1rvf

From Proteopedia

(Difference between revisions)

Current revision

FAB COMPLEXED WITH INTACT HUMAN RHINOVIRUS

Structural highlights

1rvf is a 6 chain structure with sequence from Human rhinovirus sp., Mus musculus and Rhinovirus B14. The August 2001 RCSB PDB Molecule of the Month feature on Poliovirus and Rhinovirus by David S. Goodsell is 10.2210/rcsb_pdb/mom_2001_8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 4Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

POLG_HRV14 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 (By similarity). The capsid interacts with human ICAM1 to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis. VP0 precursor is a component of immature procapsids (By similarity). 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 (By similarity). Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity). Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity). Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity). 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). RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The three-dimensional structure of intact human rhinovirus 14 (HRV-14) complexed with Fab fragments (Fab17-IA) from a strongly neutralizing antibody that binds bivalently to the virion has been determined to 4.0 angstrom resolution by a combination of X-ray crystallography and cryo-electron microscopy. In contradiction to the most commonly held model of antibody-mediated neutralization, Fab17-IA does not induce a conformational change in the HRV-14 capsid. Instead, the paratope of the antibody undergoes a large conformational change to accommodate the epitope. Unlike any previously described antibody-antigen structure, the conserved framework region of the antibody makes extensive contact with the viral surface. Fab17-IA penetrates deep within the canyon in which the cellular receptor for HRV-14 binds. Hence, it is unlikely that viral quaternary structure evolves merely to evade immune recognition. Instead, the shape and position of the receptor-binding region on a virus probably dictates receptor binding and subsequent uncoating events and has little or no influence on concealing the virus from the immune system.

Neutralizing antibody to human rhinovirus 14 penetrates the receptor-binding canyon.,Smith TJ, Chase ES, Schmidt TJ, Olson NH, Baker TS Nature. 1996 Sep 26;383(6598):350-4. PMID:8848050^[1]

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

References

↑ Smith TJ, Chase ES, Schmidt TJ, Olson NH, Baker TS. Neutralizing antibody to human rhinovirus 14 penetrates the receptor-binding canyon. Nature. 1996 Sep 26;383(6598):350-4. PMID:8848050 doi:10.1038/383350a0

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1rvf"

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1rvf]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_rhinovirus_sp. Human rhinovirus sp.], [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Rhinovirus_B14 Rhinovirus B14]. The August 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Poliovirus and Rhinovirus''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_8 10.2210/rcsb_pdb/mom_2001_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RVF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RVF FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rvf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvf OCA], [https://pdbe.org/1rvf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rvf RCSB], [https://www.ebi.ac.uk/pdbsum/1rvf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rvf ProSAT]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 4&#8491;</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rvf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rvf OCA], [https://pdbe.org/1rvf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rvf RCSB], [https://www.ebi.ac.uk/pdbsum/1rvf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rvf ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rv/1rvf_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 31: / Line 32: @@
 *[[Antibody 3D structures|Antibody 3D structures]]
 *[[Human rhinovirus|Human rhinovirus]]
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
 *[[3D structures of non-human antibody|3D structures of non-human antibody]]
 == References ==

1rvf

From Proteopedia

Current revision

FAB COMPLEXED WITH INTACT HUMAN RHINOVIRUS

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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