1upn

From Proteopedia

(Difference between revisions)

Current revision

COMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR DECAY ACCELERATING FACTOR (CD55) BY CRYO ELECTRON MICROSCOPY AT 16 A

1upn, resolution 16.00Å

Structural highlights

1upn is a 5 chain structure with sequence from Echovirus E11 and Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 16Å
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q8JKE8_9ENTO Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).[SAAS:SAAS000199_004_016611] 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).[SAAS:SAAS000199_004_042266] RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).[SAAS:SAAS000199_004_010047]

Evolutionary Conservation

Checkto colour the structure by Evolutionary Conservation, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF consisting of short consensus repeat domains 3 and 4 from cryo-negative stain electron microscopy data (EMD code 1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the 2-fold symmetry axes. Despite this general similarity our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF(34) and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB code 1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF binding phenotype in these viruses.

The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55).,Bhella D, Goodfellow IG, Roversi P, Pettigrew D, Chaudhry Y, Evans DJ, Lea SM J Biol Chem. 2004 Feb 27;279(9):8325-32. Epub 2003 Nov 21. PMID:14634014^[1]

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

References

↑ Bhella D, Goodfellow IG, Roversi P, Pettigrew D, Chaudhry Y, Evans DJ, Lea SM. The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55). J Biol Chem. 2004 Feb 27;279(9):8325-32. Epub 2003 Nov 21. PMID:14634014 doi:10.1074/jbc.M311334200

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/1upn"

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1upn.png|left|200px]]
-<!--
+==COMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR DECAY ACCELERATING FACTOR (CD55) BY CRYO ELECTRON MICROSCOPY AT 16 A==
-The line below this paragraph, containing "STRUCTURE_1upn", creates the "Structure Box" on the page.
+<SX load='1upn' size='340' side='right' viewer='molstar' caption='[[1upn]], [[Resolution|resolution]] 16.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1upn]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Echovirus_E11 Echovirus E11] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UPN FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 16&#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=1upn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1upn OCA], [https://pdbe.org/1upn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1upn RCSB], [https://www.ebi.ac.uk/pdbsum/1upn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1upn ProSAT]</span></td></tr>
-{{STRUCTURE_1upn|  PDB=1upn  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8JKE8_9ENTO Q8JKE8_9ENTO] Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).[SAAS:SAAS000199_004_016611]  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).[SAAS:SAAS000199_004_042266]  RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).[SAAS:SAAS000199_004_010047]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/up/1upn_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1upn ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF consisting of short consensus repeat domains 3 and 4 from cryo-negative stain electron microscopy data (EMD code 1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the 2-fold symmetry axes. Despite this general similarity our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF(34) and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB code 1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF binding phenotype in these viruses.
-===COMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR DECAY ACCELERATING FACTOR (CD55) BY CRYO ELECTRON MICROSCOPY AT 16 A===
+The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55).,Bhella D, Goodfellow IG, Roversi P, Pettigrew D, Chaudhry Y, Evans DJ, Lea SM J Biol Chem. 2004 Feb 27;279(9):8325-32. Epub 2003 Nov 21. PMID:14634014<ref>PMID:14634014</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1upn" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_14634014}}, adds the Publication Abstract to the page
+*[[CD55|CD55]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14634014 is the PubMed ID number.
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_14634014}}
+<references/>
+__TOC__
-==About this Structure==
+</SX>
-UPN is a 5 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_echovirus_11 Human echovirus 11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPN OCA].
+[[Category: Echovirus E11]]
-==Reference==
-<ref group="xtra">PMID:14634014</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Human echovirus 11]]
+[[Category: Large Structures]]
-[[Category: Bhella, D.]]
+[[Category: Bhella D]]
-[[Category: Chaudry, Y.]]
+[[Category: Chaudry Y]]
-[[Category: Evans, D J.]]
+[[Category: Evans DJ]]
-[[Category: Goodfellow, I G.]]
+[[Category: Goodfellow IG]]
-[[Category: Lea, S M.]]
+[[Category: Lea SM]]
-[[Category: Pettigrew, D.]]
+[[Category: Pettigrew D]]
-[[Category: Roversi, P.]]
+[[Category: Roversi P]]
-[[Category: Cd55]]
-[[Category: Daf]]
-[[Category: Echovirus]]
-[[Category: Electron microscopy]]
-[[Category: Icosahedral virus]]
-[[Category: Picornavirus]]
-[[Category: Virus-receptor complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:02:45 2009''

1upn

From Proteopedia

Current revision

COMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR DECAY ACCELERATING FACTOR (CD55) BY CRYO ELECTRON MICROSCOPY AT 16 A

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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