3qqc: Difference between revisions

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<StructureSection load='3qqc' size='340' side='right'caption='[[3qqc]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
<StructureSection load='3qqc' size='340' side='right'caption='[[3qqc]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3qqc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QQC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QQC FirstGlance]. <br>
<table><tr><td colspan='2'>[[3qqc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QQC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QQC FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.3&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PF1563 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU]), PF1990 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU]), PF0255 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=3qqc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qqc OCA], [https://pdbe.org/3qqc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qqc RCSB], [https://www.ebi.ac.uk/pdbsum/3qqc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qqc ProSAT]</span></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=3qqc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qqc OCA], [https://pdbe.org/3qqc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qqc RCSB], [https://www.ebi.ac.uk/pdbsum/3qqc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qqc ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/SPT4_PYRFU SPT4_PYRFU]] Stimulates transcription elongation.<ref>PMID:21386817</ref> <ref>PMID:21187417</ref>  [[https://www.uniprot.org/uniprot/SPT5_PYRFU SPT5_PYRFU]] Stimulates transcription elongation.<ref>PMID:21386817</ref> <ref>PMID:21187417</ref> 
[https://www.uniprot.org/uniprot/RPO1C_PYRFU RPO1C_PYRFU] DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Forms part of the jaw domain.[HAMAP-Rule:MF_00411]<ref>PMID:21386817</ref> [https://www.uniprot.org/uniprot/Q8U0M4_PYRFU Q8U0M4_PYRFU] DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Forms the clamp head domain.[HAMAP-Rule:MF_00863]  DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279][https://www.uniprot.org/uniprot/Q8U0M3_PYRFU Q8U0M3_PYRFU]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Related RNA polymerases (RNAPs) carry out cellular gene transcription in all three kingdoms of life. The universal conservation of the transcription machinery extends to a single RNAP-associated factor, Spt5 (or NusG in bacteria), which renders RNAP processive and may have arisen early to permit evolution of long genes. Spt5 associates with Spt4 to form the Spt4/5 heterodimer. Here, we present the crystal structure of archaeal Spt4/5 bound to the RNAP clamp domain, which forms one side of the RNAP active centre cleft. The structure revealed a conserved Spt5-RNAP interface and enabled modelling of complexes of Spt4/5 counterparts with RNAPs from all kingdoms of life, and of the complete yeast RNAP II elongation complex with bound Spt4/5. The N-terminal NGN domain of Spt5/NusG closes the RNAP active centre cleft to lock nucleic acids and render the elongation complex stable and processive. The C-terminal KOW1 domain is mobile, but its location is restricted to a region between the RNAP clamp and wall above the RNA exit tunnel, where it may interact with RNA and/or other factors.
 
Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity.,Martinez-Rucobo FW, Sainsbury S, Cheung AC, Cramer P EMBO J. 2011 Mar 8. PMID:21386817<ref>PMID:21386817</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3qqc" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Pyrfu]]
[[Category: Pyrococcus furiosus]]
[[Category: Martinez-Rucobo, F W]]
[[Category: Martinez-Rucobo FW]]
[[Category: Chimera protein]]
[[Category: Fusion protein]]
[[Category: Multiprotein complex]]
[[Category: Transcription]]

Latest revision as of 14:54, 14 March 2024

Crystal structure of archaeal Spt4/5 bound to the RNAP clamp domainCrystal structure of archaeal Spt4/5 bound to the RNAP clamp domain

Structural highlights

3qqc is a 3 chain structure with sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.3Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPO1C_PYRFU DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Forms part of the jaw domain.[HAMAP-Rule:MF_00411][1] Q8U0M4_PYRFU DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Forms the clamp head domain.[HAMAP-Rule:MF_00863] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279]Q8U0M3_PYRFU

See Also

References

  1. ↑ Martinez-Rucobo FW, Sainsbury S, Cheung AC, Cramer P. Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity. EMBO J. 2011 Mar 8. PMID:21386817 doi:10.1038/emboj.2011.64

3qqc, resolution 3.30Å

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