9BOP | pdb_00009bop

A broadly-neutralizing antibody against Ebolavirus glycoprotein that can potentiate the breadth and neutralization potency of other anti-glycoprotein antibodies

PDB DOI: https://doi.org/10.2210/pdb9BOP/pdb
EM Map EMD-44747: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Oryctolagus cuniculus, Ebolavirus
Expression System: Homo sapiens, Drosophila melanogaster
Mutation(s): No

Deposited: 2024-05-05 Released: 2025-11-05
Deposition Author(s): Donnellan, F.R., Rayaprolu, V., Rijal, P., O'Dowd, V., Parvate, A., Callaway, H., Hariharan, C., Parekh, D., Hui, S., Shaffer, K., Hastie, K., Shimanski, L., Muller-Krauter, H., Stecker, T., Balaram, A., Halfmann, P., Saphire, E.O., Lightwood, D.J., Townsend, A.R., Draper, S.J.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 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

A broadly-neutralizing antibody against Ebolavirus glycoprotein that can potentiate the breadth and neutralization potency of other anti-glycoprotein antibodies

Donnellan, F.R., Rayaprolu, V., Rijal, P., O'Dowd, V., Parvate, A., Callaway, H., Hariharan, C., Parekh, D., Hui, S., Shaffer, K., Hastie, K., Shimanski, L., Muller-Krauter, H., Stecker, T., Balaram, A., Halfmann, P., Saphire, E.O., Lightwood, D.J., Townsend, A.R., Draper, S.J.

To be published.

Macromolecule Content

Total Structure Weight: 298.51 kDa
Atom Count: 16,858
Modeled Residue Count: 2,162
Deposited Residue Count: 2,680
Unique protein chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
11883 heavy chain	A, I [auth C], J [auth E]	148	Oryctolagus cuniculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
11883 light chain	B, K [auth D], L [auth F]	140	Oryctolagus cuniculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
11886 heavy chain	C [auth M], E [auth O]	146	Oryctolagus cuniculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
11886 light chain	D [auth N], F [auth P]	141	Oryctolagus cuniculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Virion spike glycoprotein GP1	G [auth S], O [auth T], P [auth U]	279	Ebolavirus	Mutation(s): 0 Gene Names: GP
UniProt
Find proteins for A0A8G0KJC2 (Zaire ebolavirus) Explore A0A8G0KJC2 Go to UniProtKB: A0A8G0KJC2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8G0KJC2
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain G [auth S] Focus chain O [auth T] Focus chain P [auth U]
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Virion spike glycoprotein GP2	H [auth V], M [auth W], N [auth X]	135	Ebolavirus	Mutation(s): 0 Gene Names: GP
UniProt
Find proteins for A0A8G0KMX8 (Zaire ebolavirus) Explore A0A8G0KMX8 Go to UniProtKB: A0A8G0KMX8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8G0KMX8
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain H [auth V] Focus chain M [auth W] Focus chain N [auth X]
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Reference Sequence

Oligosaccharides

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Entity ID: 7
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	Q [auth G], R [auth H], S [auth I]	5		N-Glycosylation	Interactions Focus chain Q [auth G] Focus chain R [auth H] Focus chain S [auth I] Interactions & Density Focus chain Q [auth G] Focus chain R [auth H] Focus chain S [auth I]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth U] SDF format, chain BA [auth U] SDF format, chain T [auth S] SDF format, chain U [auth S] SDF format, chain V [auth S] SDF format, chain W [auth T] SDF format, chain X [auth T] SDF format, chain Y [auth T] SDF format, chain Z [auth U] MOL2 format, chain AA [auth U] MOL2 format, chain BA [auth U] MOL2 format, chain T [auth S] MOL2 format, chain U [auth S] MOL2 format, chain V [auth S] MOL2 format, chain W [auth T] MOL2 format, chain X [auth T] MOL2 format, chain Y [auth T] MOL2 format, chain Z [auth U] mmCIF format, chain AA [auth U] mmCIF format, chain BA [auth U] mmCIF format, chain T [auth S] mmCIF format, chain U [auth S] mmCIF format, chain V [auth S] mmCIF format, chain W [auth T] mmCIF format, chain X [auth T] mmCIF format, chain Y [auth T] mmCIF format, chain Z [auth U]	AA [auth U] BA [auth U] T [auth S] U [auth S] V [auth S] AA [auth U], BA [auth U], T [auth S], U [auth S], V [auth S], W [auth T], X [auth T], Y [auth T], Z [auth U]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth U] Focus chain BA [auth U] Focus chain T [auth S] Focus chain U [auth S] Focus chain V [auth S] Focus chain W [auth T] Focus chain X [auth T] Focus chain Y [auth T] Focus chain Z [auth U] Interactions & Density Focus chain AA [auth U] Focus chain BA [auth U] Focus chain T [auth S] Focus chain U [auth S] Focus chain V [auth S] Focus chain W [auth T] Focus chain X [auth T] Focus chain Y [auth T] Focus chain Z [auth U]