1ffk

<StructureSection load='1ffk' size='340' side='right' caption='[[1ffk]], [[Resolution|resolution]] 2.40&Aring;' scene=''>

<table><tr><td colspan='2'>[[1ffk]] is a 28 chain structure with sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. The October 2000 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Ribosome'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2000_10 10.2210/rcsb_pdb/mom_2000_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FFK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FFK FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>

<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1c04|1c04]]</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=1ffk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ffk OCA], [http://pdbe.org/1ffk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ffk RCSB], [http://www.ebi.ac.uk/pdbsum/1ffk PDBsum]</span></td></tr>

[[http://www.uniprot.org/uniprot/RL29_HALMA RL29_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL7A_HALMA RL7A_HALMA]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA and box C/D sRNAs (By similarity).[HAMAP-Rule:MF_00326] [[http://www.uniprot.org/uniprot/RL37_HALMA RL37_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00547] [[http://www.uniprot.org/uniprot/RL22_HALMA RL22_HALMA]] This protein binds specifically to 23S rRNA. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331] Contacts all 6 domains of the 23S rRNA, helping stabilize their relative orientation. An extended beta-hairpin in the C-terminus forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L4, while most of the rest of the protein is located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/RL30_HALMA RL30_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01371] [[http://www.uniprot.org/uniprot/RL23_HALMA RL23_HALMA]] Binds to a specific region on the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL31_HALMA RL31_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00410] [[http://www.uniprot.org/uniprot/RL18_HALMA RL18_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, where it forms part of the central protuberance and stabilizes the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01337_A] [[http://www.uniprot.org/uniprot/RL21_HALMA RL21_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_00369] [[http://www.uniprot.org/uniprot/RL6_HALMA RL6_HALMA]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL5_HALMA RL5_HALMA]] This is 1 of 5 proteins that mediates the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Forms part of the central protuberance. Modeling places the A and P site tRNAs in close proximity to this protein; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. In the 70S ribosome it is thought to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement.[HAMAP-Rule:MF_01333_A] [[http://www.uniprot.org/uniprot/RL39_HALMA RL39_HALMA]] Binds to the 23S rRNA. Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_00629] [[http://www.uniprot.org/uniprot/RL44E_HALMA RL44E_HALMA]] Binds to the 23S rRNA. Binds deacetylated tRNA in the E site; when the tRNA binds a stretch of 7 amino acids are displaced to allow binding.[HAMAP-Rule:MF_01476] [[http://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A] [[http://www.uniprot.org/uniprot/RL13_HALMA RL13_HALMA]] This protein is one of the early assembly proteins of the 50S ribosomal subunit (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL15_HALMA RL15_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_A] [[http://www.uniprot.org/uniprot/RL18E_HALMA RL18E_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain II) to which it binds.[HAMAP-Rule:MF_00329] [[http://www.uniprot.org/uniprot/RL19E_HALMA RL19E_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01475] [[http://www.uniprot.org/uniprot/RL24E_HALMA RL24E_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00773] [[http://www.uniprot.org/uniprot/RL3_HALMA RL3_HALMA]] 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_A] [[http://www.uniprot.org/uniprot/RL32_HALMA RL32_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00810] [[http://www.uniprot.org/uniprot/RL14_HALMA RL14_HALMA]] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367] [[http://www.uniprot.org/uniprot/RL24_HALMA RL24_HALMA]] 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_A] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_A] [[http://www.uniprot.org/uniprot/RL4_HALMA RL4_HALMA]] 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 (By similarity).[HAMAP-Rule:MF_01328_A] Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_A] Forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L22. Contacts the macrolide antibiotic spiramycin in the polypeptide exit tunnel.[HAMAP-Rule:MF_01328_A]

<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ff/1ffk_consurf.spt"</scriptWhenChecked>

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== Publication Abstract from PubMed ==

The large ribosomal subunit catalyzes peptide bond formation and binds initiation, termination, and elongation factors. We have determined the crystal structure of the large ribosomal subunit from Haloarcula marismortui at 2.4 angstrom resolution, and it includes 2833 of the subunit's 3045 nucleotides and 27 of its 31 proteins. The domains of its RNAs all have irregular shapes and fit together in the ribosome like the pieces of a three-dimensional jigsaw puzzle to form a large, monolithic structure. Proteins are abundant everywhere on its surface except in the active site where peptide bond formation occurs and where it contacts the small subunit. Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the subunit's interior.

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.,Ban N, Nissen P, Hansen J, Moore PB, Steitz TA Science. 2000 Aug 11;289(5481):905-20. PMID:10937989<ref>PMID:10937989</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>

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<div class="pdbe-citations 1ffk" style="background-color:#fffaf0;"></div>

*[[Nobel Prizes for 3D Molecular Structure|Nobel Prizes for 3D Molecular Structure]]

*[[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit|User:Wayne Decatur/Haloarcula Large Ribosomal Subunit]]

== References ==

<references/>

[[Category: Ban, N]]

[[Category: Hansen, J]]

[[Category: Moore, P B]]

[[Category: Nissen, P]]

[[Category: Steitz, T A]]

[[Category: Rna-rna]]