Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 18-mer - A3B3C3D3E3F3 Pseudo Symmetry: Cyclic - C3  (3D View)
Pseudo Stoichiometry: Hetero 18-mer - A12B3C3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 360.00 kDa 
• Atom Count: 19278 
• Residue Count: 2409 
• Unique protein chains: 6

5KEL

EBOV GP in complex with variable Fab domains of IgGs c2G4 and c13C6

• DOI: 10.2210/pdb5KEL/pdb
• EMDataResource: EMD-8240

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Ebola virus - Mayinga, Zaire, 1976, Homo sapiens
• Expression System: Drosophila melanogaster, Nicotiana benthamiana
• Mutation(s): No 


• Deposited: 2016-06-09 Released: 2016-09-07 
• Deposition Author(s): Pallesen, J., Murin, C.D., de Val, N., Cottrell, C.A., Hastie, K.M., Turner, H.L., Fusco, M.L., Flyak, A.I., Zeitlin, L., Crowe Jr., J.E., Andersen, K.G., Saphire, E.O., Ward, A.B.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structures of Ebola virus GP and sGP in complex with therapeutic antibodies.

Pallesen, J., Murin, C.D., de Val, N., Cottrell, C.A., Hastie, K.M., Turner, H.L., Fusco, M.L., Flyak, A.I., Zeitlin, L., Crowe, J.E., Andersen, K.G., Saphire, E.O., Ward, A.B.

(2016) Nat Microbiol 1: 16128-16128

• PubMed: 27562261 
• DOI: 10.1038/nmicrobiol.2016.128
• Primary Citation of Related Structures:  
  5KEL, 5KEN, 5KEM


• PubMed Abstract: 
  

The Ebola virus (EBOV) GP gene encodes two glycoproteins. The major product is a soluble, dimeric glycoprotein (sGP) that is secreted abundantly. Despite the abundance of sGP during infection, little is known regarding its structure or functional role. A minor product, resulting from transcriptional editing, is the transmembrane-anchored, trimeric viral surface glycoprotein (GP). GP mediates attachment to and entry into host cells, and is the intended target of antibody therapeutics. Because large portions of sequence are shared between GP and sGP, it has been hypothesized that sGP may potentially subvert the immune response or may contribute to pathogenicity. In this study, we present cryo-electron microscopy structures of GP and sGP in complex with GP-specific and GP/sGP cross-reactive antibodies undergoing human clinical trials. The structure of the sGP dimer presented here, in complex with both an sGP-specific antibody and a GP/sGP cross-reactive antibody, permits us to unambiguously assign the oligomeric arrangement of sGP and compare its structure and epitope presentation to those of GP. We also provide biophysical evaluation of naturally occurring GP/sGP mutations that fall within the footprints identified by our high-resolution structures. Taken together, our data provide a detailed and more complete picture of the accessible Ebolavirus glycoprotein landscape and a structural basis to evaluate patient and vaccine antibody responses towards differently structured products of the GP gene.

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Organizational Affiliation: 

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ebola surface glycoprotein, GP1	A, E, F	469	Ebola virus - Mayinga, Zaire, 1976	Mutation(s): 0  Gene Names: GP
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ebola surface glycoprotein, GP2	B, G, I	143	Ebola virus - Mayinga, Zaire, 1976	Mutation(s): 0  Gene Names: GP
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
c2G4 variable Fab domain heavy chain	H, P, Q	120	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
c2G4 variable Fab domain light chain	L, T, U	107	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
c13C6 variable Fab domain heavy chain	C, J, M	121	Homo sapiens	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
c13C6 variable Fab domain light chain	D, N, O	107	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 7
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, W, a	2		N-Glycosylation

Entity ID: 8
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	R, X, b	3		N-Glycosylation

Entity ID: 9
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	S, Y, c	4		N-Glycosylation

Entity ID: 10
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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	V, Z, d	5		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, E, F	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-06-09 
• Released Date: 2016-09-07 
Deposition Author(s): Pallesen, J., Murin, C.D., de Val, N., Cottrell, C.A., Hastie, K.M., Turner, H.L., Fusco, M.L., Flyak, A.I., Zeitlin, L., Crowe Jr., J.E., Andersen, K.G., Saphire, E.O., Ward, A.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI067927
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19 AI109762
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19 AI1097 11

Revision History 

• Version 1.0: 2016-09-07
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2018-07-18
  Changes: Data collection, Experimental preparation
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary