Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 16.06 kDa 
• Atom Count: 1254 
• Residue Count: 140 
• Unique protein chains: 2

6E5X

Crystal structure of Ebola virus VP30 C-terminus/RBBP6 peptide complex

• DOI: 10.2210/pdb6E5X/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Ebola virus - Zaire (1995), Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-07-23 Released: 2018-12-12 
• Deposition Author(s): Liu, D., Small, G.I., Leung, D.W., Amarasinghe, G.K.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.230 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication.

Batra, J., Hultquist, J.F., Liu, D., Shtanko, O., Von Dollen, J., Satkamp, L., Jang, G.M., Luthra, P., Schwarz, T.M., Small, G.I., Arnett, E., Anantpadma, M., Reyes, A., Leung, D.W., Kaake, R., Haas, P., Schmidt, C.B., Schlesinger, L.S., LaCount, D.J., Davey, R.A., Amarasinghe, G.K., Basler, C.F., Krogan, N.J.

(2018) Cell 175: 1917-1930.e13

• PubMed: 30550789 
• DOI: 10.1016/j.cell.2018.08.044
• Primary Citation of Related Structures:  
  6E5X


• PubMed Abstract: 
  

Ebola virus (EBOV) infection often results in fatal illness in humans, yet little is known about how EBOV usurps host pathways during infection. To address this, we used affinity tag-purification mass spectrometry (AP-MS) to generate an EBOV-host protein-protein interaction (PPI) map. We uncovered 194 high-confidence EBOV-human PPIs, including one between the viral transcription regulator VP30 and the host ubiquitin ligase RBBP6. Domain mapping identified a 23 amino acid region within RBBP6 that binds to VP30. A crystal structure of the VP30-RBBP6 peptide complex revealed that RBBP6 mimics the viral nucleoprotein (NP) binding to the same interface of VP30. Knockdown of endogenous RBBP6 stimulated viral transcription and increased EBOV replication, whereas overexpression of either RBBP6 or the peptide strongly inhibited both. These results demonstrate the therapeutic potential of biologics that target this interface and identify additional PPIs that may be leveraged for novel therapeutic strategies.

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Organizational Affiliation: 

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Minor nucleoprotein VP30	A	127	Ebola virus - Zaire (1995)	Mutation(s): 0  Gene Names: VP30
Find proteins for Q77DJ5 (Zaire ebolavirus (strain Kikwit-95)) Explore Q77DJ5  Go to UniProtKB:  Q77DJ5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RBBP6	B	15	Homo sapiens	Mutation(s): 0  Gene Names: RBBP6, P2PR, PACT, RBQ1, My038 EC: 2.3.2.27
Find proteins for Q7Z6E9 (Homo sapiens) Explore Q7Z6E9  Go to UniProtKB:  Q7Z6E9
NIH Common Fund Data Resources
PHAROS  Q7Z6E9 GTEx  ENSG00000122257

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.230 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.6	α = 90
b = 45.6	β = 90
c = 158.71	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-07-23 
• Released Date: 2018-12-12 
Deposition Author(s): Liu, D., Small, G.I., Leung, D.W., Amarasinghe, G.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI120943
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	AI123926

Revision History 

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence