6H9C | pdb_00006h9c

Cryo-EM structure of archaeal extremophilic internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) at 3.74 Angstroms resolution.

PDB DOI: https://doi.org/10.2210/pdb6H9C/pdb
EM Map EMD-0174: EMDB EMDataResource

Classification: VIRUS
Organism(s): Haloarcula marismortui ATCC 33799
Mutation(s): No

Deposited: 2018-08-03 Released: 2019-03-27
Deposition Author(s): Abrescia, N.G., Santos-Perez, I., Charro, D.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness, Academy of Finland, Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.74 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural basis for assembly of vertical single beta-barrel viruses.

Santos-Perez, I., Charro, D., Gil-Carton, D., Azkargorta, M., Elortza, F., Bamford, D.H., Oksanen, H.M., Abrescia, N.G.A.

(2019) Nat Commun 10: 1184-1184

PubMed: 30862777 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-019-08927-2
Primary Citation Related Structures:
6H82, 6H9C

PubMed 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 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.

Organizational Affiliation

Molecular Recognition and Host-pathogen Interactions Programme, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, 48160, Derio, Spain.

Macromolecule Content

Total Structure Weight: 648 kDa
Atom Count: 43,691
Modeled Residue Count: 5,703
Deposited Residue Count: 5,937
Unique protein chains: 7

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP7	A [auth D] AA [auth M] BA [auth N] CA [auth I] DA [auth L] A [auth D], AA [auth M], BA [auth N], CA [auth I], DA [auth L], EA [auth a], FA [auth Y], S [auth F], T [auth E], U [auth R], V [auth T], W [auth S], X [auth W], Y [auth K], Z [auth J]	184	Haloarcula marismortui ATCC 33799	Mutation(s): 0
UniProt
Find proteins for A0A1C7A3R1 (Haloarcula californiae icosahedral virus 1) Explore A0A1C7A3R1 Go to UniProtKB: A0A1C7A3R1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1C7A3R1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VP9	B [auth b]	146	Haloarcula marismortui ATCC 33799	Mutation(s): 0
UniProt
Find proteins for A0A1C7A3R7 (Haloarcula californiae icosahedral virus 1) Explore A0A1C7A3R7 Go to UniProtKB: A0A1C7A3R7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1C7A3R7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GPS-III molecule located underneath the capsomer close to the icosahedral three-fold axis.	C [auth c]	108	Haloarcula marismortui ATCC 33799	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
GPS-II protein located underneath the two-tower capsomer NOT sitting on the icosahedral 2-fold axis.	D [auth d]	75	Haloarcula marismortui ATCC 33799	Mutation(s): 0

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
(Half) GPS-II protein located underneath the two-tower capsomer sitting ON the icosahedral 2-fold axis.	E [auth e]	46	Haloarcula marismortui ATCC 33799	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Peripentonal unknown polypeptide	F [auth f]	18	Haloarcula marismortui ATCC 33799	Mutation(s): 0

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
VP4	G [auth Z] H [auth A] I [auth B] J [auth C] K [auth P] G [auth Z], H [auth A], I [auth B], J [auth C], K [auth P], L [auth Q], M [auth O], N [auth V], O [auth U], P [auth H], Q [auth G], R [auth X]	232	Haloarcula marismortui ATCC 33799	Mutation(s): 0
UniProt
Find proteins for A0A1C7A3R2 (Haloarcula californiae icosahedral virus 1) Explore A0A1C7A3R2 Go to UniProtKB: A0A1C7A3R2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1C7A3R2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.74 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.0
MODEL REFINEMENT	Coot	0.8.8
MODEL REFINEMENT	RosettaEM	3.8
MODEL REFINEMENT	PHENIX	1.13-2988

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-03-27

Deposition Author(s):

Abrescia, N.G.

Santos-Perez, I.

Charro, D.

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2015-64541-R
Spanish Ministry of Economy and Competitiveness	Spain	SEV-2016-0644
Academy of Finland	Finland	1306833, 255342,256518,283072
Other government	Spain	Basque Governament PRE_2016_2_0151