7LUX

AALALL segment from the Nucleoprotein of SARS-CoV-2, residues 217-222, crystal form 2

• PDB DOI: https://doi.org/10.2210/pdb7LUX/pdb

• Classification: PROTEIN FIBRIL
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Mutation(s): No 


• Deposited: 2021-02-23 Released: 2021-03-17 
• Deposition Author(s): Lu, J., Zee, C.-T., Sawaya, M.R., Rodriguez, J.A., Eisenberg, D.S.
• Funding Organization(s): Department of Energy (DOE, United States), National Science Foundation (NSF, United States), National Institutes of Health/National Institute on Aging (NIH/NIA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.236 
• R-Value Work: 0.195 

Literature

Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2.

Tayeb-Fligelman, E., Cheng, X., Tai, C., Bowler, J.T., Griner, S., Sawaya, M.R., Seidler, P.M., Jiang, Y.X., Lu, J., Rosenberg, G.M., Salwinski, L., Abskharon, R., Zee, C.T., Hou, K., Li, Y., Boyer, D.R., Murray, K.A., Falcon, G., Anderson, D.H., Cascio, D., Saelices, L., Damoiseaux, R., Guo, F., Eisenberg, D.S.

(2021) Biorxiv 

• PubMed: 33688654 
• DOI: https://doi.org/10.1101/2021.03.05.434000
• Primary Citation of Related Structures:  
  7LTU, 7LUX, 7LUZ, 7LV2


• PubMed Abstract: 
  

  The SARS-CoV-2 Nucleoprotein (NCAP) functions in RNA packaging during viral replication and assembly. Computational analysis of its amino acid sequence reveals a central low-complexity domain (LCD) having sequence features akin to LCDs in other proteins known to function in liquid-liquid phase separation. Here we show that in the presence of viral RNA, NCAP, and also its LCD segment alone, form amyloid-like fibrils when undergoing liquid-liquid phase separation. Within the LCD we identified three 6-residue segments that drive amyloid fibril formation. We determined atomic structures for fibrils formed by each of the three identified segments. These structures informed our design of peptide inhibitors of NCAP fibril formation and liquid-liquid phase separation, suggesting a therapeutic route for Covid-19.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 18-mer - A18 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 0.96 kDa 
• Atom Count: 67 
• Modelled Residue Count: 6 
• Deposited Residue Count: 6 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein AALALL	A	6	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9  Go to UniProtKB:  P0DTC9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	B [auth A], C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.236 
• R-Value Work: 0.195 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.46	α = 90
b = 9.54	β = 90
c = 10.95	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Lu, J., Zee, C.-T., Sawaya, M.R., Rodriguez, J.A., Eisenberg, D.S.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-FC02-02ER63421
National Science Foundation (NSF, United States)	United States	MCB 1616265
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	R01 AG048120

Revision History  

• Version 1.0: 2021-03-17
  Type: Initial release
  
• Version 1.1: 2021-03-24
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references
• Version 1.3: 2024-04-03
  Changes: Refinement description