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- PDB-6qt9: Cryo-EM structure of SH1 full particle. -

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Basic information

Entry
Database: PDB / ID: 6qt9
TitleCryo-EM structure of SH1 full particle.
Components
  • (ORF 24) x 3
  • (ORF 25) x 2
  • ORF 31
  • VP12
  • VP13
KeywordsVIRUS / euryarcheal virus / SH1
Function / homologyORF 31 / ORF 25 / ORF 24
Function and homology information
Biological speciesHaloarcula hispanica virus SH1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDe Colibus, L. / Roine, E. / Walter, T.S. / Ilca, S.L. / Wang, X. / Wang, N. / Roseman, A.M. / Bamford, D. / Huiskonen, J.T. / Stuart, D.I.
Funding support United Kingdom, Finland, 4items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N00065X/1 United Kingdom
European Research Council649053 United Kingdom
Academy of Finland255342 Finland
Academy of Finland256518 Finland
CitationJournal: Nat Commun / Year: 2019
Title: Assembly of complex viruses exemplified by a halophilic euryarchaeal virus.
Authors: Luigi De Colibus / Elina Roine / Thomas S Walter / Serban L Ilca / Xiangxi Wang / Nan Wang / Alan M Roseman / Dennis Bamford / Juha T Huiskonen / David I Stuart /
Abstract: Many of the largest known viruses belong to the PRD1-adeno structural lineage characterised by conserved pseudo-hexameric capsomers composed of three copies of a single major capsid protein (MCP). ...Many of the largest known viruses belong to the PRD1-adeno structural lineage characterised by conserved pseudo-hexameric capsomers composed of three copies of a single major capsid protein (MCP). Here, by high-resolution cryo-EM analysis, we show that a class of archaeal viruses possess hetero-hexameric MCPs which mimic the PRD1-adeno lineage trimer. These hetero-hexamers are built from heterodimers and utilise a jigsaw-puzzle system of pegs and holes, and underlying minor capsid proteins, to assemble the capsid laterally from the 5-fold vertices. At these vertices proteins engage inwards with the internal membrane vesicle whilst 2-fold symmetric horn-like structures protrude outwards. The horns are assembled from repeated globular domains attached to a central spine, presumably facilitating multimeric attachment to the cell receptor. Such viruses may represent precursors of the main PRD1-adeno lineage, similarly engaging cell-receptors via 5-fold spikes and using minor proteins to define particle size.
History
DepositionFeb 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Refinement description / Category: em_3d_fitting / Item: _em_3d_fitting.target_criteria
Revision 1.2Nov 27, 2019Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.3Dec 18, 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]

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Structure visualization

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  • Biological unit as software_defined_assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-4633
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Assembly

Deposited unit
A: ORF 25
C: ORF 25
D: ORF 25
E: ORF 25
F: ORF 25
G: ORF 25
H: ORF 25
I: ORF 25
J: ORF 25
K: ORF 25
L: ORF 25
M: ORF 25
a: ORF 24
b: ORF 24
c: ORF 24
d: ORF 24
e: ORF 24
f: ORF 24
g: ORF 24
h: ORF 24
i: ORF 24
j: ORF 24
k: ORF 24
l: ORF 24
m: ORF 24
n: ORF 24
o: ORF 24
Y: ORF 31
X: VP12
W: VP13


Theoretical massNumber of molelcules
Total (without water)604,18830
Polymers604,18830
Non-polymers00
Water0
1
A: ORF 25
C: ORF 25
D: ORF 25
E: ORF 25
F: ORF 25
G: ORF 25
H: ORF 25
I: ORF 25
J: ORF 25
K: ORF 25
L: ORF 25
M: ORF 25
a: ORF 24
b: ORF 24
c: ORF 24
d: ORF 24
e: ORF 24
f: ORF 24
g: ORF 24
h: ORF 24
i: ORF 24
j: ORF 24
k: ORF 24
l: ORF 24
m: ORF 24
n: ORF 24
o: ORF 24
Y: ORF 31
X: VP12
W: VP13
x 60


Theoretical massNumber of molelcules
Total (without water)36,251,3051800
Polymers36,251,3051800
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation59
Buried area68770 Å2
ΔGint-68 kcal/mol
Surface area233330 Å2
MethodPISA

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Components

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Protein , 7 types, 29 molecules ADCEFGHIJKLMabcdefijkmoglnhYW

#1: Protein ORF 25


Mass: 25042.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Haloarcula hispanica virus SH1 / References: UniProt: Q4KPG2
#2: Protein
ORF 25


Mass: 24913.094 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Haloarcula hispanica virus SH1 / References: UniProt: Q4KPG2
#3: Protein
ORF 24


Mass: 18840.627 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Haloarcula hispanica virus SH1 / References: UniProt: Q4KPG3
#4: Protein ORF 24


Mass: 18272.000 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Haloarcula hispanica virus SH1 / References: UniProt: Q4KPG3
#5: Protein ORF 24


Mass: 19040.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula hispanica virus SH1 / References: UniProt: Q4KPG3
#6: Protein ORF 31


Mass: 14982.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula hispanica virus SH1 / References: UniProt: Q4KPF6
#8: Protein VP13


Mass: 6826.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula hispanica virus SH1

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Protein/peptide , 1 types, 1 molecules X

#7: Protein/peptide VP12


Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula hispanica virus SH1

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Haloarcula hispanica virus SH1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Haloarcula hispanica virus SH1
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Haloarcula hispanica virus SH1
Virus shellName: Capsid / Diameter: 1000 nm / Triangulation number (T number): 28
Buffer solutionpH: 7.2 / Details: 20mM Tris-HCl pH 7.2, 1M NaCl, 10 mM MnCl2
SpecimenConc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K

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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 FIELDBright-field microscopy / Nominal magnification: 160000 X / Calibrated magnification: 37037 X
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingAverage exposure time: 4.4 sec. / Electron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 22

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1ETHANparticle selection
2SerialEMimage acquisition
4CTFFIND4.1.5CTF correction
7Rosetta2018.33.60351model fitting
8Coot0.8.9.1model fitting
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignmentcustom
12RELION2.1classificationcustom
13cisTEM3D reconstruction
20PHENIX1.14_3260model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 16185
Details: This number of particle was generated by merging the datasets of full particles with and without spikes.
SymmetryPoint symmetry: C532 (532 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16185 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingB value: 144.281 / Protocol: BACKBONE TRACE / Space: REAL / Target criteria: Cross-correlation coefficient

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