2GIC | pdb_00002gic

Crystal Structure of a vesicular stomatitis virus nucleocapsid-RNA complex

• PDB DOI: https://doi.org/10.2210/pdb2GIC/pdb
• NAKB: 2GIC

• Classification: VIRUS/VIRAL PROTEIN/RNA
• Organism(s): Vesicular stomatitis Indiana virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-03-28 Released: 2006-08-22 
• Deposition Author(s): Green, T.J., Zhang, X., Wertz, G.W., Luo, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free: 
  0.306 (Depositor) 
• R-Value Work: 
  0.255 (Depositor) 
• R-Value Observed: 
  0.258 (Depositor) 

Literature

Structure of the vesicular stomatitis virus nucleoprotein-RNA complex unveils how the RNA is sequestered

Green, T.J., Zhang, X., Wertz, G.W., Luo, M.

(2006) Science 313: 357-360

• PubMed: 16778022 
• DOI: https://doi.org/10.1126/science.1126953
• Primary Citation Related Structures: 
  2GIC


• PubMed Abstract: 
  

  Vesicular stomatitis virus is a negative-stranded RNA virus. Its nucleoprotein (N) binds the viral genomic RNA and is involved in multiple functions including transcription, replication, and assembly. We have determined a 2.9 angstrom structure of a complex containing 10 molecules of the N protein and 90 bases of RNA. The RNA is tightly sequestered in a cavity at the interface between two lobes of the N protein. This serves to protect the RNA in the absence of polynucleotide synthesis. For the RNA to be accessed, some conformational change in the N protein should be necessary.

---

Organizational Affiliation: 
• Department of Microbiology, School of Medicine, University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35294, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C10  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 255.1 kDa 
• Atom Count: 17,432 
• Modeled Residue Count: 2,131 
• Deposited Residue Count: 2,155 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleocapsid protein	B [auth A], C [auth B], D [auth C], E [auth D], F [auth E]	422	Vesicular stomatitis Indiana virus	Mutation(s): 0  Gene Names: N
UniProt
Find proteins for P03521 (Vesicular stomatitis Indiana virus (strain San Juan)) Explore P03521  Go to UniProtKB:  P03521

Entity ID: 1
Molecule	Chains	Length	Organism	Image
45-MER	A [auth R]	45	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IUM	G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth C], O [auth C], P [auth C], Q [auth D], R [auth D], S [auth E], T [auth E], U [auth E]	URANYL (VI) ION O2 U IZLHQJIUOZHTLW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.92 Å
• R-Value Free:  0.306 (Depositor) 
• R-Value Work:  0.255 (Depositor) 
• R-Value Observed: 0.258 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.16	α = 90
b = 236.316	β = 90
c = 75.651	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-22 
Deposition Author(s): Green, T.J., Zhang, X., Wertz, G.W., Luo, M.

Revision History  

• Version 1.0: 2006-08-22
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description