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- PDB-3lob: Crystal Structure of Flock House Virus calcium mutant -

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Basic information

Entry
Database: PDB / ID: 3lob
TitleCrystal Structure of Flock House Virus calcium mutant
Components
  • Coat protein beta
  • Coat protein gamma
  • RNA (5'-R(*UP*UP*U*AP*UP*CP*UP*(P))-3')
KeywordsVIRUS / Flock House Virus / RNA / beta-barrel / jellyroll / Aspartyl protease / Capsid protein / Hydrolase / Protease / Virion / icosahedral virus
Function / homology
Function and homology information


nodavirus endopeptidase / symbiont entry into host cell via permeabilization of host membrane / T=3 icosahedral viral capsid / aspartic-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase A6, nodavirus coat protein / Peptidase A6 family / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
RNA / Capsid protein alpha
Similarity search - Component
Biological speciesFlock house virus
Spodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsJohnson, J.E. / Banerjee, M. / Speir, J.A. / Huang, R.
CitationJournal: J.Virol. / Year: 2010
Title: Structure and function of a genetically engineered mimic of a nonenveloped virus entry intermediate.
Authors: Banerjee, M. / Speir, J.A. / Kwan, M.H. / Huang, R. / Aryanpur, P.P. / Bothner, B. / Johnson, J.E.
History
DepositionFeb 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 13, 2021Group: Database references / Derived calculations / Polymer sequence
Category: database_2 / entity_poly ...database_2 / entity_poly / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coat protein beta
B: Coat protein beta
C: Coat protein beta
D: Coat protein gamma
E: Coat protein gamma
F: Coat protein gamma
R: RNA (5'-R(*UP*UP*U*AP*UP*CP*UP*(P))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,25412
Polymers133,7747
Non-polymers4805
Water00
1
A: Coat protein beta
B: Coat protein beta
C: Coat protein beta
D: Coat protein gamma
E: Coat protein gamma
F: Coat protein gamma
R: RNA (5'-R(*UP*UP*U*AP*UP*CP*UP*(P))-3')
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,055,257720
Polymers8,026,439420
Non-polymers28,819300
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: Coat protein beta
B: Coat protein beta
C: Coat protein beta
D: Coat protein gamma
E: Coat protein gamma
F: Coat protein gamma
R: RNA (5'-R(*UP*UP*U*AP*UP*CP*UP*(P))-3')
hetero molecules
x 5


  • icosahedral pentamer
  • 671 kDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)671,27160
Polymers668,87035
Non-polymers2,40225
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein beta
B: Coat protein beta
C: Coat protein beta
D: Coat protein gamma
E: Coat protein gamma
F: Coat protein gamma
R: RNA (5'-R(*UP*UP*U*AP*UP*CP*UP*(P))-3')
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 806 kDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)805,52672
Polymers802,64442
Non-polymers2,88230
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: Coat protein beta
B: Coat protein beta
C: Coat protein beta
D: Coat protein gamma
E: Coat protein gamma
F: Coat protein gamma
R: RNA (5'-R(*UP*UP*U*AP*UP*CP*UP*(P))-3')
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 8.06 MDa, 420 polymers
Theoretical massNumber of molelcules
Total (without water)8,055,257720
Polymers8,026,439420
Non-polymers28,819300
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)477.088, 404.929, 476.189
Angle α, β, γ (deg.)90.00, 90.63, 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(0.51689463, -0.4191281, 0.74642586), (0.81763078, 0.5, -0.28544685), (-0.25357414, 0.75784671, 0.60113936)-33.01818, -60.52054, 76.78796
3generate(-0.26478627, 0.13946726, 0.95416828), (0.90382629, -0.30901699, 0.29598401), (0.33613429, 0.94077488, -0.04423072)32.59727, -139.69637, 85.4555
4generate(-0.26478627, 0.90382629, 0.33613429), (0.13946726, -0.30901699, 0.94077489), (0.95416828, 0.295984, -0.04423072)106.16804, -128.10919, 14.02437
5generate(0.51689463, 0.81763078, -0.25357414), (-0.41912811, 0.5, 0.75784671), (0.74642586, -0.28544685, 0.60113936)86.02182, -41.77209, -38.79004
6generate(-0.16848945, 0.98570346), (-1), (0.98570346, 0.16848945)17.71353, -14.94262
7generate(-0.33704019, 0.81763078, 0.46678026), (-0.81763078, -0.5, 0.28544685), (0.46678026, -0.28544685, 0.83704019)98.96691, 60.52054, -34.55079
8generate(0.37594243, 0.90382629, -0.20436566), (-0.90382629, 0.30901699, -0.29598401), (-0.20436566, 0.295984, 0.93307457)96.45501, 139.69637, 31.58698
9generate(0.98514067, 0.13946726, -0.10023346), (-0.13946726, 0.30901699, -0.94077489), (-0.10023346, 0.94077488, 0.32387633)13.6492, 128.10919, 92.07055
10generate(0.64866326, -0.4191281, 0.63526971), (0.41912811, -0.5, -0.75784671), (0.63526971, 0.75784671, -0.14866326)-35.01571, 41.77209, 63.31368
11generate(-1), (1), (-1)231.156, 238.08
12generate(-0.51689463, 0.4191281, -0.74642586), (0.81763078, 0.5, -0.28544685), (0.25357414, -0.75784671, -0.60113936)264.17418, -60.52054, 161.29204
13generate(0.26478627, -0.13946726, -0.95416828), (0.90382629, -0.30901699, 0.29598401), (-0.33613429, -0.94077488, 0.04423072)198.55873, -139.69637, 152.62451
14generate(0.26478627, -0.90382629, -0.33613429), (0.13946726, -0.30901699, 0.94077489), (-0.95416828, -0.295984, 0.04423072)124.98796, -128.10919, 224.05564
15generate(-0.51689463, -0.81763078, 0.25357414), (-0.41912811, 0.5, 0.75784671), (-0.74642586, 0.28544685, -0.60113936)145.13418, -41.77209, 276.87004
16generate(0.16848945, -0.98570346), (-1), (-0.98570346, -0.16848945)213.44247, 253.02262
17generate(0.33704019, -0.81763078, -0.46678026), (-0.81763078, -0.5, 0.28544685), (-0.46678026, 0.28544685, -0.83704019)132.18909, 60.52054, 272.6308
18generate(-0.37594243, -0.90382629, 0.20436566), (-0.90382629, 0.30901699, -0.29598401), (0.20436566, -0.295984, -0.93307457)134.70098, 139.69637, 206.49303
19generate(-0.98514067, -0.13946726, 0.10023346), (-0.13946726, 0.30901699, -0.94077489), (0.10023346, -0.94077488, -0.32387633)217.5068, 128.10919, 146.00946
20generate(-0.64866326, 0.4191281, -0.63526971), (0.41912811, -0.5, -0.75784671), (-0.63526971, -0.75784671, 0.14866326)266.17171, 41.77209, 174.76633
21generate(0.49285173, 0.64479088, 0.58424472), (0.76435903, -0.64479088), (-0.41575528, 0.76435903, -0.49285173)-10.93331, -11.58718, 225.76124
22generate(0.63380393, 0.55859537, 0.53503625), (0.55859537, -0.80901699, 0.18292818), (0.53503625, 0.18292817, -0.82478694)-21.36651, -86.33711, 155.38422
23generate(0.64866326, 0.4191281, 0.63526971), (-0.41912811, -0.5, 0.75784671), (0.63526971, -0.75784671, -0.14866326)-35.01571, -41.77209, 63.31368
24generate(0.51689463, 0.4191281, 0.74642586), (-0.81763078, 0.5, 0.28544685), (-0.25357414, -0.75784671, 0.60113936)-33.01818, 60.52054, 76.78796
25generate(0.42059781, 0.55859537, 0.71489069), (-0.08619551, 0.80901699, -0.58143085), (-0.9031433, 0.18292817, 0.38841919)-18.13444, 79.17583, 177.18608
26generate(0.49285173, -0.64479088, 0.58424472), (-0.76435903, 0.64479088), (-0.41575528, -0.76435903, -0.49285173)-10.93331, 11.58718, 225.76124
27generate(-0.42059781, -0.08619551, 0.9031433), (-0.55859537, 0.80901699, -0.18292818), (-0.71489069, -0.58143085, -0.38841919)56.67967, 86.33711, 247.90306
28generate(-0.51689463, 0.81763078, 0.25357414), (0.41912811, 0.5, -0.75784671), (-0.74642586, -0.28544685, -0.60113936)145.13418, 41.77209, 276.87004
29generate(0.33704019, 0.81763078, -0.46678026), (0.81763078, -0.5, -0.28544685), (-0.46678026, -0.28544685, -0.83704019)132.18909, -60.52054, 272.6308
30generate(0.96109776, -0.08619551, -0.2624146), (0.08619551, -0.80901699, 0.58143085), (-0.2624146, -0.58143085, -0.77011476)35.73408, -79.17583, 241.04382
31generate(-0.49285173, 0.64479088, -0.58424472), (-0.76435903, 0.64479088), (0.41575528, 0.76435903, 0.49285173)242.08931, 11.58718, 12.31877
32generate(0.42059781, 0.08619551, -0.9031433), (-0.55859537, 0.80901699, -0.18292818), (0.71489069, 0.58143085, 0.38841919)174.47633, 86.33711, -9.82305
33generate(0.51689463, -0.81763078, -0.25357414), (0.41912811, 0.5, -0.75784671), (0.74642586, 0.28544685, 0.60113936)86.02182, 41.77209, -38.79004
34generate(-0.33704019, -0.81763078, 0.46678026), (0.81763078, -0.5, -0.28544685), (0.46678026, 0.28544685, 0.83704019)98.96691, -60.52054, -34.55079
35generate(-0.96109776, 0.08619551, 0.2624146), (0.08619551, -0.80901699, 0.58143085), (0.2624146, 0.58143085, 0.77011476)195.42192, -79.17583, -2.96381
36generate(-0.49285173, -0.64479088, -0.58424472), (0.76435903, -0.64479088), (0.41575528, -0.76435903, 0.49285173)242.08931, -11.58718, 12.31877
37generate(-0.63380393, -0.55859537, -0.53503625), (0.55859537, -0.80901699, 0.18292818), (-0.53503625, -0.18292817, 0.82478694)252.52251, -86.33711, 82.69578
38generate(-0.64866326, -0.4191281, -0.63526971), (-0.41912811, -0.5, 0.75784671), (-0.63526971, 0.75784671, 0.14866326)266.17171, -41.77209, 174.76633
39generate(-0.51689463, -0.4191281, -0.74642586), (-0.81763078, 0.5, 0.28544685), (0.25357414, 0.75784671, -0.60113936)264.17418, 60.52054, 161.29204
40generate(-0.42059781, -0.55859537, -0.71489069), (-0.08619551, 0.80901699, -0.58143085), (0.9031433, -0.18292817, -0.38841919)249.29044, 79.17583, 60.89393
41generate(0.49285173, 0.76435903, -0.41575528), (0.64479088, 0.76435903), (0.58424472, -0.64479088, -0.49285173)108.10669, -165.51294, 110.18324
42generate(0.98514067, -0.13946726, -0.10023346), (0.13946726, 0.30901699, 0.94077489), (-0.10023346, -0.94077488, 0.32387633)13.6492, -128.10919, 92.07055
43generate(0.42059781, -0.55859537, 0.71489069), (0.08619551, 0.80901699, 0.58143085), (-0.9031433, -0.18292817, 0.38841919)-18.13444, -79.17583, 177.18608
44generate(-0.42059781, 0.08619551, 0.9031433), (0.55859537, 0.80901699, 0.18292818), (-0.71489069, 0.58143085, -0.38841919)56.67967, -86.33711, 247.90306
45generate(-0.37594243, 0.90382629, 0.20436566), (0.90382629, 0.30901699, 0.29598401), (0.20436566, 0.295984, -0.93307457)134.70098, -139.69637, 206.49303
46generate(-0.49285173, -0.76435903, 0.41575528), (0.64479088, 0.76435903), (-0.58424472, 0.64479088, 0.49285173)123.04931, -165.51294, 127.89677
47generate(-0.98514067, 0.13946726, 0.10023346), (0.13946726, 0.30901699, 0.94077489), (0.10023346, 0.94077488, -0.32387633)217.5068, -128.10919, 146.00946
48generate(-0.42059781, 0.55859537, -0.71489069), (0.08619551, 0.80901699, 0.58143085), (0.9031433, 0.18292817, -0.38841919)249.29044, -79.17583, 60.89393
49generate(0.42059781, -0.08619551, -0.9031433), (0.55859537, 0.80901699, 0.18292818), (0.71489069, -0.58143085, 0.38841919)174.47633, -86.33711, -9.82305
50generate(0.37594243, -0.90382629, -0.20436566), (0.90382629, 0.30901699, 0.29598401), (-0.20436566, -0.295984, 0.93307457)96.45501, -139.69637, 31.58698
51generate(-0.49285173, 0.76435903, 0.41575528), (-0.64479088, -0.76435903), (-0.58424472, -0.64479088, 0.49285173)123.04931, 165.51294, 127.89677
52generate(0.26478627, 0.90382629, -0.33613429), (-0.13946726, -0.30901699, -0.94077489), (-0.95416828, 0.295984, 0.04423072)124.98796, 128.10919, 224.05564
53generate(0.96109776, 0.08619551, -0.2624146), (-0.08619551, -0.80901699, -0.58143085), (-0.2624146, 0.58143085, -0.77011476)35.73408, 79.17583, 241.04382
54generate(0.63380393, -0.55859537, 0.53503625), (-0.55859537, -0.80901699, -0.18292818), (0.53503625, -0.18292817, -0.82478694)-21.36651, 86.33711, 155.38422
55generate(-0.26478627, -0.13946726, 0.95416828), (-0.90382629, -0.30901699, -0.29598401), (0.33613429, -0.94077488, -0.04423072)32.59727, 139.69637, 85.4555
56generate(0.49285173, -0.76435903, -0.41575528), (-0.64479088, -0.76435903), (0.58424472, 0.64479088, -0.49285173)108.10669, 165.51294, 110.18324
57generate(-0.26478627, -0.90382629, 0.33613429), (-0.13946726, -0.30901699, -0.94077489), (0.95416828, -0.295984, -0.04423072)106.16804, 128.10919, 14.02437
58generate(-0.96109776, -0.08619551, 0.2624146), (-0.08619551, -0.80901699, -0.58143085), (0.2624146, -0.58143085, 0.77011476)195.42192, 79.17583, -2.96381
59generate(-0.63380393, 0.55859537, -0.53503625), (-0.55859537, -0.80901699, -0.18292818), (-0.53503625, 0.18292817, 0.82478694)252.52251, 86.33711, 82.69578
60generate(0.26478627, 0.13946726, -0.95416828), (-0.90382629, -0.30901699, -0.29598401), (-0.33613429, 0.94077488, 0.04423072)198.55873, 139.69637, 152.62451
DetailsThe biological unit is a virus capsid. The biological assembly can be generated by treating the contents of the asymmetric unit with the virus matrices uploaded in the "supplemental information" section.

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Components

#1: Protein Coat protein beta / Coat protein beta / Nodavirus endopeptidase / Coat protein gamma


Mass: 39362.426 Da / Num. of mol.: 3 / Mutation: D161N, D221N, D249N, E251Q, E257Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flock house virus / Gene: alpha, Flock House Virus coat protein alpha / Plasmid: pBacPAK9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12870, nodavirus endopeptidase
#2: Protein/peptide Coat protein gamma / Coat protein beta / Nodavirus endopeptidase / Coat protein gamma


Mass: 4399.056 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flock house virus / Gene: alpha, Flock House Virus coat protein alpha / Plasmid: pBacPAK9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12870
#3: RNA chain RNA (5'-R(*UP*UP*U*AP*UP*CP*UP*(P))-3')


Mass: 2489.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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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: 295 K / Method: vapor diffusion / pH: 4
Details: 100 mM sodium citrate, pH 4.0, 4% PEG 8000 and 100 mM lithium sulfate, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.6→40 Å / Num. all: 474211 / Num. obs: 372968 / % possible obs: 35.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.3 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 5.73
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 1.37 / % possible all: 17.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
GLRFphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FHV wildtype structure

Resolution: 3.6→40 Å / Isotropic thermal model: UNRESTRAINED GROUPS / Cross valid method: NOT USED / σ(F): 0
Details: CROSS-VALIDATION NOT USED DUE TO 60-FOLD NON-CRYSTALLOGRAPHIC SYMMETRY
RfactorNum. reflection% reflectionSelection details
Rwork0.347 ---
obs0.347 327303 31.5 %-
all-327303 --
Rfree---NOT USED
Solvent computationSolvent model: FLAT / Bsol: 135.4 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 182.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å270.32 Å2
2---56.17 Å20 Å2
3---57.83 Å2
Refine analyzeLuzzati coordinate error obs: 1.13 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 1.6 Å
Refinement stepCycle: LAST / Resolution: 3.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7138 136 25 0 7299
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.49
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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: CONSTRAINED
LS refinement shellResolution: 3.6→3.76 Å /
Rfactor% reflection
Rwork0.545 -
obs-16.7 %

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