7A5A | pdb_00007a5a

Crimean-Congo Hemorrhagic Fever Virus Envelope Glycoprotein Gc W1191H/W1197A/W1199A Mutant in Postfusion Conformation (Monoclinic Crystal Form)

PDB DOI: https://doi.org/10.2210/pdb7A5A/pdb

Classification: VIRAL PROTEIN
Organism(s): Crimean-Congo hemorrhagic fever virus strain IbAr10200
Expression System: Drosophila melanogaster
Mutation(s): Yes

Deposited: 2020-08-20 Released: 2021-10-06
Deposition Author(s): Hellert, J., Guardado-Calvo, P., Rey, F.A.
Funding Organization(s): Laboratories of Excellence (LabEx)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.99 Å
R-Value Free:
0.239 (Depositor), 0.234 (DCC)
R-Value Work:
0.204 (Depositor), 0.203 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural basis of synergistic neutralization of Crimean-Congo hemorrhagic fever virus by human antibodies.

Mishra, A.K., Hellert, J., Freitas, N., Guardado-Calvo, P., Haouz, A., Fels, J.M., Maurer, D.P., Abelson, D.M., Bornholdt, Z.A., Walker, L.M., Chandran, K., Cosset, F.L., McLellan, J.S., Rey, F.A.

(2022) Science 375: 104-109

PubMed: 34793197 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.abl6502
Primary Citation Related Structures:
7A59, 7A5A, 7KX4, 7L7R

PubMed Abstract:
Crimean-Congo hemorrhagic fever virus (CCHFV) is the most widespread tick-borne zoonotic virus, with a 30% case fatality rate in humans. Structural information is lacking in regard to the CCHFV membrane fusion glycoprotein Gc—the main target of the host neutralizing antibody response—as well as antibody–mediated neutralization mechanisms. We describe the structure of prefusion Gc bound to the antigen-binding fragments (Fabs) of two neutralizing antibodies that display synergy when combined, as well as the structure of trimeric, postfusion Gc. The structures show the two Fabs acting in concert to block membrane fusion, with one targeting the fusion loops and the other blocking Gc trimer formation. The structures also revealed the neutralization mechanism of previously reported antibodies against CCHFV, providing the molecular underpinnings essential for developing CCHFV–specific medical countermeasures for epidemic preparedness.

Organizational Affiliation

Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.

Macromolecule Content

Total Structure Weight: 361.91 kDa
Atom Count: 23,452
Modeled Residue Count: 3,005
Deposited Residue Count: 3,240
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelopment polyprotein	A, B, C, D, E A, B, C, D, E, F	540	Crimean-Congo hemorrhagic fever virus strain IbAr10200	Mutation(s): 3 Gene Names: GP
UniProt
Find proteins for Q8JSZ3 (Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)) Explore Q8JSZ3 Go to UniProtKB: Q8JSZ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8JSZ3
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F
Sequence Annotations Expand
Reference Sequence

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 T [auth F] SDF format, chain S [auth E] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] K [auth B] L [auth B] M [auth C] G [auth A], H [auth A], K [auth B], L [auth B], M [auth C], N [auth C], P [auth D], S [auth E], T [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain T [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain T [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], O [auth C], Q [auth D], R [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D]