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- PDB-6h9c: Cryo-EM structure of archaeal extremophilic internal membrane-con... -

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Basic information

Entry
Database: PDB / ID: 6h9c
TitleCryo-EM structure of archaeal extremophilic internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) at 3.74 Angstroms resolution.
Components
  • (Half) GPS-II protein located underneath the two-tower capsomer sitting ON the icosahedral 2-fold axis.
  • GPS-II protein located underneath the two-tower capsomer NOT sitting on the icosahedral 2-fold axis.
  • GPS-III molecule located underneath the capsomer close to the icosahedral three-fold axis.
  • Peripentonal unknown polypeptide
  • VP4
  • VP7
  • VP9
KeywordsVIRUS / vertical single beta-barrel virus / internal membrane-containing archaeal virus.
Function / homologyVP7 / VP4 / VP9
Function and homology information
Biological speciesHaloarcula californiae ATCC 33799 (Halophile)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsAbrescia, N.G. / Santos-Perez, I. / Charro, D.
Funding support Spain, Finland, 4items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2015-64541-R Spain
Spanish Ministry of Economy and CompetitivenessSEV-2016-0644 Spain
Academy of Finland1306833, 255342,256518,283072 Finland
Other governmentBasque Governament PRE_2016_2_0151 Spain
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for assembly of vertical single β-barrel viruses.
Authors: Isaac Santos-Pérez / Diego Charro / David Gil-Carton / Mikel Azkargorta / Felix Elortza / Dennis H Bamford / Hanna M Oksanen / Nicola G A Abrescia /
Abstract: The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The ...The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The discovery of PRD1-like viruses with two MCPs challenged the known assembly principles. Here, we present the cryo-electron microscopy (cryo-EM) structures of the archaeal, halophilic, internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) and Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.7 and 3.8 Å resolution, respectively. Our structures reveal proteins located beneath the morphologically distinct two- and three-tower capsomers and homopentameric membrane proteins at the vertices that orchestrate the positioning of pre-formed vertical single β-barrel MCP heterodimers. The cryo-EM based structures together with the proteomics data provide insights into the assembly mechanism of this type of viruses and into those with membrane-less double β-barrel MCPs.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Data processing
Category: em_3d_reconstruction / pdbx_seq_map_depositor_info
Item: _em_3d_reconstruction.resolution / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Dec 14, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
D: VP7
b: VP9
c: GPS-III molecule located underneath the capsomer close to the icosahedral three-fold axis.
d: GPS-II protein located underneath the two-tower capsomer NOT sitting on the icosahedral 2-fold axis.
e: (Half) GPS-II protein located underneath the two-tower capsomer sitting ON the icosahedral 2-fold axis.
f: Peripentonal unknown polypeptide
Z: VP4
A: VP4
B: VP4
C: VP4
P: VP4
Q: VP4
O: VP4
V: VP4
U: VP4
H: VP4
G: VP4
X: VP4
F: VP7
E: VP7
R: VP7
T: VP7
S: VP7
W: VP7
K: VP7
J: VP7
M: VP7
N: VP7
I: VP7
L: VP7
a: VP7
Y: VP7


Theoretical massNumber of molelcules
Total (without water)648,00032
Polymers648,00032
Non-polymers00
Water00
1
D: VP7
b: VP9
c: GPS-III molecule located underneath the capsomer close to the icosahedral three-fold axis.
d: GPS-II protein located underneath the two-tower capsomer NOT sitting on the icosahedral 2-fold axis.
e: (Half) GPS-II protein located underneath the two-tower capsomer sitting ON the icosahedral 2-fold axis.
f: Peripentonal unknown polypeptide
Z: VP4
A: VP4
B: VP4
C: VP4
P: VP4
Q: VP4
O: VP4
V: VP4
U: VP4
H: VP4
G: VP4
X: VP4
F: VP7
E: VP7
R: VP7
T: VP7
S: VP7
W: VP7
K: VP7
J: VP7
M: VP7
N: VP7
I: VP7
L: VP7
a: VP7
Y: VP7
x 60


Theoretical massNumber of molelcules
Total (without water)38,880,0191920
Polymers38,880,0191920
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

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Protein , 5 types, 30 molecules DFERTSWKJMNILaYbcdZABCPQOVUHGX

#1: Protein
VP7


Mass: 19912.832 Da / Num. of mol.: 15 / Source method: isolated from a natural source
Source: (natural) Haloarcula californiae ATCC 33799 (Halophile)
Plasmid details: Haloarcula californiae icosahedral virus 1 / References: UniProt: A0A1C7A3R1
#2: Protein VP9


Mass: 16271.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloarcula californiae ATCC 33799 (Halophile)
References: UniProt: A0A1C7A3R7
#3: Protein GPS-III molecule located underneath the capsomer close to the icosahedral three-fold axis.


Mass: 9209.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloarcula californiae ATCC 33799 (Halophile)
#4: Protein GPS-II protein located underneath the two-tower capsomer NOT sitting on the icosahedral 2-fold axis.


Mass: 6400.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloarcula californiae ATCC 33799 (Halophile)
Plasmid details: Haloarcula californiae icosahedral virus 1
#7: Protein
VP4


Mass: 25995.318 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Haloarcula californiae ATCC 33799 (Halophile)
Plasmid details: Haloarcula californiae icosahedral virus 1 / References: UniProt: A0A1C7A3R2

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Protein/peptide , 2 types, 2 molecules ef

#5: Protein/peptide (Half) GPS-II protein located underneath the two-tower capsomer sitting ON the icosahedral 2-fold axis.


Mass: 3932.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloarcula californiae ATCC 33799 (Halophile)
Plasmid details: Haloarcula californiae icosahedral virus 1
#6: Protein/peptide Peripentonal unknown polypeptide


Mass: 1549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Haloarcula californiae ATCC 33799 (Halophile)

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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 californiae icosahedral virus 1 / Type: VIRUS / Details: Haloarcula californiae icosahedral virus - 1 / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Haloarcula californiae icosahedral virus 1
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Haloarcula californiae ATCC 33799
Virus shellDiameter: 800 nm / Triangulation number (T number): 28
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
11 MSodium ChlorideNaCl1
270 mMMagnesium ChlorideMgCl21
320 mMPotasium ChlorideKCl1
41 mMCalcium ChlorideCaCl21
550 mMTris-HClC4H11NO31
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Haloarcula californiae icosahedral virus 1. Taxonomic identifier 1735722 NCBI.
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3900 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 36 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3218
Image scansMovie frames/image: 27 / Used frames/image: 1-26

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1RELION2particle selection
4CTFFIND4CTF correction
7Coot0.8.8model fittingInitial model building software
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
19Coot0.8.8model refinementInitial fixing of geometry
20RosettaEM3.8model refinementInitial EM model refinement
21PHENIX1.13-2988model refinementModel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4584
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3414 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 89.1 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient
Details: The HCIV-1 VP7 and VP4 MCPs were manually built aided by beta-barrel core templates derived from the crystal structures of Thermus bacteriophage P23-77 MCPs (PDB ID 3ZN6).
RefinementHighest resolution: 3.74 Å

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