Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 240-mer - A60B60C60D60 Pseudo Symmetry: Icosahedral - I  (3D View)
Pseudo Stoichiometry: Hetero 240-mer - A120B60C60 

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

Macromolecule Content

• Total Structure Weight: 94.96 kDa 
• Atom Count: 6299 
• Modelled Residue Count: 804 
• Deposited Residue Count: 855 
• Unique protein chains: 4

1R08

STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES

• DOI: 10.2210/pdb1R08/pdb

• Classification: VIRUS
• Organism(s): Rhinovirus B14
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 1988-10-03 Released: 1990-01-15 
• Deposition Author(s): Badger, J., Smith, T.J., Rossmann, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å

Literature

Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses.

Badger, J., Minor, I., Oliveira, M.A., Smith, T.J., Rossmann, M.G.

(1989) Proteins 6: 1-19

• PubMed: 2558377 
• DOI: 10.1002/prot.340060102
• Primary Citation of Related Structures:  
  2RR1, 2RS1, 2RS5, 2RS3, 2RM2, 2R07, 2R06, 2R04, 1R08


• PubMed Abstract: 
  

X-Ray diffraction data have been obtained for nine related antiviral agents ("WIN compounds") while bound to human rhinovirus 14 (HRV14). These compounds can inhibit both viral attachment to host cells and uncoating. To calculate interpretable electron density maps it was necessary to account for (1) the low (approximately 60%) occupancies of these compounds in the crystal, (2) the large (up to 7.9 A) conformational changes induced at the attachment site, and (3) the incomplete diffraction data. Application of a density difference map technique, which exploits the 20-fold noncrystallographic redundancy in HRV14, resulted in clear images of the HRV14:WIN complexes. A real-space refinement procedure was used to fit atomic models to these maps. The binding site of WIN compounds in HRV14 is a hydrophobic pocket composed mainly from residues that form the beta-barrel of VP1. Among rhinoviruses, the residues associated with the binding pocket are far more conserved than external residues and are mostly contained within regular secondary structural elements. Molecular dynamics simulations of three HRV14:WIN complexes suggest that portions of the WIN compounds and viral protein near the entrance of the binding pocket are more flexible than portions deeper within the beta-barrel.

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Related Citations: 

• The Use of Molecular Replacement Phases for the Refinement of the Human Rhinovirus 14 Structure
  Arnold, E., Rossmann, M.G.
  () To be published --: --

• Analysis of the Structure of a Common Cold Virus, Human Rhinovirus 14, Refined at a Resolution of 3.0 Angstroms
  Arnold, E., Rossmann, M.G.
  () To be published --: --

• Three-Dimensional Structures of Drug-Resistant Mutants of Human Rhinovirus 14
  Badger, J., Krishnaswamy, S., Kremer, M.J., Oliveira, M.A., Rossmann, M.G., Heinz, B.A., Rueckert, R.R., Dutko, F.J., Mckinlay, M.A.
  (1989) J Mol Biol 207: 163

• Structural Analysis of a Series of Antiviral Agents Complexed with Human Rhinovirus 14
  Badger, J., Minor, I., Kremer, M.J., Oliveira, M.A., Smith, T.J., Griffith, J.P., Guerin, D.M.A., Krishnaswamy, S., Luo, M., Rossmann, M.G., Mckinlay, M.A., Diana, G.D., Dutko, F.J., Fancher, M., Rueckert, R.R., Heinz, B.A.
  (1988) Proc Natl Acad Sci U S A 85: 3304

• The Structure Determination of a Common Cold Virus, Human Rhinovirus 14
  Arnold, E., Vriend, G., Luo, M., Griffith, J.P., Kamer, G., Erickson, J.W., Johnson, J.E., Rossmann, M.G.
  (1987) Acta Crystallogr A 43: 346

• Implications of the Picornavirus Capsid Structure for Polyprotein Structure
  Arnold, E., Luo, M., Vriend, G., Rossmann, M.G., Palmenberg, A.C., Parks, G.D., Nicklin, M.J.H., Wimmer, E.
  (1987) Proc Natl Acad Sci U S A 84: 21

• The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating
  Smith, T.J., Kremer, M.J., Luo, M., Vriend, G., Arnold, E., Kamer, G., Rossmann, M.G., Mckinlay, M.A., Diana, G.D., Otto, M.J.
  (1986) Science 233: 1286

• The Structure of a Human Common Cold Virus (Rhinovirus 14) and its Evolutionary Relations to Other Viruses
  Rossmann, M.G., Arnold, E., Erickson, J.W., Frankenberger, E.A., Griffith, J.P., Hecht, H.-J., Johnson, J.E., Kamer, G., Luo, M., Vriend, G.
  (1987) Chem Scr 26: 313

• Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
  Rossmann, M.G., Arnold, E., Erickson, J.W., Frankenberger, E.A., Griffith, J.P., Hecht, H.-J., Johnson, J.E., Kamer, G., Luo, M., Mosser, A.G., Rueckert, R.R., Sherry, B., Vriend, G.
  (1985) Nature 317: 145

• Virion Orientation in Cubic Crystals of the Human Common Cold Virus Hrv14
  Arnold, E., Erickson, J.W., Fout, G.S., Frankenberger, E.A., Hecht, H.-J., Luo, M., Rossmann, M.G., Rueckert, R.R.
  (1984) J Mol Biol 177: 417

• Picornaviruses of Two Different Genera Have Similar Structures
  Luo, M., Arnold, E., Erickson, J.W., Rossmann, M.G., Boege, U., Scraba, D.G.
  (1984) J Mol Biol 180: 703

• Crystallization of a Common Cold Virus, Human Rhinovirus 14. (Quote)Isomorphism(Quote) with Poliovirus Crystals
  Erickson, J.W., Frankenberger, E.A., Rossmann, M.G., Fout, G.S., Medappa, K.C., Rueckert, R.R.
  (1983) Proc Natl Acad Sci U S A 80: 931

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Organizational Affiliation: 

Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1)	A [auth 1]	289	Rhinovirus B14	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 P03303 (Human rhinovirus 14) Explore P03303  Go to UniProtKB:  P03303

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP2)	B [auth 2]	262	Rhinovirus B14	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 P03303 (Human rhinovirus 14) Explore P03303  Go to UniProtKB:  P03303

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP3)	C [auth 3]	236	Rhinovirus B14	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 P03303 (Human rhinovirus 14) Explore P03303  Go to UniProtKB:  P03303

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP4)	D [auth 4]	68	Rhinovirus B14	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 P03303 (Human rhinovirus 14) Explore P03303  Go to UniProtKB:  P03303

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W42	E [auth 1]	5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PENTYL)-3-(HYDROXYETHYL OXYMETHYLENEOXYMETHYL) ISOXAZOLE C21 H26 Cl2 N2 O6 JLSNWEWWUSOSMP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 445.1	α = 90
b = 445.1	β = 90
c = 445.1	γ = 90

Software Package:

Software Name	Purpose
REAL-SPACE	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1988-10-03 
• Released Date: 1990-01-15 
Deposition Author(s): Badger, J., Smith, T.J., Rossmann, M.G.

Revision History  

• Version 1.0: 1990-01-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance