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 1.0 of the entry. See complete history.

Literature

Structure of the Sabia Virus spike complex in a closed conformation

Diskin, R., Cohen-Dvashi, H.

To be published.

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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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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]

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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]

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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]

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 BA [auth a] SDF format, chain CA [auth a] SDF format, chain DA [auth a] SDF format, chain FA [auth A] SDF format, chain GA [auth c] SDF format, chain HA [auth c] SDF format, chain IA [auth c] SDF format, chain JA [auth b] SDF format, chain KA [auth b] SDF format, chain LA [auth b] SDF format, chain MA [auth C] SDF format, chain NA [auth B] MOL2 format, chain BA [auth a] MOL2 format, chain CA [auth a] MOL2 format, chain DA [auth a] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth c] MOL2 format, chain HA [auth c] MOL2 format, chain IA [auth c] MOL2 format, chain JA [auth b] MOL2 format, chain KA [auth b] MOL2 format, chain LA [auth b] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth B] mmCIF format, chain BA [auth a] mmCIF format, chain CA [auth a] mmCIF format, chain DA [auth a] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth c] mmCIF format, chain HA [auth c] mmCIF format, chain IA [auth c] mmCIF format, chain JA [auth b] mmCIF format, chain KA [auth b] mmCIF format, chain LA [auth b] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth B]	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]