1D3E Virus Receptor date Sep 29, 1999
title Cryo-Em Structure Of Human Rhinovirus 16 (Hrv16) Complexed W Domain Fragment Of Its Cellular Receptor, Intercellular Adh Molecule-1 (D1d2-Icam-1). Implications For Virus-Receptor Interactions. Alpha Carbons Only
authors J.Bella, M.G.Rossmann
compound source
Molecule: Protein (Intercellular Adhesion Molecule-1)
Chain: I
Fragment: First Two Domains, Residues 1-185
Synonym: D1d2-Icam-1
Fragment: 1 - 185
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Protein (Rhinovirus 16 Coat Protein Vp1)
Chain: 1
Synonym: Hrv16 Vp1

Organism_scientific: Human Rhinovirus Sp.
Organism_taxid: 169066
Strain: Serotype 16

Molecule: Protein (Rhinovirus 16 Coat Protein Vp2)
Chain: 2
Synonym: Hrv16 Vp2

Organism_scientific: Human Rhinovirus Sp.
Organism_taxid: 169066
Strain: Serotype 16

Molecule: Protein (Rhinovirus 16 Coat Protein Vp3)
Chain: 3
Synonym: Hrv16 Vp3

Organism_scientific: Human Rhinovirus Sp.
Organism_taxid: 169066
Strain: Serotype 16

Molecule: Protein (Rhinovirus 16 Coat Protein Vp4)
Chain: 4
Synonym: Hrv16 Vp4

Organism_scientific: Human Rhinovirus Sp.
Organism_taxid: 169066
Strain: Serotype 16
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 28.00 Å
Gene
Ontology
ChainFunctionProcessComponent
1, 3, 2


4


I


Primary referenceStructural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor., Kolatkar PR, Bella J, Olson NH, Bator CM, Baker TS, Rossmann MG, EMBO J 1999 Nov 15;18(22):6249-59. PMID:10562537
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (26 Kb) [Save to disk]
  • Biological Unit Coordinates (1d3e.pdb1.gz) 1083 Kb
  • CSU: Contacts of Structural Units for 1D3E
  • Likely Quarternary Molecular Structure file(s) for 1D3E
  • Structure Factors (77 Kb)
  • Retrieve 1D3E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D3E from S2C, [Save to disk]
  • View 1D3E in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1D3E
  • VIPERdb: visual, structural and computational analysis of 1D3E
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1D3E, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d3e1_, region 1 [Jmol] [rasmolscript] [script source]
        - Domain d1d3e2_, region 2 [Jmol] [rasmolscript] [script source]
        - Domain d1d3e3_, region 3 [Jmol] [rasmolscript] [script source]
        - Domain d1d3e4_, region 4 [Jmol] [rasmolscript] [script source]
        - Domain d1d3ei_, region I [Jmol] [rasmolscript] [script source]
  • Fold representative 1d3e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1d3e_4] [1d3e_1] [1d3e_I] [1d3e] [1d3e_2] [1d3e_3]
  • SWISS-PROT database: [P05362] [Q82122]
  • Domain organization of [ICAM1_HUMAN] [POLG_HRV16] by SWISSPFAM
  • Other resources with information on 1D3E
  • Community annotation for 1D3E at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1D3E from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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