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| | ==Crystal structure of human PDGF-BB in complex with a modified nucleotide aptamer (SOMAmer SL5)== | | ==Crystal structure of human PDGF-BB in complex with a modified nucleotide aptamer (SOMAmer SL5)== |
| - | <StructureSection load='4hqu' size='340' side='right' caption='[[4hqu]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='4hqu' size='340' side='right'caption='[[4hqu]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4hqu]] is a 2 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=4HQU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HQU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4hqu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HQU FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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]] 2.2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=18M:2-O-METHYLGUANOSINE+3,5-BIS(DIHYDROGEN+PHOSPHATE)'>18M</scene>, <scene name='pdbligand=18Q:2-DEOXY-5-[(THIOPHEN-2-YLMETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>18Q</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=DUZ:5-(BENZYLCARBAMOYL)-2-DEOXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>DUZ</scene>, <scene name='pdbligand=PE6:PHOSPHORYL-HEXAETHYLENE+GLYCOL'>PE6</scene>, <scene name='pdbligand=UPE:2-DEOXY-5-[(2-PHENYLETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UPE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=18M:2-O-METHYLGUANOSINE+3,5-BIS(DIHYDROGEN+PHOSPHATE)'>18M</scene>, <scene name='pdbligand=18Q:2-DEOXY-5-[(THIOPHEN-2-YLMETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>18Q</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=DUZ:5-(BENZYLCARBAMOYL)-2-DEOXYURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>DUZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PE6:PHOSPHORYL-HEXAETHYLENE+GLYCOL'>PE6</scene>, <scene name='pdbligand=UPE:2-DEOXY-5-[(2-PHENYLETHYL)CARBAMOYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UPE</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3mjg|3mjg]], [[4hqx|4hqx]]</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=4hqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqu OCA], [https://pdbe.org/4hqu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hqu RCSB], [https://www.ebi.ac.uk/pdbsum/4hqu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hqu ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDGFB, PDGF2, SIS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=4hqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4hqu RCSB], [http://www.ebi.ac.uk/pdbsum/4hqu PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Disease == | | == Disease == |
| - | [[http://www.uniprot.org/uniprot/PDGFB_HUMAN PDGFB_HUMAN]] Note=A chromosomal aberration involving PDGFB is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGFB.<ref>PMID:12660034</ref> | + | [https://www.uniprot.org/uniprot/PDGFB_HUMAN PDGFB_HUMAN] Note=A chromosomal aberration involving PDGFB is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGFB.<ref>PMID:12660034</ref> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PDGFB_HUMAN PDGFB_HUMAN]] Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Required for normal proliferation and recruitment of pericytes and vascular smooth muscle cells in the central nervous system, skin, lung, heart and placenta. Required for normal blood vessel development, and for normal development of kidney glomeruli. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFA (By similarity). | + | [https://www.uniprot.org/uniprot/PDGFB_HUMAN PDGFB_HUMAN] Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Required for normal proliferation and recruitment of pericytes and vascular smooth muscle cells in the central nervous system, skin, lung, heart and placenta. Required for normal blood vessel development, and for normal development of kidney glomeruli. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFA (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4hqu" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Homo sapiens]] | | [[Category: Homo sapiens]] |
| - | [[Category: Davies, D R]] | + | [[Category: Large Structures]] |
| - | [[Category: Edwards, T E]] | + | [[Category: Davies DR]] |
| - | [[Category: Gelinas, A D]] | + | [[Category: Edwards TE]] |
| - | [[Category: Janjic, N]] | + | [[Category: Gelinas AD]] |
| - | [[Category: Jarvis, T C]] | + | [[Category: Janjic N]] |
| - | [[Category: Zhang, C]] | + | [[Category: Jarvis TC]] |
| - | [[Category: 5-modified deoxyuridine]]
| + | [[Category: Zhang C]] |
| - | [[Category: Aptamer]]
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| - | [[Category: Growth factor]]
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| - | [[Category: Hormone-dna complex]]
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| - | [[Category: Selex]]
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| Structural highlights
4hqu is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.2Å |
| Ligands: | , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Disease
PDGFB_HUMAN Note=A chromosomal aberration involving PDGFB is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGFB.[1]
Function
PDGFB_HUMAN Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Required for normal proliferation and recruitment of pericytes and vascular smooth muscle cells in the central nervous system, skin, lung, heart and placenta. Required for normal blood vessel development, and for normal development of kidney glomeruli. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFA (By similarity).
Publication Abstract from PubMed
Selection of aptamers from nucleic acid libraries by in vitro evolution represents a powerful method of identifying high-affinity ligands for a broad range of molecular targets. Nevertheless, a sizeable fraction of proteins remain difficult targets due to inherently limited chemical diversity of nucleic acids. We have exploited synthetic nucleotide modifications that confer protein-like diversity on a nucleic acid scaffold, resulting in a new generation of binding reagents called SOMAmers (Slow Off-rate Modified Aptamers). Here we report a unique crystal structure of a SOMAmer bound to its target, platelet-derived growth factor B (PDGF-BB). The SOMAmer folds into a compact structure and exhibits a hydrophobic binding surface that mimics the interface between PDGF-BB and its receptor, contrasting sharply with mainly polar interactions seen in traditional protein-binding aptamers. The modified nucleotides circumvent the intrinsic diversity constraints of natural nucleic acids, thereby greatly expanding the structural vocabulary of nucleic acid ligands and considerably broadening the range of accessible protein targets.
Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets.,Davies DR, Gelinas AD, Zhang C, Rohloff JC, Carter JD, O'Connell D, Waugh SM, Wolk SK, Mayfield WS, Burgin AB, Edwards TE, Stewart LJ, Gold L, Janjic N, Jarvis TC Proc Natl Acad Sci U S A. 2012 Nov 8. PMID:23139410[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Sandberg AA, Anderson WD, Fredenberg C, Hashimoto H. Dermatofibrosarcoma protuberans of breast. Cancer Genet Cytogenet. 2003 Apr 1;142(1):56-9. PMID:12660034
- ↑ Davies DR, Gelinas AD, Zhang C, Rohloff JC, Carter JD, O'Connell D, Waugh SM, Wolk SK, Mayfield WS, Burgin AB, Edwards TE, Stewart LJ, Gold L, Janjic N, Jarvis TC. Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets. Proc Natl Acad Sci U S A. 2012 Nov 8. PMID:23139410 doi:http://dx.doi.org/10.1073/pnas.1213933109
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