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

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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 / homologyintegral component of membrane / Major virion protein
Function and homology information
Specimen sourceAeropyrum pernix bacilliform virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsHuiskonen, J.T. / Ptchelkine, D. / Phillpps, S.E.V.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 6, 2017 / Release: Nov 22, 2017
RevisionDateData content typeGroupCategoryProviderType
1.0Nov 22, 2017Structure modelrepositoryInitial release
1.1Oct 17, 2018Structure modelData collection / Refinement descriptionrefine

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Deposited unit
A: Major virion protein

Theoretical massNumber of molelcules
Total (without water)8,2731
A: Major virion protein
x 135

Theoretical massNumber of molelcules
Total (without water)1,116,836135
TypeNameSymmetry operationNumber
point symmetry operation135


#1: Protein/peptide Major virion protein

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

Experimental details


EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: single particle reconstruction

Sample preparation

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

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 37037 / Cs: 2 mm / C2 aperture diameter: 5 mm
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


SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
EM software
2SerialEMimage acquisition
4CTFFIND3CTF correction
7Cootmodel fitting
9SPRINGinitial Euler assignment
10SPRINGfinal Euler assignment
12SPRING3D reconstruction
13REFMACmodel refinement
14PHENIXmodel refinement
Particle selectionDetails: Overlapping segments extracted from helical particles
Number of particles selected: 169316
SymmetryPoint symmetry: C5
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 94645 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL
RefineCorrelation coeff Fo to Fc: 0.898 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall ESU R: 0.328
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 86.033 Å2 / Aniso B11: 0.95 Å2 / Aniso B12: 2.73 Å2 / Aniso B13: 0.16 Å2 / Aniso B22: -0.7 Å2 / Aniso B23: 1.59 Å2 / Aniso B33: -0.25 Å2
Least-squares processR factor R work: 0.27071 / R factor obs: 0.27071 / Highest resolution: 3.5 Å / Lowest resolution: 113.4 Å / Number reflection obs: 43610 / Percent reflection obs: 1
Number of atoms included #1Total: 3528
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0120.0193598
ELECTRON MICROSCOPYr_bond_other_d0.0000.0203591
ELECTRON MICROSCOPYr_angle_refined_deg1.9841.9864886
ELECTRON MICROSCOPYr_angle_other_deg3.7423.0008232
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.0115.000483
ELECTRON MICROSCOPYr_dihedral_angle_2_deg31.72621.42998
ELECTRON MICROSCOPYr_dihedral_angle_3_deg24.64415.000539
ELECTRON MICROSCOPYr_dihedral_angle_4_deg15.73115.00014
ELECTRON MICROSCOPYr_chiral_restr0.1230.200588
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0213997
ELECTRON MICROSCOPYr_gen_planes_other0.0060.020749
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_other11.6509.4001646
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
Refine LS shellHighest resolution: 3.5 Å / R factor R work: 0.773 / Lowest resolution: 3.591 Å / Number reflection R free: 0 / Number reflection R work: 3199 / Total number of bins used: 20 / Percent reflection obs: 1

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