7UOV | pdb_00007uov

Native Lassa glycoprotein in complex with neutralizing antibodies 12.1F and 37.2D

PDB DOI: https://doi.org/10.2210/pdb7UOV/pdb
EM Map EMD-26655: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Homo sapiens, Lassa virus Josiah
Expression System: Drosophila melanogaster, Homo sapiens
Mutation(s): No

Deposited: 2022-04-14 Released: 2022-11-02
Deposition Author(s): Li, H., Saphire, E.O.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.75 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

A cocktail of protective antibodies subverts the dense glycan shield of Lassa virus.

Li, H., Buck, T., Zandonatti, M., Yin, J., Moon-Walker, A., Fang, J., Koval, A., Heinrich, M.L., Rowland, M.M., Diaz Avalos, R., Schendel, S.L., Parekh, D., Zyla, D., Enriquez, A., Harkins, S., Sullivan, B., Smith, V., Chukwudozie, O., Watanabe, R., Robinson, J.E., Garry, R.F., Branco, L.M., Hastie, K.M., Saphire, E.O.

(2022) Sci Transl Med 14: eabq0991-eabq0991

PubMed: 36288283 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/scitranslmed.abq0991
Primary Citation Related Structures:
7UOT, 7UOV

PubMed Abstract:
Developing potent therapeutics and effective vaccines are the ultimate goals in controlling infectious diseases. Lassa virus (LASV), the causative pathogen of Lassa fever (LF), infects hundreds of thousands annually, but effective antivirals or vaccines against LASV infection are still lacking. Furthermore, neutralizing antibodies against LASV are rare. Here, we describe biochemical analyses and high-resolution cryo-electron microscopy structures of a therapeutic cocktail of three broadly protective antibodies that target the LASV glycoprotein complex (GPC), previously identified from survivors of multiple LASV infections. Structural and mechanistic analyses reveal compatible neutralizing epitopes and complementary neutralization mechanisms that offer high potency, broad range, and resistance to escape. These antibodies either circumvent or exploit specific glycans comprising the extensive glycan shield of GPC. Further, they require mammalian glycosylation, native GPC cleavage, and proper GPC trimerization. These findings guided engineering of a next-generation GPC antigen suitable for future neutralizing antibody and vaccine discovery. Together, these results explain protective mechanisms of rare, broad, and potent antibodies and identify a strategy for the rational design of therapeutic modalities against LF and related infectious diseases.

Organizational Affiliation

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 340.33 kDa
Atom Count: 19,757
Modeled Residue Count: 2,304
Deposited Residue Count: 2,826
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
12.1F heavy chain (variable domain)	A [auth H], G [auth D], M [auth F]	114	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
12.1F light chain (variable domain)	B [auth L], H [auth E], N [auth G]	106	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein G1	C [auth A], I [auth B], O [auth C]	259	Lassa virus Josiah	Mutation(s): 0 Gene Names: GPC, GP-C
UniProt
Find proteins for P08669 (Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)) Explore P08669 Go to UniProtKB: P08669
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08669
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain C [auth A] Focus chain I [auth B] Focus chain O [auth C]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein G2	D [auth a], J [auth b], P [auth c]	232	Lassa virus Josiah	Mutation(s): 0 Gene Names: GPC, GP-C
UniProt
Find proteins for P08669 (Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)) Explore P08669 Go to UniProtKB: P08669
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08669
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain D [auth a] Focus chain J [auth b] Focus chain P [auth c]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
37.2D light chain (variable domain)	E [auth T], K [auth P], Q [auth R]	105	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
37.2D heavy chain (variable domain)	F [auth S], L [auth O], R [auth Q]	126	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 7
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	FA [auth f], GA [auth g], OA [auth o], S [auth I], SA [auth s], FA [auth f], GA [auth g], OA [auth o], S [auth I], SA [auth s], W [auth N]	3		N-Glycosylation	Interactions Focus chain FA [auth f] Focus chain GA [auth g] Focus chain OA [auth o] Focus chain S [auth I] Focus chain SA [auth s] Focus chain W [auth N] Interactions & Density Focus chain FA [auth f] Focus chain GA [auth g] Focus chain OA [auth o] Focus chain S [auth I] Focus chain SA [auth s] Focus chain W [auth N]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-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	CA [auth Z], JA [auth j], PA [auth p], T [auth J], UA [auth u], CA [auth Z], JA [auth j], PA [auth p], T [auth J], UA [auth u], Y [auth V]	6		N-Glycosylation	Interactions Focus chain CA [auth Z] Focus chain JA [auth j] Focus chain PA [auth p] Focus chain T [auth J] Focus chain UA [auth u] Focus chain Y [auth V] Interactions & Density Focus chain CA [auth Z] Focus chain JA [auth j] Focus chain PA [auth p] Focus chain T [auth J] Focus chain UA [auth u] Focus chain Y [auth V]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	NA [auth n], U [auth K]	5		N-Glycosylation	Interactions Focus chain NA [auth n] Focus chain U [auth K] Interactions & Density Focus chain NA [auth n] Focus chain U [auth K]
Glycosylation Resources
GlyTouCan: G42466VF GlyCosmos: G42466VF GlyGen: G42466VF

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth X], DA [auth d], EA [auth e], LA [auth l], RA [auth r], AA [auth X], DA [auth d], EA [auth e], LA [auth l], RA [auth r], V [auth M], WA [auth w]	4		N-Glycosylation	Interactions Focus chain AA [auth X] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain LA [auth l] Focus chain RA [auth r] Focus chain V [auth M] Focus chain WA [auth w] Interactions & Density Focus chain AA [auth X] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain LA [auth l] Focus chain RA [auth r] Focus chain V [auth M] Focus chain WA [auth w]
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	HA [auth h], IA [auth i], KA [auth k], QA [auth q], TA [auth t], HA [auth h], IA [auth i], KA [auth k], QA [auth q], TA [auth t], VA [auth v], X [auth U], Z [auth W]	2		N-Glycosylation	Interactions Focus chain HA [auth h] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain QA [auth q] Focus chain TA [auth t] Focus chain VA [auth v] Focus chain X [auth U] Focus chain Z [auth W] Interactions & Density Focus chain HA [auth h] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain QA [auth q] Focus chain TA [auth t] Focus chain VA [auth v] Focus chain X [auth U] Focus chain Z [auth W]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 12
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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth Y], MA [auth m], XA [auth x]	6		N-Glycosylation	Interactions Focus chain BA [auth Y] Focus chain MA [auth m] Focus chain XA [auth x] Interactions & Density Focus chain BA [auth Y] Focus chain MA [auth m] Focus chain XA [auth x]
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain YA [auth A] MOL2 format, chain YA [auth A] mmCIF format, chain YA [auth A]	YA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain YA [auth A] Interactions & Density Focus chain YA [auth A]