6QD8

EM structure of a EBOV-GP bound to 4M0368 neutralizing antibody

• PDB DOI: https://doi.org/10.2210/pdb6QD8/pdb
• EM Map EMD-4521: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Ebola virus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-01-01 Released: 2019-10-02 
• Deposition Author(s): Diskin, R., Cohen-Dvashi, H.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

rVSV-ZEBOV induces a polyclonal and convergent B cell response with potent Ebola virus-neutralizing antibodies

Diskin, R., Cohen-Dvashi, H., Ehrhardt, S., Zehner, M., Krahling, V., Kreer, C., Dahlke, C., Ercanoglu, M.S., Gruell, H., Addo, M.M., Becker, S., Klein, F.

(2019) Nat Med 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 303.57 kDa 
• Atom Count: 14,154 
• Modelled Residue Count: 1,812 
• Deposited Residue Count: 2,769 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain	A [auth Z], C [auth Y], E [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein,Virion spike glycoprotein,EBOV-GP1	B [auth A], G [auth C], H [auth E]	322	Ebola virus	Mutation(s): 0  Gene Names: GP
UniProt
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
Envelope glycoprotein	D [auth B], I [auth F], J [auth D]	168	Ebola virus	Mutation(s): 0  Gene Names: GP
UniProt
Find proteins for Q05320 (Zaire ebolavirus (strain Mayinga-76)) Explore Q05320  Go to UniProtKB:  Q05320
Glycosylation
Glycosylation Sites: 2

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain	F [auth H], K [auth W], L [auth Q]	219	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth G], N [auth I], O [auth J]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	P [auth B], Q [auth F], R [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	V2
MODEL REFINEMENT	PHENIX	3297

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-02 
Deposition Author(s): Diskin, R., Cohen-Dvashi, H.

Revision History  

• Version 1.0: 2019-10-02
  Type: Initial release
  
• Version 1.1: 2019-10-23
  Changes: Data collection, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary