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- PDB-4qpg: Crystal structure of empty hepatitis A virus -

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Basic information

Entry
Database: PDB / ID: 4qpg
TitleCrystal structure of empty hepatitis A virus
Components
  • Capsid protein VP0
  • Capsid protein VP1
  • Capsid protein VP3
KeywordsVIRUS / evolution / insect picorna-like viruses / ICOSAHEDRAL / domain swap / beta-barrel / PICORNAVIRUS / pathogen / Liver
Function / homology
Function and homology information


host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / : / nucleoside-triphosphate phosphatase / protein complex oligomerization ...host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
: / 2B protein soluble domain / Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) ...: / 2B protein soluble domain / Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman hepatitis A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsWang, X. / Ren, J. / Gao, Q. / Hu, Z. / Sun, Y. / Li, X. / Rowlands, D.J. / Yin, W. / Wang, J. / Stuart, D.I. ...Wang, X. / Ren, J. / Gao, Q. / Hu, Z. / Sun, Y. / Li, X. / Rowlands, D.J. / Yin, W. / Wang, J. / Stuart, D.I. / Rao, Z. / Fry, E.E.
CitationJournal: Nature / Year: 2015
Title: Hepatitis A virus and the origins of picornaviruses.
Authors: Wang, X. / Ren, J. / Gao, Q. / Hu, Z. / Sun, Y. / Li, X. / Rowlands, D.J. / Yin, W. / Wang, J. / Stuart, D.I. / Rao, Z. / Fry, E.E.
History
DepositionJun 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Sep 20, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP0
C: Capsid protein VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1807
Polymers75,9173
Non-polymers2634
Water0
1
A: Capsid protein VP1
B: Capsid protein VP0
C: Capsid protein VP3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,570,806420
Polymers4,555,025180
Non-polymers15,782240
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 VP1
B: Capsid protein VP0
C: Capsid protein VP3
hetero molecules
x 5


  • icosahedral pentamer
  • 381 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)380,90135
Polymers379,58515
Non-polymers1,31520
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
B: Capsid protein VP0
C: Capsid protein VP3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 457 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)457,08142
Polymers455,50218
Non-polymers1,57824
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 VP1
B: Capsid protein VP0
C: Capsid protein VP3
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 2.29 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)2,285,403210
Polymers2,277,51290
Non-polymers7,891120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)366.114, 442.914, 289.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.5613, -0.2494, -0.7891), (0.751, 0.5542, 0.359), (0.3478, -0.7941, 0.4984)60.05, 97.26, 179.5
3generate(-0.141, 0.3509, -0.9257), (0.9636, -0.1658, -0.2096), (-0.227, -0.9216, -0.3148)-72.15, 260.3, 212.9
4generate(-0.133, 0.9638, -0.2311), (0.349, -0.1727, -0.9211), (-0.9276, -0.2032, -0.3134)-211.5, 265.5, 53.51
5generate(0.5648, 0.7508, 0.3424), (-0.2509, 0.5515, -0.7955), (-0.7862, 0.3634, 0.4999)-168.2, 104, -77.46
6generate(-0.4994, -0.4866, -0.7168), (0.515, 0.4987, -0.6972), (0.6967, -0.7173, 0.001543)112.1, 115.5, 164.6
7generate(-0.8949, 0.4242, -0.1388), (0.4218, 0.7019, -0.574), (-0.1461, -0.5722, -0.807)-93.78, 69.73, 137
8generate(-0.237, 0.571, 0.786), (0.571, 0.7364, -0.3628), (-0.786, 0.3628, -0.5006)-131.7, 60.84, -71.3
9generate(0.5648, -0.2485, 0.7869), (0.7511, 0.5498, -0.3655), (-0.3418, 0.7975, 0.4972)50.09, 102.2, -173
10generate(0.403, -0.9038, -0.1438), (0.7104, 0.408, -0.5735), (0.577, 0.129, 0.8065)201.2, 134.8, -26.77
11generate(-0.4996, 0.5127, 0.6983), (-0.4868, 0.5006, -0.7158), (-0.7166, -0.6975, -0.000474)-117.8, 114.9, 160.6
12generate(0.3453, -0.1445, 0.9273), (-0.1478, 0.9674, 0.2058), (-0.9268, -0.2081, 0.3127)26.91, 5.953, 49.85
13generate(0.4042, -0.904, 0.1396), (0.7125, 0.4068, 0.5717), (-0.5736, -0.1316, 0.8085)199.8, 127.7, 29.91
14generate(-0.4026, -0.7134, -0.5736), (0.9039, -0.4089, -0.1258), (-0.1448, -0.5691, 0.8094)161.4, 312.5, 127
15generate(-0.9602, 0.1616, -0.2278), (0.1602, -0.3495, -0.9231), (-0.2288, -0.9229, 0.3097)-34.84, 304.3, 208.6
16generate(-0.8928, 0.4278, 0.1411), (0.4266, 0.7025, 0.5697), (0.1446, 0.5688, -0.8097)-95.34, 62.61, -114.8
17generate(-0.1356, 0.3451, 0.9287), (0.964, -0.1705, 0.2041), (0.2287, 0.9229, -0.3096)-81.96, 258.4, -196.6
18generate(0.4986, -0.5134, 0.6984), (0.4882, -0.4994, -0.7157), (0.7162, 0.6979, 0.001678)109.2, 336.5, -148.7
19generate(0.138, -0.963, -0.2314), (-0.3495, 0.1712, -0.9212), (0.9267, 0.208, -0.313)214.8, 188.6, -37.75
20generate(-0.7236, -0.3828, -0.5743), (-0.3847, 0.9146, -0.1249), (0.573, 0.1305, -0.8091)88.28, 19.31, -17.64
21generate(0.7642, 0.5488, 0.3389), (0.5424, -0.2626, -0.798), (-0.349, 0.7936, -0.4983)-122.9, 284.7, -167.4
22generate(0.9606, -0.1589, -0.228), (-0.1604, 0.3532, -0.9217), (0.227, 0.922, 0.3138)36.85, 149.4, -200.8
23generate(0.3428, -0.148, -0.9277), (-0.1436, 0.9677, -0.2074), (0.9284, 0.2043, 0.3104)38.41, 8.845, -41.27
24generate(-0.237, 0.571, -0.786), (0.5722, 0.7359, 0.3621), (0.7851, -0.3639, -0.5012)-121.9, 56.61, 89.69
25generate(0.02659, 0.9996, -0.001041), (0.9996, -0.02659, -0.000731), (-0.000759, -0.001021, -1)-221.2, 227.5, 12.21
26generate(-0.3981, -0.7143, 0.5755), (0.9058, -0.4052, 0.1237), (0.1449, 0.5706, 0.8084)154.7, 311.1, -124.9
27generate(-0.562, -0.7537, 0.3407), (0.2514, -0.5481, -0.7977), (0.788, -0.3627, 0.4975)164.9, 348.4, 83.86
28generate(-0.767, -0.5438, 0.3406), (-0.5426, 0.2664, -0.7966), (0.3424, -0.7958, -0.4994)118.3, 167.8, 185.1
29generate(-0.7219, -0.384, 0.5756), (-0.384, 0.9144, 0.1283), (-0.5756, -0.1284, -0.8076)81.47, 18.06, 38.99
30generate(-0.4997, -0.4864, 0.7168), (0.5131, 0.5004, 0.6973), (-0.6979, 0.7162, -0.000503)103.3, 106.5, -152.5

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Components

#1: Protein Capsid protein VP1 / / HAV


Mass: 25258.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human hepatitis A virus / Strain: TZ84 / References: UniProt: Q8QXR6*PLUS
#2: Protein Capsid protein VP0 / / HAV


Mass: 22822.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human hepatitis A virus / Strain: TZ84 / References: UniProt: P08617*PLUS
#3: Protein Capsid protein VP3 / / HAV


Mass: 27835.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human hepatitis A virus / Strain: TZ84 / References: UniProt: P08617*PLUS
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 17

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% MPD and 0.5 M ammonium sulphate as precipitants and 0.1 M HEPES-Na buffer at pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 404893 / % possible obs: 68 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 155.1 Å2 / Rmerge(I) obs: 0.363 / Net I/σ(I): 3
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 0.3 / Num. unique all: 2925 / % possible all: 9.9

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Processing

Software
NameVersionClassification
GDAdata collection
MOLREPphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FMD

1fmd


Resolution: 3.5→49.67 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 13718776.56 / 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
Rfree0.263 3880 1 %RANDOM
Rwork0.264 ---
obs0.264 396724 67.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 119.226 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 180.3 Å2
Baniso -1Baniso -2Baniso -3
1--6.3 Å20 Å2-0 Å2
2---24.59 Å2-0 Å2
3---30.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.65 Å0.64 Å
Luzzati d res low-6 Å
Luzzati sigma a0.89 Å0.96 Å
Refinement stepCycle: LAST / Resolution: 3.5→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5356 0 12 0 5368
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it5.676
X-RAY DIFFRACTIONc_mcangle_it9.1512
X-RAY DIFFRACTIONc_scbond_it9.238
X-RAY DIFFRACTIONc_scangle_it13.6616
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 264 1 %
Rwork0.404 26357 -
obs--27.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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