Score = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 47/80 (58%)
Query: 1 MNSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKF 60
+N+ I L G +W ++ Y+ H+GYPGG+ A QL + +P +++ AV+ LP++++
Sbjct: 64 INADKIKLTGKKWDQKIYYRHSGYPGGIKEFTARQLQQRNPEKLIQLAVKRMLPKTILGR 123
Query: 61 RLMARLHIFPDQEVPEDLLK 80
+ + RL I+ E P K
Sbjct: 124 KALKRLKIYAGSEHPHSAQK 143
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.
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.
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.
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 45/77 (58%)
Query: 1 MNSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKF 60
+N+ IAL G + ++Y+ H+G+PGG+ A +L E P ++K+AV+ LP++ +
Sbjct: 57 VNAEKIALTGRKLADKSYYSHSGFPGGLKEISAGKLLEKKPEELIKRAVKGMLPKNKLSR 116
Query: 61 RLMARLHIFPDQEVPED 77
++ +L I+ P D
Sbjct: 117 HMLKKLKIYAGSSHPHD 133
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.
Score = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 45/77 (58%)
Query: 1 MNSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKF 60
+N+ + L G + + Y+HHTG+PGG+ A +L E P +++KAV+ LP++ +
Sbjct: 58 VNAAKLQLTGNKLADKMYYHHTGFPGGIKSITAGKLIEKKPEDLIRKAVKGMLPKNKLAR 117
Query: 61 RLMARLHIFPDQEVPED 77
++ +L ++ E P +
Sbjct: 118 HMLKKLKVYAGPEHPHE 134
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.
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.
Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies. Length = 114
>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed
Score = 47.7 bits (114), Expect = 5e-08
Identities = 20/74 (27%), Positives = 41/74 (55%)
Query: 2 NSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFR 61
N+ + L G + +++ Y+ H+GYPGG+ ++ P V++ AV+ LP++ + +
Sbjct: 56 NAEKVRLTGKKLEQKVYYRHSGYPGGLKSRTFEEMIARKPERVLEHAVKGMLPKNRLGRK 115
Query: 62 LMARLHIFPDQEVP 75
L +L ++ E P
Sbjct: 116 LFKKLKVYAGSEHP 129
This model distinguishes ribosomal protein L13 of bacteria and organelles from its eukarytotic and archaeal counterparts [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 140
>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
>PF00572 Ribosomal_L13: Ribosomal protein L13; InterPro: IPR005822 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms
Probab=99.97 E-value=9.5e-33 Score=200.01 Aligned_cols=84 Identities=37% Similarity=0.715 Sum_probs=81.7
Q ss_pred CccceeEeeCccccceEEEEecCCCCCccccChhhhhhcChHHHHHHHHHhcCCCChhHHHHhccccccCCCCCChhhhc
Q psy6264 1 MNSRHIALPGYEWKKRAYFHHTGYPGGVSWTLAWQLHEIDPTLVMKKAVRWELPRSLIKFRLMARLHIFPDQEVPEDLLK 80 (120)
Q Consensus 1 vNaeki~itG~k~~~K~y~~htgypGglk~~~~~~~~~r~P~~il~~AVrgMLPkn~lgr~~l~rLkvy~G~~hP~~~~~ 80 (120)
||||+|+|||++|.+|.|++|||||||+++.+++++++++|++||++||+||||+|.+|+++|+||+||+|++|||+.|+
T Consensus 43 iNae~i~~tG~k~~~k~y~~h~~~~g~~~~~~~~~~~~~~P~~i~~~aVrgMLP~n~~g~~~l~rL~vy~g~~hp~~~~~ 122 (128)
T PF00572_consen 43 INAEKIVLTGKKWRQKVYYRHTGYPGGLKNPTAKGLHEKDPSRILKRAVRGMLPKNKLGREALKRLKVYPGEPHPHAAQK 122 (128)
T ss_dssp ECGGGBEESSHHHHHHHHHHEHSSSTSCEEEECHHHHCSSHHHHHHHHHHTTSTTSHHHHHHHTTEEEESSSSCSTTSSS
T ss_pred EcCeeeEecCCeecceEEEeecccchhhcccchhhhhhcCHHHHHHHHHHHHCCCChhhhHHhhceEEECCCCCChhccC
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchh
Q psy6264 81 NVSS 84 (120)
Q Consensus 81 ~~~~ 84 (120)
++..
T Consensus 123 ~~~~ 126 (128)
T PF00572_consen 123 PVVL 126 (128)
T ss_dssp CBEE
T ss_pred CEeC
Confidence 8764
The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L13 is one of the proteins from the large ribosomal subunit []. In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 4A17_I 4A1E_I 4A1A_I 4A1C_I 3D5B_N 3MS1_J 1VSP_H 3PYT_J 3PYO_J 3PYV_J ....
>TIGR01077 L13_A_E ribosomal protein L13, archaeal/eukaryotic
This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol. Bacterial and organellar forms are represented by TIGR01066.
Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies.
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
>pdb|1P85|H Chain H, Real Space Refined Coordinates Of The 50s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome Length = 142
>pdb|1VSA|H Chain H, Crystal Structure Of A 70s Ribosome-Trna Complex Reveals Functional Interactions And Rearrangements. This File, 1vsa, Contains The 50s Ribosome Subunit. 30s Ribosome Subunit Is In The File 2ow8 Length = 163
>pdb|1VSP|H Chain H, Interactions And Dynamics Of The Shine-Dalgarno Helix In The 70s Ribosome. This File, 1vsp, Contains The 50s Ribosome Subunit. 30s Ribosome Subunit Is In The File 2qnh Length = 140
>pdb|3MRZ|J Chain J, Recognition Of The Amber Stop Codon By Release Factor Rf1. This Entry 3mrz Contains 50s Ribosomal Subunit. The 30s Ribosomal Subunit Can Be Found In Pdb Entry 3ms0. Molecule A In The Same Asymmetric Unit Is Deposited As 3mr8 (50s) And 3ms1 (30s). Length = 139
>pdb|3FIN|N Chain N, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A 6.4 A Cryo-Em Map. This File Contains The 50s Subunit Length = 139
>pdb|2J01|N Chain N, Structure Of The Thermus Thermophilus 70s Ribosome Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4). This File Contains The 50s Subunit From Molecule I. Length = 140
>pdb|3PYO|J Chain J, Crystal Structure Of A Complex Containing Domain 3 From The Psiv Igr Ires Rna Bound To The 70s Ribosome. This File Contains The 50s Subunit Of The First 70s Ribosome. Length = 137
>pdb|3TVE|M Chain M, Crystal Structure Analysis Of Ribosomal Decoding. This Entry Contains The 50s Ribosomal Subunit Of The First 70s Molecule In The Asymmetric Unit For The Cognate Trna-Leu Complex Length = 138
