3j3q

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
 
+
====
-
<div style="background-color:yellow;" border="1" cellpadding="5">''Warning: this is a large structure, and loading might take a long time or not happen at all.''</div>
+
<StructureSection load='3j3q' size='340' side='right' caption='[[3j3q]]' scene=''>
-
== Atomic-level structure of the entire HIV-1 capsid ==
+
-
<StructureSection load='3j3q-pdb-bundle1.pdb.gz' size='340' side='right' caption='[[3j3q]]' scene=''>
+
== Structural highlights ==
== Structural highlights ==
-
[[3j3q]] is a 1355 chain structure, available for rendering on Proteopedia in 25 parts.
+
<table><tr><td colspan='2'>This structure supersedes and combines the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vu4 1vu4], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vu5 1vu5], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vu6 1vu6], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vu7 1vu7], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vu8 1vu8], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vu9 1vu9], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vua 1vua], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuc 1vuc], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vud 1vud], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vue 1vue], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuf 1vuf], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vug 1vug], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuh 1vuh], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vui 1vui], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuj 1vuj], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuk 1vuk], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vul 1vul], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vum 1vum], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vun 1vun], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuo 1vuo], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vup 1vup], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vuq 1vuq], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vur 1vur], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vus 1vus] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vut 1vut]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol= FirstGlance]. <br>
-
You may render each one of these parts individually by selecting here: <jmol><jmolMenu>
+
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3j3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j3q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j3q RCSB], [http://www.ebi.ac.uk/pdbsum/3j3q PDBsum]</span></td></tr>
-
<item>
+
</table>
-
<script>
+
{{Large structure}}
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
__TOC__
-
echo Loading part 1 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle1.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 1</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 2 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle2.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 2</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 3 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle3.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 3</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 4 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle4.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 4</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 5 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle5.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 5</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 6 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle6.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 6</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 7 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle7.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 7</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 8 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle8.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 8</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 9 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle9.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 9</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 10 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle10.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 10</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 11 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle11.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 11</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 12 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle12.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 12</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 13 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle13.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 13</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 14 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle14.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 14</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 15 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle15.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 15</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 16 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle16.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 16</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 17 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle17.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 17</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 18 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle18.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 18</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 19 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle19.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 19</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 20 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle20.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 20</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 21 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle21.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 21</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 22 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle22.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 22</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 23 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle23.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 23</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 24 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle24.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 24</text>
+
-
</item>
+
-
<item>
+
-
<script>
+
-
set echo off; set echo loading 50% 50%; set echo loading center; color echo [xffa500]; background echo translucent 0.7 gray;
+
-
echo Loading part 25 ...; refresh;
+
-
load models {0 0 1} /cgi-bin/getlateststructure?3j3q-pdb-bundle25.pdb.gz filter "*.CA,*.P|HETATM,![HOH]";
+
-
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
+
-
</script>
+
-
<text>render part 25</text>
+
-
</item>
+
-
</jmolMenu></jmol>
+
-
 
+
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven alpha-helices and a beta-hairpin, a carboxy-terminal domain (CTD) comprising four alpha-helices, and a flexible linker with a 310-helix connecting the two structural domains. Structures of the capsid-protein assembly units have been determined by X-ray crystallography; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 A resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. Incorporation of pentamers results in closer trimer contacts and induces acute surface curvature. The complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention.
+
-
 
+
-
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.,Zhao G, Perilla JR, Yufenyuy EL, Meng X, Chen B, Ning J, Ahn J, Gronenborn AM, Schulten K, Aiken C, Zhang P Nature. 2013 May 30;497(7451):643-6. doi: 10.1038/nature12162. PMID:23719463<ref>PMID:23719463</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
 
+
-
== References ==
+
-
<references/>
+
</StructureSection>
</StructureSection>
-
[[Category: Zhao, G]]
+
[[Category: Z-disk]]
-
[[Category: Zhang, P]]
+
-
[[Category: Schulten, K.J]]
+
-
[[Category: Perilla, J.R]]
+

Revision as of 13:28, 1 September 2015

==

3j3q

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3j3q"
Personal tools