Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 180-mer - A60B60C60 Pseudo Symmetry: Icosahedral - I  (3D View)
Pseudo Stoichiometry: Hetero 180-mer - A120B60 

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

Macromolecule Content

• Total Structure Weight: 98.01 kDa 
• Atom Count: 6281 
• Modelled Residue Count: 773 
• Deposited Residue Count: 880 
• Unique protein chains: 3

1POV

ROLE AND MECHANISM OF THE MATURATION CLEAVAGE OF VP0 IN POLIOVIRUS ASSEMBLY: STRUCTURE OF THE EMPTY CAPSID ASSEMBLY INTERMEDIATE AT 2.9 ANGSTROMS RESOLUTION

• PDB DOI: 10.2210/pdb1POV/pdb

• Classification: VIRUS
• Organism(s): Human poliovirus 1 Mahoney
• Mutation(s): No 


• Deposited: 1995-08-10 Released: 1995-12-07 
• Deposition Author(s): Basavappa, R., Filman, D.J., Hogle, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Observed: 0.281 

Literature

Role and mechanism of the maturation cleavage of VP0 in poliovirus assembly: structure of the empty capsid assembly intermediate at 2.9 A resolution.

Basavappa, R., Syed, R., Flore, O., Icenogle, J.P., Filman, D.J., Hogle, J.M.

(1994) Protein Sci 3: 1651-1669

• PubMed: 7849583 
• DOI: 10.1002/pro.5560031005
• Primary Citation of Related Structures:  
  1POV


• PubMed Abstract: 
  

The crystal structure of the P1/Mahoney poliovirus empty capsid has been determined at 2.9 A resolution. The empty capsids differ from mature virions in that they lack the viral RNA and have yet to undergo a stabilizing maturation cleavage of VP0 to yield the mature capsid proteins VP4 and VP2. The outer surface and the bulk of the protein shell are very similar to those of the mature virion. The major differences between the 2 structures are focused in a network formed by the N-terminal extensions of the capsid proteins on the inner surface of the shell. In the empty capsids, the entire N-terminal extension of VP1, as well as portions corresponding to VP4 and the N-terminal extension of VP2, are disordered, and many stabilizing interactions that are present in the mature virion are missing. In the empty capsid, the VP0 scissile bond is located some 20 A away from the positions in the mature virion of the termini generated by VP0 cleavage. The scissile bond is located on the rim of a trefoil-shaped depression in the inner surface of the shell that is highly reminiscent of an RNA binding site in bean pod mottle virus. The structure suggests plausible (and ultimately testable) models for the initiation of encapsidation, for the RNA-dependent autocatalytic cleavage of VP0, and for the role of the cleavage in establishing the ordered N-terminal network and in generating stable virions.

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Related Citations: 

• Three-Dimensional Structure of a Mouse-Adapted Type 2(Slash)Type 1 Poliovirus Chimera
  Yeates, T.O., Jacobson, D.H., Martin, A., Wychowski, C., Girard, M., Filman, D.J., Hogle, J.M.
  (1991) EMBO J 10: 2331

• Structural Factors that Control Conformational Transitions and Serotype Specificity in Type 3 Poliovirus
  Filman, D.J., Syed, R., Chow, M., Macadam, A.J., Minor, P.D., Hogle, J.M.
  (1989) EMBO J 8: 1567

• Myristylation of Picornavirus Capsid Protein Vp4 and its Structural Significance
  Chow, M., Newman, J.F.E., Filman, D., Hogle, J.M., Rowlands, D.J., Brown, F.
  (1987) Nature 327: 482

• Three-Dimensional Structure of Poliovirus at 2.9 Angstroms Resolution
  Hogle, J.M., Chow, M., Filman, D.J.
  (1985) Science 229: 1358

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Organizational Affiliation: 

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)	A [auth 0]	340	Human poliovirus 1 Mahoney	Mutation(s): 0  EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney)) Explore P03300  Go to UniProtKB:  P03300

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)	B [auth 1]	302	Human poliovirus 1 Mahoney	Mutation(s): 0  EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney)) Explore P03300  Go to UniProtKB:  P03300

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)	C [auth 3]	238	Human poliovirus 1 Mahoney	Mutation(s): 0  EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney)) Explore P03300  Go to UniProtKB:  P03300

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPH	E [auth 1]	SPHINGOSINE C18 H37 N O2 WWUZIQQURGPMPG-MSOLQXFVSA-N
MYR	D [auth 0]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Observed: 0.281 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 322.9	α = 90
b = 358	β = 90
c = 380.1	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-08-10 
• Released Date: 1995-12-07 
Deposition Author(s): Basavappa, R., Filman, D.J., Hogle, J.M.

Revision History  

• Version 1.0: 1995-12-07
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance