6QD8 | pdb_00006qd8

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.

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05320
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05320
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain D [auth B] Focus chain I [auth F] Focus chain J [auth D]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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	D 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	Interactions Focus chain M [auth G] Focus chain N [auth I] Focus chain O [auth J] Interactions & Density Focus chain M [auth G] Focus chain N [auth I] Focus chain O [auth J]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain Q [auth F] SDF format, chain R [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth D]	P [auth B], Q [auth F], R [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth B] Focus chain Q [auth F] Focus chain R [auth D] Interactions & Density Focus chain P [auth B] Focus chain Q [auth F] Focus chain R [auth D]

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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-10-02

Deposition Author(s):

Diskin, R.

Cohen-Dvashi, H.

Revision History (Full details and data files)

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
Version 2.1: 2024-11-20
Changes: Data collection, Database references, Refinement description, Structure summary