2qa4

A more complete structure of the the L7/L12 stalk of the Haloarcula marismortui 50S large ribosomal subunitA more complete structure of the the L7/L12 stalk of the Haloarcula marismortui 50S large ribosomal subunit

Structural highlights 2qa4 is a 30 chain structure with sequence from Haloarcula marismortui. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: , , , , NonStd Res: , , , Resources: FirstGlance, OCA, RCSB, PDBsum Function [RL11_HALMA] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736_A] [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] [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] [RL31_HALMA] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00410] [RL18E_HALMA] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain II) to which it binds.[HAMAP-Rule:MF_00329] [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] [RL19_HALMA] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01475] [RL39_HALMA] Binds to the 23S rRNA. Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_00629] [RL24E_HALMA] Binds to the 23S rRNA.[HAMAP-Rule:MF_00773] [RL14_HALMA] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367] [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] [RL37_HALMA] Binds to the 23S rRNA.[HAMAP-Rule:MF_00547] [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] [RL32_HALMA] Binds to the 23S rRNA.[HAMAP-Rule:MF_00810] [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] [RL37A_HALMA] Binds to the 23S rRNA.[HAMAP-Rule:MF_00327] [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] [RLA0_HALMA] Ribosomal protein L10e is the functional equivalent of E.coli protein L10.[HAMAP-Rule:MF_00280] [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] [RL15_HALMA] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_A] [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] [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] [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] [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] [RL10_HALMA] This is 1 of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Modeling places the A and P site tRNAs in close proximity to this protein.[HAMAP-Rule:MF_00448] [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] [RL44_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] [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] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed Initiation factors, elongation factors, and release factors all interact with the L7/L12 stalk of the large ribosomal subunit during their respective GTP-dependent cycles on the ribosome. Electron density corresponding to the stalk is not present in previous crystal structures of either 50 S subunits or 70 S ribosomes. We have now discovered conditions that result in a more ordered factor-binding center in the Haloarcula marismortui (H.ma) large ribosomal subunit crystals and consequently allows the visualization of the full-length L11, the N-terminal domain (NTD) of L10 and helices 43 and 44 of 23 S rRNA. The resulting model is currently the most complete reported structure of a L7/L12 stalk in the context of a ribosome. This region contains a series of intermolecular interfaces that are smaller than those typically seen in other ribonucleoprotein interactions within the 50 S subunit. Comparisons of the L11 NTD position between the current structure, which is has an NTD splayed out with respect to previous structures, and other structures of ribosomes in different functional states demonstrates a dynamic range of L11 NTD movements. We propose that the L11 NTD moves through three different relative positions during the translational cycle: apo-ribosome, factor-bound pre-GTP hydrolysis and post-GTP hydrolysis. These positions outline a pathway for L11 NTD movements that are dependent on the specific nucleotide state of the bound ligand. These three states are represented by the orientations of the L11 NTD relative to the ribosome and suggest that L11 may play a more specialized role in the factor binding cycle than previously appreciated. Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements.,Kavran JM, Steitz TA J Mol Biol. 2007 Aug 24;371(4):1047-59. Epub 2007 Jun 4. PMID:17599351 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Large Ribosomal Subunit of Haloarcula Ribosome 3D structures User:Wayne Decatur/Haloarcula Large Ribosomal Subunit

spinqualitylabelsall models 2qa4, resolution 3.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image