9I59 | pdb_00009i59

RVFV GnH complexed with RVFV-379 Fab

PDB DOI: https://doi.org/10.2210/pdb9I59/pdb

Classification: VIRAL PROTEIN
Organism(s): Rift Valley fever virus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-01-27 Released: 2025-11-26
Deposition Author(s): Paesen, G.C., Bowden, T.A.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.251 (Depositor), 0.251 (DCC)
R-Value Work:
0.212 (Depositor), 0.212 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural basis for recognition of Rift Valley fever virus Gn protein by a human neutralizing monoclonal antibody with a kappa light chain.

Paesen, G.C., Chapman, N.S., Westover, J.B., McMillen, C.M., Kuzmina, N.A., Dews, E.A., Myers, L., Stass, R., Montgomery, J.M., Bukreyev, A., Hartman, A.L., Gowen, B.B., Crowe Jr., J.E., Bowden, T.A.

(2026) PLoS Pathog 22: e1013926-e1013926

PubMed: 41701720 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.ppat.1013926
Primary Citation of Related Structures:
9I59

PubMed Abstract:
Rift Valley fever virus (RVFV) poses a continued threat to human health and animal husbandry. Two neutralizing and protective human monoclonal antibodies (mAbs), RVFV-268 and RVFV-379, exhibit similar affinities and epitope footprints on the Gn glycoprotein component of the RVFV Gn-Gc capsomeric lattice. Here, we define fine details of the biophysical determinants of Gn recognition used by RVFV human monoclonal antibodies through studying an antibody encoded by a set of recombined genes not previously identified in RVFV antibodies. We find that RVFV-379 exhibits a larger footprint than that observed for RVFV-268 and other antibodies targeting the same region, which involves major contributions of both the light and heavy chains. RVFV-379 also uses an oblique angle of approach towards the virion surface that contrasts with the perpendicular angle of engagement observed for some other potently neutralizing human mAbs. Further, consistent with amino acid sequence variation within and proximal to the RVFV-379 epitope, in vitro neutralization screening reveals a limited degree of neutralization breadth across prevalent RVFV strains, suggesting that RVFV has fewer functional constraints at this region of the virus envelope. By dissecting the molecular determinants of mAb recognition of Gn, this integrated analysis refines strategies needed for the rational design of vaccines that can elicit a potent and species-wide protective antibody immune response to this important re-emerging pathogen.

Organizational Affiliation

Division of Structural Biology, Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

Macromolecule Content

Total Structure Weight: 172.2 kDa
Atom Count: 11,339
Modeled Residue Count: 1,400
Deposited Residue Count: 1,566
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelopment polyprotein	A, B	345	Rift Valley fever virus	Mutation(s): 0
UniProt
Find proteins for A2T080 (Rift valley fever virus) Explore A2T080 Go to UniProtKB: A2T080
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2T080
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of Fab	C [auth H], E [auth X]	223	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of Fab	D [auth L], F [auth Y]	215	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain K [auth L] MOL2 format, chain K [auth L] mmCIF format, chain K [auth L]	K [auth L]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth L] Interactions & Density Focus chain K [auth L]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth Y] SDF format, chain L [auth X] SDF format, chain J [auth L] SDF format, chain I [auth H] SDF format, chain H MOL2 format, chain G [auth A] MOL2 format, chain M [auth Y] MOL2 format, chain L [auth X] MOL2 format, chain J [auth L] MOL2 format, chain I [auth H] MOL2 format, chain H mmCIF format, chain G [auth A] mmCIF format, chain M [auth Y] mmCIF format, chain L [auth X] mmCIF format, chain J [auth L] mmCIF format, chain I [auth H] mmCIF format, chain H	G [auth A] H I [auth H] J [auth L] L [auth X] G [auth A], H, I [auth H], J [auth L], L [auth X], M [auth Y]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H Focus chain I [auth H] Focus chain J [auth L] Focus chain L [auth X] Focus chain M [auth Y] Interactions & Density Focus chain G [auth A] Focus chain H Focus chain I [auth H] Focus chain J [auth L] Focus chain L [auth X] Focus chain M [auth Y]