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| | <StructureSection load='6p4f' size='340' side='right'caption='[[6p4f]], [[Resolution|resolution]] 3.55Å' scene=''> | | <StructureSection load='6p4f' size='340' side='right'caption='[[6p4f]], [[Resolution|resolution]] 3.55Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6p4f]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulto Sulto]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P4F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6P4F FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6p4f]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii_str._7 Sulfurisphaera tokodaii str. 7] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P4F FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 3.55Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4ern|4ern]], [[2fwr|2fwr]], [[5tnu|5tnu]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xpb2, ST1613, STK_16130 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273063 SULTO]), bax1, ST1614, STK_16140 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273063 SULTO])</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=6p4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p4f OCA], [https://pdbe.org/6p4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p4f RCSB], [https://www.ebi.ac.uk/pdbsum/6p4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p4f ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6p4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p4f OCA], [http://pdbe.org/6p4f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p4f RCSB], [http://www.ebi.ac.uk/pdbsum/6p4f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p4f ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q970I2_SULTO Q970I2_SULTO] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6p4f" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6p4f" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Sulto]] | + | [[Category: Sulfurisphaera tokodaii str. 7]] |
| - | [[Category: Fan, L]] | + | [[Category: Synthetic construct]] |
| - | [[Category: He, F]] | + | [[Category: Fan L]] |
| - | [[Category: Hilario, E]] | + | [[Category: He F]] |
| - | [[Category: Atpase]] | + | [[Category: Hilario E]] |
| - | [[Category: Endonuclease]]
| + | |
| - | [[Category: Helicase]]
| + | |
| - | [[Category: Hydrolase-dna complex]]
| + | |
| - | [[Category: Stxpb:bax1 complex]]
| + | |
| Structural highlights
Function
Q970I2_SULTO
Publication Abstract from PubMed
Nucleotide excision repair (NER) removes various DNA lesions caused by UV light and chemical carcinogens. The DNA helicase XPB plays a key role in DNA opening and coordinating damage incision by nucleases during NER, but the underlying mechanisms remain unclear. Here, we report crystal structures of XPB from Sulfurisphaera tokodaii (St) bound to the nuclease Bax1 and their complex with a bubble DNA having one arm unwound in the crystal. StXPB and Bax1 together spirally encircle 10 base pairs of duplex DNA at the double-/single-stranded (ds-ss) junction. Furthermore, StXPB has its ThM motif intruding between the two DNA strands and gripping the 3'-overhang while Bax1 interacts with the 5'-overhang. This ternary complex likely reflects the state of repair bubble extension by the XPB and nuclease machine. ATP binding and hydrolysis by StXPB could lead to a spiral translocation along dsDNA and DNA strand separation by the ThM motif, revealing an unconventional DNA unwinding mechanism. Interestingly, the DNA is kept away from the nuclease domain of Bax1, potentially preventing DNA incision by Bax1 during repair bubble extension.
Structural basis of the XPB helicase-Bax1 nuclease complex interacting with the repair bubble DNA.,He F, DuPrez K, Hilario E, Chen Z, Fan L Nucleic Acids Res. 2020 Nov 18;48(20):11695-11705. doi: 10.1093/nar/gkaa801. PMID:32986831[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ He F, DuPrez K, Hilario E, Chen Z, Fan L. Structural basis of the XPB helicase-Bax1 nuclease complex interacting with the repair bubble DNA. Nucleic Acids Res. 2020 Nov 18;48(20):11695-11705. doi: 10.1093/nar/gkaa801. PMID:32986831 doi:http://dx.doi.org/10.1093/nar/gkaa801
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