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- PDB-6h82: Cryo-EM structure of the archaeal extremophilic internal membrane... -

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Entry
Database: PDB / ID: 6h82
TitleCryo-EM structure of the archaeal extremophilic internal membrane containing Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.78 Angstroms resolution.
Components
  • (VP7) x 3
  • GPS III
  • Uncharacterized protein
  • VP16 (vertex complex)
  • VP4
  • polypeptide stretch (vertex complex)
KeywordsVIRUS / single vertical beta-barrel virus / archaeal / membrane-containing / quasi-atomic resolution
Function / homologyVP7 / VP4 / Uncharacterized protein
Function and homology information
Biological speciesHaloarcula hispanica icosahedral virus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.78 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_151) Spain
Citation
Journal: 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.
#1: Journal: Structure / Year: 2015
Title: Insight into the Assembly of Viruses with Vertical Single β-barrel Major Capsid Proteins.
Authors: David Gil-Carton / Salla T Jaakkola / Diego Charro / Bibiana Peralta / Daniel Castaño-Díez / Hanna M Oksanen / Dennis H Bamford / Nicola G A Abrescia /
Abstract: Archaeal viruses constitute the least explored niche within the virosphere. Structure-based approaches have revealed close relationships between viruses infecting organisms from different domains of ...Archaeal viruses constitute the least explored niche within the virosphere. Structure-based approaches have revealed close relationships between viruses infecting organisms from different domains of life. Here, using biochemical and cryo-electron microscopy techniques, we solved the structure of euryarchaeal, halophilic, internal membrane-containing Haloarcula hispanica icosahedral virus 2 (HHIV-2). We show that the density of the two major capsid proteins (MCPs) recapitulates vertical single β-barrel proteins and that disulfide bridges stabilize the capsid. Below, ordered density is visible close to the membrane and at the five-fold vertices underneath the host-interacting vertex complex underpinning membrane-protein interactions. The HHIV-2 structure exemplifies the division of conserved architectural elements of a virion, such as the capsid, from those that evolve rapidly due to selective environmental pressure such as host-recognizing structures. We propose that in viruses with two vertical single β-barrel MCPs the vesicle is indispensable, and membrane-protein interactions serve as protein-railings for guiding the assembly.
History
DepositionAug 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Other / Category: atom_sites / em_image_scans
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.2Jun 17, 2020Group: Refinement description / Category: struct_ncs_oper / Item: _struct_ncs_oper.code
Revision 1.3May 15, 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
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

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Assembly

Deposited unit
A: VP4
D: VP7
C: VP4
E: VP7
B: VP4
F: VP7
Q: VP4
T: VP7
P: VP4
R: VP7
O: VP4
S: VP7
U: VP4
J: VP7
Z: VP4
K: VP7
V: VP4
W: VP7
H: VP4
M: VP7
G: VP4
N: VP7
L: VP7
I: VP7
X: VP4
a: VP7
Y: VP7
b: Uncharacterized protein
g: VP16 (vertex complex)
c: GPS III
d: GPS III
m: polypeptide stretch (vertex complex)


Theoretical massNumber of molelcules
Total (without water)636,57232
Polymers636,57232
Non-polymers00
Water00
1
A: VP4
D: VP7
C: VP4
E: VP7
B: VP4
F: VP7
Q: VP4
T: VP7
P: VP4
R: VP7
O: VP4
S: VP7
U: VP4
J: VP7
Z: VP4
K: VP7
V: VP4
W: VP7
H: VP4
M: VP7
G: VP4
N: VP7
L: VP7
I: VP7
X: VP4
a: VP7
Y: VP7
b: Uncharacterized protein
g: VP16 (vertex complex)
c: GPS III
d: GPS III
m: polypeptide stretch (vertex complex)
x 60


Theoretical massNumber of molelcules
Total (without water)38,194,3361920
Polymers38,194,3361920
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(1), (-1), (-1)
3generate(0.80902, -0.5, -0.30902), (0.5, 0.30902, 0.80902), (-0.30902, -0.80902, 0.5)
4generate(0.5, -0.30902, -0.80902), (0.30902, -0.80902, 0.5), (-0.80902, -0.5, -0.30902)
5generate(0.5, 0.30902, -0.80902), (-0.30902, -0.80902, -0.5), (-0.80902, 0.5, -0.30902)
6generate(0.80902, 0.5, -0.30902), (-0.5, 0.30902, -0.80902), (-0.30902, 0.80902, 0.5)
7generate(0.80902, 0.5, -0.30902), (0.5, -0.30902, 0.80902), (0.30902, -0.80902, -0.5)
8generate(0.80902, 0.5, 0.30902), (0.5, -0.30902, -0.80902), (-0.30902, 0.80902, -0.5)
9generate(0.80902, -0.5, -0.30902), (-0.5, -0.30902, -0.80902), (0.30902, 0.80902, -0.5)
10generate(0.5, -0.30902, -0.80902), (-0.30902, 0.80902, -0.5), (0.80902, 0.5, 0.30902)
11generate(0.5, 0.30902, 0.80902), (0.30902, 0.80902, -0.5), (-0.80902, 0.5, 0.30902)
12generate(0.5, 0.30902, -0.80902), (0.30902, 0.80902, 0.5), (0.80902, -0.5, 0.30902)
13generate(0.5, -0.30902, 0.80902), (-0.30902, 0.80902, 0.5), (-0.80902, -0.5, 0.30902)
14generate(0.80902, -0.5, 0.30902), (-0.5, -0.30902, 0.80902), (-0.30902, -0.80902, -0.5)
15generate(0.30902, 0.80902, -0.5), (0.80902, -0.5, -0.30902), (-0.5, -0.30902, -0.80902)
16generate(1), (-1), (-1)
17generate(0.30902, 0.80902, 0.5), (-0.80902, 0.5, -0.30902), (-0.5, -0.30902, 0.80902)
18generate(0.80902, 0.5, 0.30902), (-0.5, 0.30902, 0.80902), (0.30902, -0.80902, 0.5)
19generate(0.80902, -0.5, 0.30902), (0.5, 0.30902, -0.80902), (0.30902, 0.80902, 0.5)
20generate(-1), (1), (-1)
21generate(0.30902, -0.80902, -0.5), (0.80902, 0.5, -0.30902), (0.5, -0.30902, 0.80902)
22generate(0.30902, -0.80902, 0.5), (0.80902, 0.5, 0.30902), (-0.5, 0.30902, 0.80902)
23generate(-1), (1), (-1)
24generate(0.30902, -0.80902, -0.5), (-0.80902, -0.5, 0.30902), (-0.5, 0.30902, -0.80902)
25generate(0.5, 0.30902, 0.80902), (-0.30902, -0.80902, 0.5), (0.80902, -0.5, -0.30902)
26generate(0.30902, 0.80902, -0.5), (-0.80902, 0.5, 0.30902), (0.5, 0.30902, 0.80902)
27generate(-0.30902, -0.80902, -0.5), (0.80902, -0.5, 0.30902), (-0.5, -0.30902, 0.80902)
28generate(-0.5, -0.30902, -0.80902), (-0.30902, -0.80902, 0.5), (-0.80902, 0.5, 0.30902)
29generate(-1), (-1), (1)
30generate(-0.30902, -0.80902, -0.5), (-0.80902, 0.5, -0.30902), (0.5, 0.30902, -0.80902)
31generate(0.30902, -0.80902, 0.5), (-0.80902, -0.5, -0.30902), (0.5, -0.30902, -0.80902)
32generate(0.5, -0.30902, 0.80902), (0.30902, -0.80902, -0.5), (0.80902, 0.5, -0.30902)
33generate(1), (1), (1)
34generate(0.30902, 0.80902, 0.5), (0.80902, -0.5, 0.30902), (0.5, 0.30902, -0.80902)
35generate(-0.30902, 0.80902, 0.5), (0.80902, 0.5, -0.30902), (-0.5, 0.30902, -0.80902)
36generate(-0.5, 0.30902, -0.80902), (0.30902, -0.80902, -0.5), (-0.80902, -0.5, 0.30902)
37generate(-0.30902, 0.80902, -0.5), (-0.80902, -0.5, -0.30902), (-0.5, 0.30902, 0.80902)
38generate(-0.5, 0.30902, -0.80902), (-0.30902, 0.80902, 0.5), (0.80902, 0.5, -0.30902)
39generate(-0.30902, 0.80902, -0.5), (0.80902, 0.5, 0.30902), (0.5, -0.30902, -0.80902)
40generate(-0.5, -0.30902, -0.80902), (0.30902, 0.80902, -0.5), (0.80902, -0.5, -0.30902)
41generate(-1), (-1), (1)
42generate(1), (1), (1)
43generate(-0.5, -0.30902, 0.80902), (0.30902, 0.80902, 0.5), (-0.80902, 0.5, -0.30902)
44generate(-0.30902, -0.80902, 0.5), (-0.80902, 0.5, 0.30902), (-0.5, -0.30902, -0.80902)
45generate(-0.5, 0.30902, 0.80902), (-0.30902, 0.80902, -0.5), (-0.80902, -0.5, -0.30902)
46generate(1), (-1), (-1)
47generate(-0.80902, 0.5, -0.30902), (0.5, 0.30902, -0.80902), (-0.30902, -0.80902, -0.5)
48generate(-0.80902, 0.5, 0.30902), (-0.5, -0.30902, -0.80902), (-0.30902, -0.80902, 0.5)
49generate(-0.30902, 0.80902, 0.5), (-0.80902, -0.5, 0.30902), (0.5, -0.30902, 0.80902)
50generate(-0.80902, -0.5, -0.30902), (0.5, -0.30902, -0.80902), (0.30902, -0.80902, 0.5)
51generate(-0.30902, -0.80902, 0.5), (0.80902, -0.5, -0.30902), (0.5, 0.30902, 0.80902)
52generate(-0.80902, -0.5, 0.30902), (0.5, -0.30902, 0.80902), (-0.30902, 0.80902, 0.5)
53generate(-0.80902, -0.5, -0.30902), (-0.5, 0.30902, 0.80902), (-0.30902, 0.80902, -0.5)
54generate(-1), (-1), (1)
55generate(-0.80902, 0.5, -0.30902), (-0.5, -0.30902, 0.80902), (0.30902, 0.80902, 0.5)
56generate(-0.5, 0.30902, 0.80902), (0.30902, -0.80902, 0.5), (0.80902, 0.5, 0.30902)
57generate(-0.80902, 0.5, 0.30902), (0.5, 0.30902, 0.80902), (0.30902, 0.80902, -0.5)
58generate(-0.80902, -0.5, 0.30902), (-0.5, 0.30902, -0.80902), (0.30902, -0.80902, -0.5)
59generate(-0.5, -0.30902, 0.80902), (-0.30902, -0.80902, -0.5), (0.80902, -0.5, 0.30902)
60generate(-1), (1), (-1)

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Components

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Protein , 7 types, 31 molecules ACBQPOUZVHGXDTJWEFRSKMNaLIYbgcd

#1: Protein
VP4


Mass: 25585.746 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Details: http://mit.cicbiogune.int:39000/projects/P2/W1 / Source: (natural) Haloarcula hispanica icosahedral virus 2 / References: UniProt: H9AZX2
#2: Protein
VP7


Mass: 18473.355 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Haloarcula hispanica icosahedral virus 2 / References: UniProt: H9AZX1
#3: Protein
VP7


Mass: 18857.811 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Haloarcula hispanica icosahedral virus 2 / References: UniProt: H9AZX1
#4: Protein VP7


Mass: 17347.154 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Haloarcula hispanica icosahedral virus 2 / References: UniProt: H9AZX1
#5: Protein Uncharacterized protein


Mass: 14206.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula hispanica icosahedral virus 2 / References: UniProt: H9AZX8
#6: Protein VP16 (vertex complex)


Mass: 18485.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula hispanica icosahedral virus 2
#7: Protein GPS III


Mass: 8954.028 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Haloarcula hispanica icosahedral virus 2

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Protein/peptide , 1 types, 1 molecules m

#8: Protein/peptide polypeptide stretch (vertex complex)


Mass: 2145.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula hispanica icosahedral virus 2

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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 icosahedral virus 2 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Haloarcula hispanica icosahedral virus 2
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Haloarcula hispanica ATCC 33960
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HCLC4H11NO31
220 mMMagnessium clorhideMgCl21
310 mMCalcium clorhideCaCl21
40.5 Msodium clorhideNaCl1
SpecimenConc.: 1.2 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: Quantifoil R2/1
VitrificationCryogen 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
Image recordingElectron dose: 35 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1RELION1.4particle selection
4CTFFIND3CTF correction
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 14877
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11446 / Symmetry type: POINT
RefinementHighest resolution: 3.78 Å

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