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- PDB-3hag: Crystal structure of the Hepatitis E Virus-like Particle -

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Basic information

Entry
Database: PDB / ID: 3hag
TitleCrystal structure of the Hepatitis E Virus-like Particle
ComponentsCapsid proteinCapsid
KeywordsVIRUS / jelly-roll beta sheets / beta barrel / icosahedral virus
Function / homology
Function and homology information


T=1 icosahedral viral capsid / viral capsid / host cell surface / host cell cytoplasm / structural molecule activity / RNA binding / identical protein binding / cytoplasm
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #190 / Hepatitis E virus structural protein 2 / Structural protein 2 nucleoplasmin-like domain / Jelly Rolls - #20 / Elongation Factor Tu (Ef-tu); domain 3 / Viral coat protein subunit / Jelly Rolls / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein ORF2 / Capsid protein
Similarity search - Component
Biological speciesHepatitis E virus type 4
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rave / Resolution: 3.5 Å
AuthorsGuu, T.S.Y. / Liu, Z. / Ye, Q. / Mata, D.A. / Li, K. / Yin, C. / Zhang, J. / Tao, Y.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of the hepatitis E virus-like particle suggests mechanisms for virus assembly and receptor binding.
Authors: Guu, T.S. / Liu, Z. / Ye, Q. / Mata, D.A. / Li, K. / Yin, C. / Zhang, J. / Tao, Y.J.
History
DepositionMay 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)54,4471
Polymers54,4471
Non-polymers00
Water0
1
A: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,266,79460
Polymers3,266,79460
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
x 5


  • icosahedral pentamer
  • 272 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)272,2335
Polymers272,2335
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 327 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)326,6796
Polymers326,6796
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
x 20


  • crystal asymmetric unit, crystal frame
  • 1.09 MDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)1,088,93120
Polymers1,088,93120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)241.092, 241.092, 519.861
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.41774022, -0.62980264, 0.65486009), (0.88171676, 0.45493963, -0.12492192), (-0.21924566, 0.62958602, 0.74535413)
3generate(-0.52437588, -0.13732532, 0.84034023), (0.79684504, -0.42698657, 0.42745812), (0.30011316, 0.89376967, 0.33332846)
4generate(-0.52437588, 0.79684505, 0.30011317), (-0.13732532, -0.42698657, 0.89376967), (0.84034022, 0.42745813, 0.33332845)
5generate(0.41774023, 0.88171676, -0.21924566), (-0.62980264, 0.45493963, 0.62958603), (0.65486009, -0.12492191, 0.74535413)
6generate(-0.99625286, 0.07058442, 0.04998077), (0.07058442, 0.32959033, 0.94148184), (0.04998077, 0.94148184, -0.33333747)
7generate(-0.36489749, 0.69102152, -0.62397041), (0.11367546, 0.69823326, 0.70678724), (0.92408209, 0.18697477, -0.33333577)
8generate(0.5936557, 0.15134344, -0.79035946), (0.50817075, 0.69104425, 0.51402368), (0.62396746, -0.70679064, 0.33333404)
9generate(0.55471879, -0.80263307, -0.21924238), (0.7088912, 0.31795826, 0.62958384), (-0.43561489, -0.50466098, 0.74535694)
10generate(-0.42789874, -0.85254489, 0.30011645), (0.43844797, 0.09456746, 0.89376752), (-0.79035818, 0.51402744, 0.33333128)
11generate(-0.06299687, -0.60939589, 0.79035944), (-0.60939589, -0.60366904, -0.51402368), (0.79035944, -0.51402367, -0.33333409)
12generate(-0.73691377, 0.26003651, 0.62397045), (-0.67413683, -0.21445596, -0.70678722), (-0.04997631, -0.94148269, 0.33333574)
13generate(-0.21536278, 0.97525422, -0.04998073), (-0.31574345, -0.11797472, -0.94148183), (-0.92408059, -0.18697906, 0.3333375)
14generate(0.78089035, 0.54785068, -0.30011646), (-0.02950322, -0.44755912, -0.89376753), (-0.623971, 0.70678884, -0.33333123)
15generate(0.87505767, -0.43151695, 0.21924233), (-0.21099041, -0.74773472, -0.62958386), (0.43561121, 0.50466415, -0.74535694)
16generate(0.05924973, 0.53881147, -0.84034021), (0.53881147, -0.72592129, -0.42745817), (-0.84034021, -0.42745816, -0.33332844)
17generate(0.68407104, -0.32125539, -0.65486013), (-0.3212554, -0.93871694, 0.1249219), (-0.65486012, 0.12492189, -0.7453541)
18generate(0.14608296, -0.98927234, -4.0E-8), (-0.98927234, -0.14608296, 4.0E-8), (-3.0E-8, 3.0E-8, -1)
19generate(-0.81123327, -0.54206266, 0.21924567), (-0.54206265, 0.55658742, -0.62958599), (0.21924567, -0.62958599, -0.74535416)
20generate(-0.86489916, 0.40234507, -0.30011312), (0.40234508, 0.19822763, -0.89376968), (-0.30011312, -0.89376968, -0.33332847)

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Components

#1: Protein Capsid protein / Capsid


Mass: 54446.559 Da / Num. of mol.: 1 / Fragment: Hepatitis Capsid Protein 110-608
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis E virus type 4 / Strain: China/T1 / Plasmid: pFastbac 1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 / References: UniProt: Q8JVV3, UniProt: Q9IVZ8*PLUS
Sequence detailsTHESE CONFLICTS ARE DUE TO DIFFERENT STRAINS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5M Lithium Sulfate Monohydrate 0.1M Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 214104 / Num. obs: 202478 / % possible obs: 94.6 %
Reflection shellHighest resolution: 3.5 Å / % possible all: 92.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
RAVEmodel building
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RAVEphasing
RefinementMethod to determine structure: Rave
Starting model: 14A EM-map

Resolution: 3.5→50 Å / Isotropic thermal model: Isotropic / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.286 8043 random
Rwork0.2767 --
all-214104 -
obs-202478 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.444 Å20 Å20 Å2
2--4.444 Å20 Å2
3----8.887 Å2
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3589 0 0 0 3589
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.47054
X-RAY DIFFRACTIONc_bond_d0.008943
LS refinement shellResolution: 3.5→3.66 Å
RfactorNum. reflection
Rfree0.3531 1010
Rwork0.3418 -
obs-24118

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