4v5a: Difference between revisions

<table><tr><td colspan='2'>[[4v5a]] is a 112 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2v46 2v46], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2v47 2v47], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2v48 2v48] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2v49 2v49]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V5A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V5A 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene></td></tr>

<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1fjg|1fjg]], [[1gix|1gix]], [[1i94|1i94]], [[1i95|1i95]], [[1i96|1i96]], [[1i97|1i97]], [[1ibk|1ibk]], [[1ibl|1ibl]], [[1ibm|1ibm]], [[1j5e|1j5e]], [[1jgo|1jgo]], [[1jgp|1jgp]], [[1jgq|1jgq]], [[1l1u|1l1u]], [[1n32|1n32]], [[1n33|1n33]], [[1n34|1n34]], [[1n36|1n36]], [[1pns|1pns]], [[1pnx|1pnx]], [[1xmo|1xmo]], [[1xmq|1xmq]], [[1xnq|1xnq]], [[1xnr|1xnr]], [[1yl4|1yl4]], [[2b64|2b64]], [[2b9m|2b9m]], [[2b9o|2b9o]], [[2f4v|2f4v]], [[2j00|2j00]], [[2j02|2j02]], [[2uu9|2uu9]], [[2uua|2uua]], [[2uub|2uub]], [[2uuc|2uuc]], [[2uxb|2uxb]], [[2uxc|2uxc]]</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=4v5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v5a OCA], [http://pdbe.org/4v5a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v5a RCSB], [http://www.ebi.ac.uk/pdbsum/4v5a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v5a ProSAT]</span></td></tr>

[[http://www.uniprot.org/uniprot/RL34_THET8 RL34_THET8]] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00391] [[http://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385] [[http://www.uniprot.org/uniprot/RL13_THET8 RL13_THET8]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL24_THET8 RL24_THET8]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_B]  One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_B] [[http://www.uniprot.org/uniprot/RL19_THET8 RL19_THET8]] Contacts the 16S rRNA of the 30S subunit (part of bridge B6), connecting the 2 subunits.[HAMAP-Rule:MF_00402] [[http://www.uniprot.org/uniprot/RL3_THET8 RL3_THET8]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_B] [[http://www.uniprot.org/uniprot/RL21_THET8 RL21_THET8]] This protein binds to 23S rRNA in the presence of protein L20 (By similarity). Found on the solvent side of the large subunit.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RL25_THET8 RL25_THET8]] This is one of 3 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit.[HAMAP-Rule:MF_01334] [[http://www.uniprot.org/uniprot/RL14_THET8 RL14_THET8]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_01367]  Contacts the 16S rRNA of the 30S subunit in two different positions helping to form bridges B5 and B8.[HAMAP-Rule:MF_01367] [[http://www.uniprot.org/uniprot/RL23_THET8 RL23_THET8]] One of the early assembly proteins (By similarity) it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome (By similarity).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL31_THET8 RL31_THET8]] Binds the 23S rRNA (By similarity).[HAMAP-Rule:MF_00501] [[http://www.uniprot.org/uniprot/RRF_THET8 RRF_THET8]] Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another (By similarity). [[http://www.uniprot.org/uniprot/RL29_THET8 RL29_THET8]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL4_THET8 RL4_THET8]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01328_B]  Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328_B]  This protein can be incorporated into E.coli ribosomes in vivo, which resulted in decreased peptidyltransferase (Ptase) activity of the hybrid ribosomes. The hybrid 50S subunits associate less well with 30S subunits to form the ribosome.[HAMAP-Rule:MF_01328_B] [[http://www.uniprot.org/uniprot/RL22_THET8 RL22_THET8]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331_B]  The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome. This extension seems to form part of the wall of the exit tunnel.[HAMAP-Rule:MF_01331_B] [[http://www.uniprot.org/uniprot/RL15_THET8 RL15_THET8]] Binds to the 23S rRNA (By similarity).[HAMAP-Rule:MF_01341_B] [[http://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/RS9_THET2 RS9_THET2]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA (By similarity). [[http://www.uniprot.org/uniprot/RL16_THET8 RL16_THET8]] This protein binds directly to 23S rRNA. Interacts with the A site tRNA.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B] [[http://www.uniprot.org/uniprot/RL9_THET8 RL9_THET8]] Binds to the 23S rRNA. Extends more that 50 Angstroms beyond the surface of the 70S ribosome.[HAMAP-Rule:MF_00503]  

[[Category: Thermus thermophilus hb8]]

[[Category: Dunham, C M]]

[[Category: Kelley, A C]]

[[Category: Petry, S]]

[[Category: Ramakrishnan, V]]

[[Category: Selmer, M]]

[[Category: Weixlbaumer, A]]

[[Category: Zinc-finger]]