9FYA | pdb_00009fya

Structure of the Sabia Virus spike complex in a closed conformation

PDB DOI: https://doi.org/10.2210/pdb9FYA/pdb
EM Map EMD-50862: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Sabia virus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-07-03 Released: 2025-06-11
Deposition Author(s): Diskin, R., Cohen-Dvashi, H.
Funding Organization(s): Israel Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.64 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Metal-induced conformational changes in the Sabia virus spike complex.

Cohen-Dvashi, H., Katz, M., Diskin, R.

(2025) Nat Microbiol 10: 2221-2230

PubMed: 40751015 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41564-025-02075-8
Primary Citation Related Structures:
9FYA, 9FYE, 9FYG

PubMed Abstract:
Haemorrhagic fever viruses from the Arenaviridae are a source of concern owing to their potential to cause lethal outbreaks and the lack of effective therapeutics. While structures of spike proteins from 'Old World' arenaviruses are available, the differences and similarities to 'New World' arenaviruses, such as the Sabiá virus, remain unclear owing to the lack of New World spike structures. Here we present the structure of the isolated spike complex from the Sabiá virus, which mediates viral attachment and entry to the host cells, using single-particle cryo-electron microscopy. We find two distinct conformational states of the spike, representing its native closed state at 2.6 Å resolution and an open state at 2.9 Å resolution that it assumes during cell entry. In addition, we show that the opening of the spike and subsequent cell entry are dependent on acidic pH and an unidentified metal ion. Our study suggests potential differences in the cell entry mechanisms of clade B arenaviruses compared with others in the Arenaviridae family.

Organizational Affiliation

Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.

Macromolecule Content

Total Structure Weight: 169.45 kDa
Atom Count: 8,893
Modeled Residue Count: 963
Deposited Residue Count: 1,326
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein G2	A [auth a], C [auth c], D [auth b]	246	Sabia virus	Mutation(s): 0 Gene Names: GPC, GP-C
UniProt
Find proteins for Q90037 (Sabia mammarenavirus (isolate Human/Brasil/SPH114202/1990)) Explore Q90037 Go to UniProtKB: Q90037
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q90037
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A [auth a] Focus chain C [auth c] Focus chain D [auth b]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein G1	B [auth A], E [auth C], F [auth B]	196	Sabia virus	Mutation(s): 0 Gene Names: GPC, GP-C
UniProt
Find proteins for Q90037 (Sabia mammarenavirus (isolate Human/Brasil/SPH114202/1990)) Explore Q90037 Go to UniProtKB: Q90037
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q90037
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain B [auth A] Focus chain E [auth C] Focus chain F [auth B]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth D], L [auth I], N [auth K], O [auth L], T [auth Q], G [auth D], L [auth I], N [auth K], O [auth L], T [auth Q], Z [auth W]	2		N-Glycosylation	Interactions Focus chain G [auth D] Focus chain L [auth I] Focus chain N [auth K] Focus chain O [auth L] Focus chain T [auth Q] Focus chain Z [auth W] Interactions & Density Focus chain G [auth D] Focus chain L [auth I] Focus chain N [auth K] Focus chain O [auth L] Focus chain T [auth Q] Focus chain Z [auth W]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth E], J [auth G], P [auth M], R [auth O], V [auth S], H [auth E], J [auth G], P [auth M], R [auth O], V [auth S], X [auth U]	5		N-Glycosylation	Interactions Focus chain H [auth E] Focus chain J [auth G] Focus chain P [auth M] Focus chain R [auth O] Focus chain V [auth S] Focus chain X [auth U] Interactions & Density Focus chain H [auth E] Focus chain J [auth G] Focus chain P [auth M] Focus chain R [auth O] Focus chain V [auth S] Focus chain X [auth U]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth X], I [auth F], K [auth H], M [auth J], Q [auth N], AA [auth X], I [auth F], K [auth H], M [auth J], Q [auth N], S [auth P], U [auth R], W [auth T], Y [auth V]	3		N-Glycosylation	Interactions Focus chain AA [auth X] Focus chain I [auth F] Focus chain K [auth H] Focus chain M [auth J] Focus chain Q [auth N] Focus chain S [auth P] Focus chain U [auth R] Focus chain W [auth T] Focus chain Y [auth V] Interactions & Density Focus chain AA [auth X] Focus chain I [auth F] Focus chain K [auth H] Focus chain M [auth J] Focus chain Q [auth N] Focus chain S [auth P] Focus chain U [auth R] Focus chain W [auth T] Focus chain Y [auth V]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain NA [auth B] SDF format, chain MA [auth C] SDF format, chain LA [auth b] SDF format, chain KA [auth b] SDF format, chain JA [auth b] SDF format, chain IA [auth c] SDF format, chain HA [auth c] SDF format, chain GA [auth c] SDF format, chain FA [auth A] SDF format, chain DA [auth a] SDF format, chain CA [auth a] SDF format, chain BA [auth a] MOL2 format, chain NA [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain LA [auth b] MOL2 format, chain KA [auth b] MOL2 format, chain JA [auth b] MOL2 format, chain IA [auth c] MOL2 format, chain HA [auth c] MOL2 format, chain GA [auth c] MOL2 format, chain FA [auth A] MOL2 format, chain DA [auth a] MOL2 format, chain CA [auth a] MOL2 format, chain BA [auth a] mmCIF format, chain NA [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain LA [auth b] mmCIF format, chain KA [auth b] mmCIF format, chain JA [auth b] mmCIF format, chain IA [auth c] mmCIF format, chain HA [auth c] mmCIF format, chain GA [auth c] mmCIF format, chain FA [auth A] mmCIF format, chain DA [auth a] mmCIF format, chain CA [auth a] mmCIF format, chain BA [auth a]	BA [auth a] CA [auth a] DA [auth a] FA [auth A] GA [auth c] BA [auth a], CA [auth a], DA [auth a], FA [auth A], GA [auth c], HA [auth c], IA [auth c], JA [auth b], KA [auth b], LA [auth b], MA [auth C], NA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth a] Focus chain CA [auth a] Focus chain DA [auth a] Focus chain FA [auth A] Focus chain GA [auth c] Focus chain HA [auth c] Focus chain IA [auth c] Focus chain JA [auth b] Focus chain KA [auth b] Focus chain LA [auth b] Focus chain MA [auth C] Focus chain NA [auth B] Interactions & Density Focus chain BA [auth a] Focus chain CA [auth a] Focus chain DA [auth a] Focus chain FA [auth A] Focus chain GA [auth c] Focus chain HA [auth c] Focus chain IA [auth c] Focus chain JA [auth b] Focus chain KA [auth b] Focus chain LA [auth b] Focus chain MA [auth C] Focus chain NA [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain EA [auth a] MOL2 format, chain EA [auth a] mmCIF format, chain EA [auth a]	EA [auth a]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain EA [auth a] Interactions & Density Focus chain EA [auth a]