1w2b | pdb_00001w2b

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Trigger Factor ribosome binding domain in complex with 50S

spinqualitylabelsall models 1w2b, resolution 3.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1w2b is a 30 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895 and Haloarcula marismortui. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CD, CL, K, MG, NA Related: 1ffk, 1jj2, 1k73, 1k8a, 1k9m, 1kc8, 1kd1, 1kqs, 1m1k, 1m90, 1n8r, 1nji, 1q7y, 1q81, 1q82, 1q86, 1qvf, 1qvg, 1s72 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Warning: this is a large structure, and loading might take a long time or not happen at all. Function [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] [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] [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] [RL39_HALMA] Binds to the 23S rRNA. Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_00629] [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] [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] [RL37A_HALMA] Binds to the 23S rRNA.[HAMAP-Rule:MF_00327] [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] [RL15_HALMA] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_A] [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] [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] [RL24E_HALMA] Binds to the 23S rRNA.[HAMAP-Rule:MF_00773] [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] [RL31_HALMA] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00410] [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] [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] [RLA0_HALMA] Ribosomal protein L10e is the functional equivalent of E.coli protein L10.[HAMAP-Rule:MF_00280] [RL19E_HALMA] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01475] [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] [RL14_HALMA] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367] [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] [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] [RL18E_HALMA] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain II) to which it binds.[HAMAP-Rule:MF_00329] [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] [RL37_HALMA] Binds to the 23S rRNA.[HAMAP-Rule:MF_00547] 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 During protein biosynthesis, nascent polypeptide chains that emerge from the ribosomal exit tunnel encounter ribosome-associated chaperones, which assist their folding to the native state. Here we present a 2.7 A crystal structure of Escherichia coli trigger factor, the best-characterized chaperone of this type, together with the structure of its ribosome-binding domain in complex with the Haloarcula marismortui large ribosomal subunit. Trigger factor adopts a unique conformation resembling a crouching dragon with separated domains forming the amino-terminal ribosome-binding 'tail', the peptidyl-prolyl isomerase 'head', the carboxy-terminal 'arms' and connecting regions building up the 'back'. From its attachment point on the ribosome, trigger factor projects the extended domains over the exit of the ribosomal tunnel, creating a protected folding space where nascent polypeptides may be shielded from proteases and aggregation. This study sheds new light on our understanding of co-translational protein folding, and suggests an unexpected mechanism of action for ribosome-associated chaperones. Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins.,Ferbitz L, Maier T, Patzelt H, Bukau B, Deuerling E, Ban N Nature. 2004 Sep 30;431(7008):590-6. Epub 2004 Aug 29. PMID:15334087 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Ribosome 3D structures

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