1D3E

CRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 16 (HRV16) 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: 28.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 4140
    • The Refined Structure of Human Rhinovirus 16 at 2.15 Angstroms Resolution: Implications for the Viral Life Cycle
      Hadfield, A.T., Lee, W.M., Zhao, R., Oliveira, M.A., Minor, I., Rueckert, R.R., Rossmann, M.G.
      (1997) Structure 5: 427
    • 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) I185Homo sapiensMutation(s): 0 
Gene Names: ICAM1
Find proteins for P05362 (Homo sapiens)
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Go to UniProtKB:  P05362
NIH Common Fund Data Resources
PHAROS:  P05362
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP1) 1285Human 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)
Find proteins for Q82122 (Human rhinovirus 16)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP2) 2252Human 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)
Find proteins for Q82122 (Human rhinovirus 16)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP3) 3238Human 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)
Find proteins for Q82122 (Human rhinovirus 16)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RHINOVIRUS 16 COAT PROTEIN VP4) 468Human 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)
Find proteins for Q82122 (Human rhinovirus 16)
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Go to UniProtKB:  Q82122
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 28.0 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: 2019-12-18
    Changes: Data collection, Other