This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2x4r

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 09:39, 8 February 2016

CRYSTAL STRUCTURE OF MHC CLASS I HLA-A2.1 BOUND TO CYTOMEGALOVIRUS (CMV) PP65 EPITOPE

Structural highlights

2x4r is a 6 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1uqs, 1bd2, 2esv, 2ak4, 1ypz, 1im3, 1uxw, 1i7u, 1c16, 1hsa, 2axf, 1gzp, 2bnq, 1w72, 2jcc, 2bck, 1de4, 2vlk, 1exu, 1qrn, 2hla, 1mhe, 1im9, 1eez, 1jht, 1qqd, 1qr1, 1zs8, 1hla, 1jgd, 1i1y, 1vgk, 1age, 1ur7, 1hhg, 1s9x, 1a9e, 1duz, 2clr, 3hla, 1m05, 1tvb, 2v2w, 1onq, 2vlr, 2bvo, 1a1n, 1lp9, 1zsd, 1m6o, 1hhk, 1hsb, 1zt4, 1x7q, 1ce6, 1py4, 1syv, 2j8u, 1sys, 1ogt, 1cg9, 1p7q, 1q94, 1jnj, 1agb, 2d31, 1aqd, 1xz0, 1lds, 1hhh, 1tvh, 1xr8, 2bss, 1e28, 1a1m, 2bvp, 2v2x, 1xr9, 2gj6, 1qlf, 1efx, 2av1, 1tmc, 1qsf, 1duy, 1kpr, 1jge, 2hjl, 1qew, 1w0v, 1k5n, 1ao7, 2bnr, 1xh3, 2bst, 1mi5, 2h26, 1s9y, 1a1o, 2a83, 1agf, 1oga, 2f8o, 2cii, 1i7r, 1jf1, 2c7u, 2f74, 1e27, 1w0w, 1gzq, 1uxs, 1akj, 2hjk, 2vb5, 1agd, 1r3h, 1eey, 1i7t, 1ydp, 1i4f, 2vll, 2bsr, 1of2, 1b0g, 2vlj, 1b0r, 1hhi, 1qse, 2axg, 1a9b, 2bvq, 1agc, 1hhj, 1qvo, 1s9w, 1ktl, 1a6z, 2cik, 1i1f, 2uwe, 2av7, 2x4p, 2x4u, 2x4s, 2x4t, 2x4n, 2x4o, 2x4q
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[1A02_HUMAN] Involved in the presentation of foreign antigens to the immune system. [PP65_HCMVA] Counteracts the host antiviral immune response when activated and phosphorylated, by preventing IRF3 from entering the nucleus. Also participates in the transactivation of viral major immediate-early genes by the recruitment of host IFI16 to the promoters pf these genes.^[1] ^[2]

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

High-throughput structure determination of protein-ligand complexes is central in drug development and structural proteomics. To facilitate such high-throughput structure determination we designed an induced replacement strategy. Crystals of a protein complex bound to a photosensitive ligand are exposed to UV light, inducing the departure of the bound ligand, allowing a new ligand to soak in. We exemplify the approach for a class of protein complexes that is especially recalcitrant to high-throughput strategies: the MHC class I proteins. We developed a UV-sensitive, "conditional", peptide ligand whose UV-induced cleavage in the crystals leads to the exchange of the low-affinity lytic fragments for full-length peptides introduced in the crystallant solution. This "in crystallo" exchange is monitored by the loss of seleno-methionine anomalous diffraction signal of the conditional peptide compared to the signal of labeled MHC beta2m subunit. This method has the potential to facilitate high-throughput crystallography in various protein families.

UV-induced ligand exchange in MHC class I protein crystals.,Celie PH, Toebes M, Rodenko B, Ovaa H, Perrakis A, Schumacher TN J Am Chem Soc. 2009 Sep 2;131(34):12298-304. PMID:19655750^[3]

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

References

↑ Abate DA, Watanabe S, Mocarski ES. Major human cytomegalovirus structural protein pp65 (ppUL83) prevents interferon response factor 3 activation in the interferon response. J Virol. 2004 Oct;78(20):10995-1006. PMID:15452220 doi:10.1128/JVI.78.20.10995-11006.2004
↑ Cristea IM, Moorman NJ, Terhune SS, Cuevas CD, O'Keefe ES, Rout MP, Chait BT, Shenk T. Human cytomegalovirus pUL83 stimulates activity of the viral immediate-early promoter through its interaction with the cellular IFI16 protein. J Virol. 2010 Aug;84(15):7803-14. doi: 10.1128/JVI.00139-10. Epub 2010 May 26. PMID:20504932 doi:10.1128/JVI.00139-10
↑ Celie PH, Toebes M, Rodenko B, Ovaa H, Perrakis A, Schumacher TN. UV-induced ligand exchange in MHC class I protein crystals. J Am Chem Soc. 2009 Sep 2;131(34):12298-304. PMID:19655750 doi:10.1021/ja9037559

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/2x4r"

@@ Line 2: / Line 2: @@
 <StructureSection load='2x4r' size='340' side='right' caption='[[2x4r]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2x4r]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2X4R FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2x4r]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X4R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2X4R FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1uqs|1uqs]], [[1bd2|1bd2]], [[2esv|2esv]], [[2ak4|2ak4]], [[1ypz|1ypz]], [[1im3|1im3]], [[1uxw|1uxw]], [[1i7u|1i7u]], [[1c16|1c16]], [[1hsa|1hsa]], [[2axf|2axf]], [[1gzp|1gzp]], [[2bnq|2bnq]], [[1w72|1w72]], [[2jcc|2jcc]], [[2bck|2bck]], [[1de4|1de4]], [[2vlk|2vlk]], [[1exu|1exu]], [[1qrn|1qrn]], [[2hla|2hla]], [[1mhe|1mhe]], [[1im9|1im9]], [[1eez|1eez]], [[1jht|1jht]], [[1qqd|1qqd]], [[1qr1|1qr1]], [[1zs8|1zs8]], [[1hla|1hla]], [[1jgd|1jgd]], [[1i1y|1i1y]], [[1vgk|1vgk]], [[1age|1age]], [[1ur7|1ur7]], [[1hhg|1hhg]], [[1s9x|1s9x]], [[1a9e|1a9e]], [[1duz|1duz]], [[2clr|2clr]], [[3hla|3hla]], [[1m05|1m05]], [[1tvb|1tvb]], [[2v2w|2v2w]], [[1onq|1onq]], [[2vlr|2vlr]], [[2bvo|2bvo]], [[1a1n|1a1n]], [[1lp9|1lp9]], [[1zsd|1zsd]], [[1m6o|1m6o]], [[1hhk|1hhk]], [[1hsb|1hsb]], [[1zt4|1zt4]], [[1x7q|1x7q]], [[1ce6|1ce6]], [[1py4|1py4]], [[1syv|1syv]], [[2j8u|2j8u]], [[1sys|1sys]], [[1ogt|1ogt]], [[1cg9|1cg9]], [[1p7q|1p7q]], [[1q94|1q94]], [[1jnj|1jnj]], [[1agb|1agb]], [[2d31|2d31]], [[1aqd|1aqd]], [[1xz0|1xz0]], [[1lds|1lds]], [[1hhh|1hhh]], [[1tvh|1tvh]], [[1xr8|1xr8]], [[2bss|2bss]], [[1e28|1e28]], [[1a1m|1a1m]], [[2bvp|2bvp]], [[2v2x|2v2x]], [[1xr9|1xr9]], [[2gj6|2gj6]], [[1qlf|1qlf]], [[1efx|1efx]], [[2av1|2av1]], [[1tmc|1tmc]], [[1qsf|1qsf]], [[1duy|1duy]], [[1kpr|1kpr]], [[1jge|1jge]], [[2hjl|2hjl]], [[1qew|1qew]], [[1w0v|1w0v]], [[1k5n|1k5n]], [[1ao7|1ao7]], [[2bnr|2bnr]], [[1xh3|1xh3]], [[2bst|2bst]], [[1mi5|1mi5]], [[2h26|2h26]], [[1s9y|1s9y]], [[1a1o|1a1o]], [[2a83|2a83]], [[1agf|1agf]], [[1oga|1oga]], [[2f8o|2f8o]], [[2cii|2cii]], [[1i7r|1i7r]], [[1jf1|1jf1]], [[2c7u|2c7u]], [[2f74|2f74]], [[1e27|1e27]], [[1w0w|1w0w]], [[1gzq|1gzq]], [[1uxs|1uxs]], [[1akj|1akj]], [[2hjk|2hjk]], [[2vb5|2vb5]], [[1agd|1agd]], [[1r3h|1r3h]], [[1eey|1eey]], [[1i7t|1i7t]], [[1ydp|1ydp]], [[1i4f|1i4f]], [[2vll|2vll]], [[2bsr|2bsr]], [[1of2|1of2]], [[1b0g|1b0g]], [[2vlj|2vlj]], [[1b0r|1b0r]], [[1hhi|1hhi]], [[1qse|1qse]], [[2axg|2axg]], [[1a9b|1a9b]], [[2bvq|2bvq]], [[1agc|1agc]], [[1hhj|1hhj]], [[1qvo|1qvo]], [[1s9w|1s9w]], [[1ktl|1ktl]], [[1a6z|1a6z]], [[2cik|2cik]], [[1i1f|1i1f]], [[2uwe|2uwe]], [[2av7|2av7]], [[2x4p|2x4p]], [[2x4u|2x4u]], [[2x4s|2x4s]], [[2x4t|2x4t]], [[2x4n|2x4n]], [[2x4o|2x4o]], [[2x4q|2x4q]]</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=2x4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x4r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2x4r RCSB], [http://www.ebi.ac.uk/pdbsum/2x4r PDBsum]</span></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=2x4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x4r OCA], [http://pdbe.org/2x4r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2x4r RCSB], [http://www.ebi.ac.uk/pdbsum/2x4r PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 17: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2x4r ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2x4r" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Homo sapiens]]
+[[Category: Human]]
 [[Category: Celie, P H.N]]
 [[Category: Ovaa, H]]

2x4r

From Proteopedia

Revision as of 09:39, 8 February 2016

CRYSTAL STRUCTURE OF MHC CLASS I HLA-A2.1 BOUND TO CYTOMEGALOVIRUS (CMV) PP65 EPITOPE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox