6j4z

From Proteopedia

(Difference between revisions)

Revision as of 16:05, 27 February 2019

RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome

Structural highlights

6j4z is a 26 chain structure with sequence from Atcc 28485, Kompc and Kompg. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	PAS_chr2-1_0350 (KOMPG), H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B (KOMPG), HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 (KOMPG), HIST1H2AB, H2AFM, HIST1H2AE, H2AFA (KOMPG), HIST1H2BJ, H2BFR (KOMPG)
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[H2B1J_HUMAN] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.^[1] ^[2] ^[3] Has broad antibacterial activity. May contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.^[4] ^[5] ^[6] [C4QZQ7_KOMPG] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU363031] [C4R4Y0_KOMPG] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279] [C4R0E6_KOMPG] The SPT4-SPT5 complex mediates both activation and inhibition of transcription elongation, and plays a role in pre-mRNA processing. This complex seems to be important for the stability of the RNA polymerase II elongation machinery on the chromatin template but not for the inherent ability of this machinery to translocate down the gene.[PIRNR:PIRNR025023] [F2QPE6_KOMPC] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[PIRNR:PIRNR005586]

Publication Abstract from PubMed

RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional factors in vivo. We demonstrate that the transcription elongation factors Elf1 and Spt4/5 cooperatively lower the barriers and increase the RNAPII processivity in the nucleosome. The cryo-electron microscopy structures of the nucleosome-transcribing RNAPII elongation complexes (ECs) reveal that Elf1 and Spt4/5 reshape the EC downstream edge and intervene between RNAPII and the nucleosome. They facilitate RNAPII progression through superhelical location SHL(-1) by adjusting the nucleosome in favor of the forward progression. They suppress pausing at SHL(-5) by preventing the stable RNAPII-nucleosome interaction. Thus, the EC overcomes the nucleosomal barriers while providing a platform for various chromatin functions.

Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.,Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI Science. 2019 Feb 15;363(6428):744-747. doi: 10.1126/science.aav8912. Epub 2019, Feb 7. PMID:30733384^[7]

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

References

↑ Kim HS, Cho JH, Park HW, Yoon H, Kim MS, Kim SC. Endotoxin-neutralizing antimicrobial proteins of the human placenta. J Immunol. 2002 Mar 1;168(5):2356-64. PMID:11859126
↑ Tollin M, Bergman P, Svenberg T, Jornvall H, Gudmundsson GH, Agerberth B. Antimicrobial peptides in the first line defence of human colon mucosa. Peptides. 2003 Apr;24(4):523-30. PMID:12860195
↑ Howell SJ, Wilk D, Yadav SP, Bevins CL. Antimicrobial polypeptides of the human colonic epithelium. Peptides. 2003 Nov;24(11):1763-70. PMID:15019208 doi:10.1016/j.peptides.2003.07.028
↑ Kim HS, Cho JH, Park HW, Yoon H, Kim MS, Kim SC. Endotoxin-neutralizing antimicrobial proteins of the human placenta. J Immunol. 2002 Mar 1;168(5):2356-64. PMID:11859126
↑ Tollin M, Bergman P, Svenberg T, Jornvall H, Gudmundsson GH, Agerberth B. Antimicrobial peptides in the first line defence of human colon mucosa. Peptides. 2003 Apr;24(4):523-30. PMID:12860195
↑ Howell SJ, Wilk D, Yadav SP, Bevins CL. Antimicrobial polypeptides of the human colonic epithelium. Peptides. 2003 Nov;24(11):1763-70. PMID:15019208 doi:10.1016/j.peptides.2003.07.028
↑ Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI. Structural insight into nucleosome transcription by RNA polymerase II with elongation factors. Science. 2019 Feb 15;363(6428):744-747. doi: 10.1126/science.aav8912. Epub 2019, Feb 7. PMID:30733384 doi:http://dx.doi.org/10.1126/science.aav8912

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6j4z"

@@ Line 3: / Line 3: @@
 <StructureSection load='6j4z' size='340' side='right' caption='[[6j4z]], [[Resolution|resolution]] 4.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6j4z]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Komagataella_phaffii_(strain_atcc_76273_/_cbs_7435_/_cect_11047_/_nrrl_y-11430_/_wegner_21-1) Komagataella phaffii (strain atcc 76273 / cbs 7435 / cect 11047 / nrrl y-11430 / wegner 21-1)] and [http://en.wikipedia.org/wiki/Komagataella_phaffii_(strain_gs115_/_atcc_20864) Komagataella phaffii (strain gs115 / atcc 20864)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J4Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6j4z]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_28485 Atcc 28485], [http://en.wikipedia.org/wiki/Kompc Kompc] and [http://en.wikipedia.org/wiki/Kompg Kompg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J4Z 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=ZN:ZINC+ION'>ZN</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PAS_chr2-1_0350 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H2AB, H2AFM, HIST1H2AE, H2AFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H2BJ, H2BFR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </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=6j4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4z OCA], [http://pdbe.org/6j4z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j4z RCSB], [http://www.ebi.ac.uk/pdbsum/6j4z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4z ProSAT]</span></td></tr>
@@ Line 23: / Line 24: @@
 __TOC__
 </StructureSection>
+[[Category: Atcc 28485]]
 [[Category: DNA-directed RNA polymerase]]
+[[Category: Kompc]]
+[[Category: Kompg]]
 [[Category: Ehara, H]]
 [[Category: Fujino, Y]]

6j4z

From Proteopedia

Revision as of 16:05, 27 February 2019

RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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