthews: 4.52 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 150 mM sodium citrate, 20-25% PEG 350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→92 Å / Num. all: 1968286 / Num. obs: 1968286 / Biso Wilson estimate: 25.2 Å2 / Rsym value: 0.233 / Net I/σ(I): 6.6
Reflection shellResolution: 2.3→2.4 Å / Mean I/σ(I) obs: 0.9 / Rsym value: 0.971

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2MEV

2mev


Resolution: 2.3→88.56 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 125195906.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.26 98592 5 %RANDOM
Rwork0.258 ---
obs0.258 1968286 80.3 %-
all-1968286 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.7387 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2---0.55 Å20 Å2
3---1.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.3→88.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6253 0 1 267 6521
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.377 8993 4.9 %
Rwork0.377 173286 -
obs--44.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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