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- PDB-5oxe: Structure of major capsid protein VP1 of Aeropyrum pernix bacilli... -

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Entry
Database: PDB / ID: 5oxe
TitleStructure of major capsid protein VP1 of Aeropyrum pernix bacilliform virus 1 APBV1
ComponentsMajor virion protein
KeywordsVIRUS / archaeal virus / thermophile / capsid / helical
Function / homologymembrane / Major virion protein
Function and homology information
Biological speciesAeropyrum pernix bacilliform virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHuiskonen, J.T. / Ptchelkine, D. / Phillpps, S.E.V.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust203141/Z/16/Z United Kingdom
Wellcome Trust060208/Z/00/Z United Kingdom
Wellcome Trust093305/Z/10/Z United Kingdom
European Research Council649053 United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging.
Authors: Denis Ptchelkine / Ashley Gillum / Tomohiro Mochizuki / Soizick Lucas-Staat / Ying Liu / Mart Krupovic / Simon E V Phillips / David Prangishvili / Juha T Huiskonen /
Abstract: Archaeal viruses have evolved to infect hosts often thriving in extreme conditions such as high temperatures. However, there is a paucity of information on archaeal virion structures, genome ...Archaeal viruses have evolved to infect hosts often thriving in extreme conditions such as high temperatures. However, there is a paucity of information on archaeal virion structures, genome packaging, and determinants of temperature resistance. The rod-shaped virus APBV1 (Aeropyrum pernix bacilliform virus 1) is among the most thermostable viruses known; it infects a hyperthermophile Aeropyrum pernix, which grows optimally at 90 °C. Here we report the structure of APBV1, determined by cryo-electron microscopy at near-atomic resolution. Tight packing of the major virion glycoprotein (VP1) is ensured by extended hydrophobic interfaces, and likely contributes to the extreme thermostability of the helical capsid. The double-stranded DNA is tightly packed in the capsid as a left-handed superhelix and held in place by the interactions with positively charged residues of VP1. The assembly is closed by specific capping structures at either end, which we propose to play a role in DNA packing and delivery.
History
DepositionSep 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Refinement description / Category: refine
Revision 1.2Nov 6, 2019Group: Data collection / Category: em_software / Item: _em_software.name / _em_software.version
Revision 1.3Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.4May 15, 2024Group: 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_struct_oper_list / refine
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 / _refine.ls_d_res_high / _refine.ls_d_res_low

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Assembly

Deposited unit
A: Major virion protein


Theoretical massNumber of molelcules
Total (without water)8,2731
Polymers8,2731
Non-polymers00
Water00
1
A: Major virion protein
x 135


Theoretical massNumber of molelcules
Total (without water)1,116,836135
Polymers1,116,836135
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation134

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Components

#1: Protein Major virion protein


Mass: 8272.858 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aeropyrum pernix bacilliform virus 1 / References: UniProt: D4QF72

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Aeropyrum pernix bacilliform virus 1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Aeropyrum pernix bacilliform virus 1
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Aeropyrum pernix
Buffer solutionpH: 7 / Details: distilled water
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 37037 X / Cs: 2 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
EM imaging opticsEnergyfilter name: K2 Summit / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV

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Processing

SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND3CTF correction
7Cootmodel fitting
9SPRINGinitial Euler assignment
10SPRINGfinal Euler assignment
12SPRING3D reconstruction
13REFMACmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 169316
Details: Overlapping segments extracted from helical particles
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94645 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementResolution: 3.7→3.7 Å / Cor.coef. Fo:Fc: 0.898 / ESU R: 0.328
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.27071 --
obs0.27071 43610 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 86.033 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å22.73 Å20.16 Å2
2---0.7 Å21.59 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Total: 3528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0120.0193598
ELECTRON MICROSCOPYr_bond_other_d00.023591
ELECTRON MICROSCOPYr_angle_refined_deg1.9841.9864886
ELECTRON MICROSCOPYr_angle_other_deg3.74238232
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.0115483
ELECTRON MICROSCOPYr_dihedral_angle_2_deg31.72621.42998
ELECTRON MICROSCOPYr_dihedral_angle_3_deg24.64415539
ELECTRON MICROSCOPYr_dihedral_angle_4_deg15.7311514
ELECTRON MICROSCOPYr_chiral_restr0.1230.2588
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0213997
ELECTRON MICROSCOPYr_gen_planes_other0.0060.02749
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it8.2287.8571953
ELECTRON MICROSCOPYr_mcbond_other8.2267.8461952
ELECTRON MICROSCOPYr_mcangle_it13.87311.7092429
ELECTRON MICROSCOPYr_mcangle_other13.87211.7212430
ELECTRON MICROSCOPYr_scbond_it11.6549.3961645
ELECTRON MICROSCOPYr_scbond_other11.659.41646
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other19.05513.4122458
ELECTRON MICROSCOPYr_long_range_B_refined22.82995.9354239
ELECTRON MICROSCOPYr_long_range_B_other22.82895.9394240
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.773 3199 -
Rfree-0 -
obs--100 %

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