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1v9u

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1v9u, resolution 3.60Å ()
Ligands: ,
Related: 1fpn
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Contents

Human Rhinovirus 2 bound to a fragment of its cellular receptor protein

Publication Abstract from PubMed

Although many viral receptors have been identified, the ways in which they interact with their cognate viruses are not understood at the molecular level. We have determined the X-ray structure of a complex between calcium-containing modules of the very low-density lipoprotein receptor and the minor group human rhinovirus HRV2. The receptor binds close to the icosahedral five-fold vertex, with only one module per virus protomer. The binding face of this module is defined by acidic calcium-chelating residues and, in particular, by an exposed tryptophan that is highly conserved. The attachment site on the virus involves only residues from VP1, particularly a lysine strictly conserved in all minor group HRVs. The disposition of the attached ligand-binding repeats around the five-fold axis, together with the proximity of the N- and C-terminal ends of adjacent modules, suggests that more than one repeat in a single receptor molecule might attach simultaneously.

X-ray structure of a minor group human rhinovirus bound to a fragment of its cellular receptor protein., Verdaguer N, Fita I, Reithmayer M, Moser R, Blaas D, Nat Struct Mol Biol. 2004 May;11(5):429-34. Epub 2004 Apr 4. PMID:15064754

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

Disease

[VLDLR_HUMAN] Defects in VLDLR are the cause of cerebellar ataxia mental retardation and dysequilibrium syndrome type 1 (CMARQ1) [MIM:224050]; also known as dysequilibrium syndrome (DES) or non-progressive cerebellar disorder with mental retardation. CMARQ1 is a congenital, non-progressive cerebellar ataxia associated with disturbed equilibrium, delayed ambulation, mental retardation and cerebellar hypoplasia. Additional features include short stature, strabismus, pes planus and, rarely, seizures.[1]

Function

[POLG_HRV2] Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The capsid interacts with human VLDLR to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin-mediated endocytosis. VP4 and VP1 subsequently undergo conformational changes leading to the formation of a pore in the endosomal membrane, thereby delivering the viral genome into the cytoplasm.[2][3] VP0 precursor is a component of immature procapsids (By similarity).[4][5] Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription.[6][7] Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity).[8][9] Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).[10][11] Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity).[12][13] Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity).[14][15] RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).[16][17] [VLDLR_HUMAN] Binds VLDL and transports it into cells by endocytosis. In order to be internalized, the receptor-ligand complexes must first cluster into clathrin-coated pits. Binding to Reelin induces tyrosine phosphorylation of Dab1 and modulation of Tau phosphorylation (By similarity).

About this Structure

1v9u is a 5 chain structure with sequence from Homo sapiens and Human rhinovirus a2. Full crystallographic information is available from OCA.

Reference

  • Verdaguer N, Fita I, Reithmayer M, Moser R, Blaas D. X-ray structure of a minor group human rhinovirus bound to a fragment of its cellular receptor protein. Nat Struct Mol Biol. 2004 May;11(5):429-34. Epub 2004 Apr 4. PMID:15064754 doi:10.1038/nsmb753
  1. Boycott KM, Flavelle S, Bureau A, Glass HC, Fujiwara TM, Wirrell E, Davey K, Chudley AE, Scott JN, McLeod DR, Parboosingh JS. Homozygous deletion of the very low density lipoprotein receptor gene causes autosomal recessive cerebellar hypoplasia with cerebral gyral simplification. Am J Hum Genet. 2005 Sep;77(3):477-83. Epub 2005 Jul 22. PMID:16080122 doi:S0002-9297(07)63027-4
  2. Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
  3. Hewat EA, Neumann E, Blaas D. The concerted conformational changes during human rhinovirus 2 uncoating. Mol Cell. 2002 Aug;10(2):317-26. PMID:12191477
  4. Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
  5. Hewat EA, Neumann E, Blaas D. The concerted conformational changes during human rhinovirus 2 uncoating. Mol Cell. 2002 Aug;10(2):317-26. PMID:12191477
  6. Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
  7. Hewat EA, Neumann E, Blaas D. The concerted conformational changes during human rhinovirus 2 uncoating. Mol Cell. 2002 Aug;10(2):317-26. PMID:12191477
  8. Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
  9. Hewat EA, Neumann E, Blaas D. The concerted conformational changes during human rhinovirus 2 uncoating. Mol Cell. 2002 Aug;10(2):317-26. PMID:12191477
  10. Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
  11. Hewat EA, Neumann E, Blaas D. The concerted conformational changes during human rhinovirus 2 uncoating. Mol Cell. 2002 Aug;10(2):317-26. PMID:12191477
  12. Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
  13. Hewat EA, Neumann E, Blaas D. The concerted conformational changes during human rhinovirus 2 uncoating. Mol Cell. 2002 Aug;10(2):317-26. PMID:12191477
  14. Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
  15. Hewat EA, Neumann E, Blaas D. The concerted conformational changes during human rhinovirus 2 uncoating. Mol Cell. 2002 Aug;10(2):317-26. PMID:12191477
  16. Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
  17. Hewat EA, Neumann E, Blaas D. The concerted conformational changes during human rhinovirus 2 uncoating. Mol Cell. 2002 Aug;10(2):317-26. PMID:12191477

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