1D3I

CRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 14 (HRV14) COMPLEXED WITH A TWO-DOMAIN FRAGMENT OF ITS CELLULAR RECEPTOR, INTERCELLULAR ADHESION MOLECULE-1 (D1D2-ICAM-1). IMPLICATIONS FOR VIRUS-RECEPTOR INTERACTIONS. ALPHA CARBONS ONLY


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 26.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor.

Kolatkar, P.R.Bella, J.Olson, N.H.Bator, C.M.Baker, T.S.Rossmann, M.G.

(1999) EMBO J 18: 6249-6259

  • DOI: 10.1093/emboj/18.22.6249
  • Primary Citation of Related Structures:  
    1D3E, 1D3L, 1D3I

  • PubMed Abstract: 
  • Two human rhinovirus serotypes complexed with two- and five-domain soluble fragments of the cellular receptor, intercellular adhesion molecule-1, have been investigated by X-ray crystallographic analyses of the individual components and by cryo-electron microscopy of the complexes ...

    Two human rhinovirus serotypes complexed with two- and five-domain soluble fragments of the cellular receptor, intercellular adhesion molecule-1, have been investigated by X-ray crystallographic analyses of the individual components and by cryo-electron microscopy of the complexes. The three-dimensional image reconstructions provide a molecular envelope within which the crystal structures of the viruses and the receptor fragments can be positioned with accuracy. The N-terminal domain of the receptor binds to the rhinovirus 'canyon' surrounding the icosahedral 5-fold axes. Fitting of molecular models into the image reconstruction density identified the residues on the virus that interact with those on the receptor surface, demonstrating complementarity of the electrostatic patterns for the tip of the N-terminal receptor domain and the floor of the canyon. The complexes seen in the image reconstructions probably represent the first stage of a multistep binding process. A mechanism is proposed for the subsequent viral uncoating process.


    Related Citations: 
    • The Structure of the Two Amino-Terminal Domains of Human Icam-1 Suggests How It Functions as a Rhinovirus Receptor and as an Lfa-1 Integrin Ligand.
      Bella, J., Kolatkar, P.R., Marlor, C.W., Greve, J.M., Rossmann, M.G.
      (1998) Proc Natl Acad Sci U S A 95: 6249
    • 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.
      (1990) J Mol Biol 211: 763
    • 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
    • Structure of a Human Rhinovirus Complexed with its Receptor Molecule
      Olson, N.H., Kolatkar, P.R., Oliveira, M.A., Cheng, R.H., Greve, J.M., Mcclelland, A., Baker, T.S., Rossmann, M.G.
      (1993) Proc Natl Acad Sci U S A 90: 507
    • A Dimeric Crystal Structure for the N-Terminal Two Domains of Intercellular Adhesion Molecule-1
      Casasnovas, J.M., Stehle, T., Liu, J.H., Wang, J.H., Springer, T.A.
      (1998) Proc Natl Acad Sci U S A 95: 4134

    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (INTERCELLULAR ADHESION MOLECULE-1)A [auth I]185Homo sapiensMutation(s): 0 
Gene Names: ICAM1
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PHAROS:  P05362
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1)B [auth 1]289Human rhinovirus sp.Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP2)C [auth 2]262Human rhinovirus sp.Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP3)D [auth 3]236Human rhinovirus sp.Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
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Entity ID: 5
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PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP4)E [auth 4]68Human rhinovirus sp.Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 26.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-01-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-12-18
    Changes: Other