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P29198

- RL13_HALMA

UniProt

P29198 - RL13_HALMA

Protein

50S ribosomal protein L13

Gene

rpl13

Organism
Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809) (Halobacterium marismortui)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 104 (01 Oct 2014)
      Sequence version 1 (01 Dec 1992)
      Previous versions | rss
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    Functioni

    This protein is one of the early assembly proteins of the 50S ribosomal subunit By similarity. Binds to 23S rRNA.By similarity

    GO - Molecular functioni

    1. rRNA binding Source: UniProtKB-KW
    2. structural constituent of ribosome Source: InterPro

    GO - Biological processi

    1. translation Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Ribonucleoprotein, Ribosomal protein

    Keywords - Ligandi

    RNA-binding, rRNA-binding

    Enzyme and pathway databases

    BioCyciHMAR272569:GJDH-61-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    50S ribosomal protein L13UniRule annotation
    Alternative name(s):
    Hmal13
    Gene namesi
    Name:rpl13UniRule annotation
    Ordered Locus Names:rrnAC0065
    OrganismiHaloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809) (Halobacterium marismortui)
    Taxonomic identifieri272569 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaHalobacteriaHalobacterialesHalobacteriaceaeHaloarcula
    ProteomesiUP000001169: Chromosome I

    Subcellular locationi

    GO - Cellular componenti

    1. large ribosomal subunit Source: InterPro

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 14514550S ribosomal protein L13PRO_0000133758Add
    BLAST

    Interactioni

    Subunit structurei

    Part of the 50S ribosomal subunit. Interacts weakly with proteins L3 and L6.2 PublicationsUniRule annotation

    Protein-protein interaction databases

    STRINGi272569.rrnAC0065.

    Structurei

    Secondary structure

    1
    145
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi9 – 135
    Helixi19 – 3113
    Beta strandi36 – 394
    Helixi41 – 433
    Beta strandi45 – 484
    Helixi50 – 6213
    Helixi75 – 8410
    Turni85 – 906
    Helixi92 – 998
    Beta strandi101 – 1033
    Beta strandi109 – 1113
    Turni117 – 1193
    Turni123 – 1253
    Beta strandi128 – 1314
    Helixi132 – 1398

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1FFKX-ray2.40G1-145[»]
    1JJ2X-ray2.40I1-145[»]
    1K73X-ray3.01K1-145[»]
    1K8AX-ray3.00K1-145[»]
    1K9MX-ray3.00K1-145[»]
    1KC8X-ray3.01K1-145[»]
    1KD1X-ray3.00K1-145[»]
    1KQSX-ray3.10I1-145[»]
    1M1KX-ray3.20K1-145[»]
    1M90X-ray2.80K1-145[»]
    1N8RX-ray3.00K1-145[»]
    1NJIX-ray3.00K1-145[»]
    1Q7YX-ray3.20K1-145[»]
    1Q81X-ray2.95K1-145[»]
    1Q82X-ray2.98K1-145[»]
    1Q86X-ray3.00K1-145[»]
    1QVFX-ray3.10I1-145[»]
    1QVGX-ray2.90I1-145[»]
    1S72X-ray2.40J1-145[»]
    1VQ4X-ray2.70J1-145[»]
    1VQ5X-ray2.60J1-145[»]
    1VQ6X-ray2.70J1-145[»]
    1VQ7X-ray2.50J1-145[»]
    1VQ8X-ray2.20J1-145[»]
    1VQ9X-ray2.40J1-145[»]
    1VQKX-ray2.30J1-145[»]
    1VQLX-ray2.30J1-145[»]
    1VQMX-ray2.30J1-145[»]
    1VQNX-ray2.40J1-145[»]
    1VQOX-ray2.20J1-145[»]
    1VQPX-ray2.25J1-145[»]
    1W2BX-ray3.50I1-145[»]
    1YHQX-ray2.40J1-145[»]
    1YI2X-ray2.65J1-145[»]
    1YIJX-ray2.60J1-145[»]
    1YITX-ray2.80J1-145[»]
    1YJ9X-ray2.90J1-145[»]
    1YJNX-ray3.00J1-145[»]
    1YJWX-ray2.90J1-145[»]
    2B66X-ray5.90N1-145[»]
    2B9NX-ray6.76N1-145[»]
    2OTJX-ray2.90J1-145[»]
    2OTLX-ray2.70J1-145[»]
    2QA4X-ray3.00J1-145[»]
    2QEXX-ray2.90J1-145[»]
    3CC2X-ray2.40J1-145[»]
    3CC4X-ray2.70J1-145[»]
    3CC7X-ray2.70J1-145[»]
    3CCEX-ray2.75J1-145[»]
    3CCJX-ray2.70J1-145[»]
    3CCLX-ray2.90J1-145[»]
    3CCMX-ray2.55J1-145[»]
    3CCQX-ray2.90J1-145[»]
    3CCRX-ray3.00J1-145[»]
    3CCSX-ray2.95J1-145[»]
    3CCUX-ray2.80J1-145[»]
    3CCVX-ray2.90J1-145[»]
    3CD6X-ray2.75J1-145[»]
    3CMAX-ray2.80J1-145[»]
    3CMEX-ray2.95J1-145[»]
    3CPWX-ray2.70I1-145[»]
    3CXCX-ray3.00I1-145[»]
    3G4SX-ray3.20J4-145[»]
    3G6EX-ray2.70J4-145[»]
    3G71X-ray2.85J4-145[»]
    3I55X-ray3.11J1-145[»]
    3I56X-ray2.90J1-145[»]
    3OW2X-ray2.70I4-145[»]
    4HUBX-ray2.40J1-145[»]
    ProteinModelPortaliP29198.
    SMRiP29198. Positions 4-145.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP29198.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the ribosomal protein L13P family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0102.
    HOGENOMiHOG000225287.
    KOiK02871.
    OMAiRLSRPKY.

    Family and domain databases

    Gene3Di3.90.1180.10. 1 hit.
    HAMAPiMF_01366. Ribosomal_L13.
    InterProiIPR005822. Ribosomal_L13.
    IPR023563. Ribosomal_L13_CS.
    IPR023564. Ribosomal_L13_dom.
    IPR005755. Ribosomal_L13_euk/arc.
    [Graphical view]
    PANTHERiPTHR11545. PTHR11545. 1 hit.
    PTHR11545:SF3. PTHR11545:SF3. 1 hit.
    PfamiPF00572. Ribosomal_L13. 1 hit.
    [Graphical view]
    PIRSFiPIRSF002181. Ribosomal_L13. 1 hit.
    SUPFAMiSSF52161. SSF52161. 1 hit.
    TIGRFAMsiTIGR01077. L13_A_E. 1 hit.
    PROSITEiPS00783. RIBOSOMAL_L13. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P29198-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSVAEFDADV IVDARDCIMG RVASQVAEQA LDGETVAVVN AERAVITGRE    50
    EQIVEKYEKR VDIGNDNGYF YPKRPDGIFK RTIRGMLPHK KQRGREAFES 100
    VRVYLGNPYD EDGEVLDGTS LDRLSNIKFV TLGEISETLG ANKTW 145
    Length:145
    Mass (Da):16,228
    Last modified:December 1, 1992 - v1
    Checksum:i069CE666662AE3BC
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M76567 Genomic DNA. Translation: AAA73097.1.
    AY596297 Genomic DNA. Translation: AAV45145.1.
    PIRiB41715.
    RefSeqiYP_134851.1. NC_006396.1.

    Genome annotation databases

    EnsemblBacteriaiAAV45145; AAV45145; rrnAC0065.
    GeneIDi3130528.
    KEGGihma:rrnAC0065.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M76567 Genomic DNA. Translation: AAA73097.1 .
    AY596297 Genomic DNA. Translation: AAV45145.1 .
    PIRi B41715.
    RefSeqi YP_134851.1. NC_006396.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1FFK X-ray 2.40 G 1-145 [» ]
    1JJ2 X-ray 2.40 I 1-145 [» ]
    1K73 X-ray 3.01 K 1-145 [» ]
    1K8A X-ray 3.00 K 1-145 [» ]
    1K9M X-ray 3.00 K 1-145 [» ]
    1KC8 X-ray 3.01 K 1-145 [» ]
    1KD1 X-ray 3.00 K 1-145 [» ]
    1KQS X-ray 3.10 I 1-145 [» ]
    1M1K X-ray 3.20 K 1-145 [» ]
    1M90 X-ray 2.80 K 1-145 [» ]
    1N8R X-ray 3.00 K 1-145 [» ]
    1NJI X-ray 3.00 K 1-145 [» ]
    1Q7Y X-ray 3.20 K 1-145 [» ]
    1Q81 X-ray 2.95 K 1-145 [» ]
    1Q82 X-ray 2.98 K 1-145 [» ]
    1Q86 X-ray 3.00 K 1-145 [» ]
    1QVF X-ray 3.10 I 1-145 [» ]
    1QVG X-ray 2.90 I 1-145 [» ]
    1S72 X-ray 2.40 J 1-145 [» ]
    1VQ4 X-ray 2.70 J 1-145 [» ]
    1VQ5 X-ray 2.60 J 1-145 [» ]
    1VQ6 X-ray 2.70 J 1-145 [» ]
    1VQ7 X-ray 2.50 J 1-145 [» ]
    1VQ8 X-ray 2.20 J 1-145 [» ]
    1VQ9 X-ray 2.40 J 1-145 [» ]
    1VQK X-ray 2.30 J 1-145 [» ]
    1VQL X-ray 2.30 J 1-145 [» ]
    1VQM X-ray 2.30 J 1-145 [» ]
    1VQN X-ray 2.40 J 1-145 [» ]
    1VQO X-ray 2.20 J 1-145 [» ]
    1VQP X-ray 2.25 J 1-145 [» ]
    1W2B X-ray 3.50 I 1-145 [» ]
    1YHQ X-ray 2.40 J 1-145 [» ]
    1YI2 X-ray 2.65 J 1-145 [» ]
    1YIJ X-ray 2.60 J 1-145 [» ]
    1YIT X-ray 2.80 J 1-145 [» ]
    1YJ9 X-ray 2.90 J 1-145 [» ]
    1YJN X-ray 3.00 J 1-145 [» ]
    1YJW X-ray 2.90 J 1-145 [» ]
    2B66 X-ray 5.90 N 1-145 [» ]
    2B9N X-ray 6.76 N 1-145 [» ]
    2OTJ X-ray 2.90 J 1-145 [» ]
    2OTL X-ray 2.70 J 1-145 [» ]
    2QA4 X-ray 3.00 J 1-145 [» ]
    2QEX X-ray 2.90 J 1-145 [» ]
    3CC2 X-ray 2.40 J 1-145 [» ]
    3CC4 X-ray 2.70 J 1-145 [» ]
    3CC7 X-ray 2.70 J 1-145 [» ]
    3CCE X-ray 2.75 J 1-145 [» ]
    3CCJ X-ray 2.70 J 1-145 [» ]
    3CCL X-ray 2.90 J 1-145 [» ]
    3CCM X-ray 2.55 J 1-145 [» ]
    3CCQ X-ray 2.90 J 1-145 [» ]
    3CCR X-ray 3.00 J 1-145 [» ]
    3CCS X-ray 2.95 J 1-145 [» ]
    3CCU X-ray 2.80 J 1-145 [» ]
    3CCV X-ray 2.90 J 1-145 [» ]
    3CD6 X-ray 2.75 J 1-145 [» ]
    3CMA X-ray 2.80 J 1-145 [» ]
    3CME X-ray 2.95 J 1-145 [» ]
    3CPW X-ray 2.70 I 1-145 [» ]
    3CXC X-ray 3.00 I 1-145 [» ]
    3G4S X-ray 3.20 J 4-145 [» ]
    3G6E X-ray 2.70 J 4-145 [» ]
    3G71 X-ray 2.85 J 4-145 [» ]
    3I55 X-ray 3.11 J 1-145 [» ]
    3I56 X-ray 2.90 J 1-145 [» ]
    3OW2 X-ray 2.70 I 4-145 [» ]
    4HUB X-ray 2.40 J 1-145 [» ]
    ProteinModelPortali P29198.
    SMRi P29198. Positions 4-145.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 272569.rrnAC0065.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAV45145 ; AAV45145 ; rrnAC0065 .
    GeneIDi 3130528.
    KEGGi hma:rrnAC0065.

    Phylogenomic databases

    eggNOGi COG0102.
    HOGENOMi HOG000225287.
    KOi K02871.
    OMAi RLSRPKY.

    Enzyme and pathway databases

    BioCyci HMAR272569:GJDH-61-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P29198.

    Family and domain databases

    Gene3Di 3.90.1180.10. 1 hit.
    HAMAPi MF_01366. Ribosomal_L13.
    InterProi IPR005822. Ribosomal_L13.
    IPR023563. Ribosomal_L13_CS.
    IPR023564. Ribosomal_L13_dom.
    IPR005755. Ribosomal_L13_euk/arc.
    [Graphical view ]
    PANTHERi PTHR11545. PTHR11545. 1 hit.
    PTHR11545:SF3. PTHR11545:SF3. 1 hit.
    Pfami PF00572. Ribosomal_L13. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF002181. Ribosomal_L13. 1 hit.
    SUPFAMi SSF52161. SSF52161. 1 hit.
    TIGRFAMsi TIGR01077. L13_A_E. 1 hit.
    PROSITEi PS00783. RIBOSOMAL_L13. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Halobacterial S9 operon. Three ribosomal protein genes are cotranscribed with genes encoding a tRNA(Leu), the enolase, and a putative membrane protein in the archaebacterium Haloarcula (Halobacterium) marismortui."
      Kroemer W.J., Arndt E.
      J. Biol. Chem. 266:24573-24579(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
    3. "The complete atomic structure of the large ribosomal subunit at 2.4 A resolution."
      Ban N., Nissen P., Hansen J., Moore P.B., Steitz T.A.
      Science 289:905-920(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF THE 50S SUBUNIT.
      Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
    4. "The structural basis of ribosome activity in peptide bond synthesis."
      Nissen P., Hansen J., Ban N., Moore P.B., Steitz T.A.
      Science 289:920-930(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF THE 50S SUBUNIT.
      Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
    5. "A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits."
      Schmeing T.M., Seila A.C., Hansen J.L., Freeborn B., Soukup J.K., Scaringe S.A., Strobel S.A., Moore P.B., Steitz T.A.
      Nat. Struct. Biol. 9:225-230(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT.
      Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
    6. "The kink-turn: a new RNA secondary structure motif."
      Klein D.J., Schmeing T.M., Moore P.B., Steitz T.A.
      EMBO J. 20:4214-4221(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF THE 50S SUBUNIT.
      Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
    7. "The structures of four macrolide antibiotics bound to the large ribosomal subunit."
      Hansen J.L., Ippolito J.A., Ban N., Nissen P., Moore P.B., Steitz T.A.
      Mol. Cell 10:117-128(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH FOUR MACROLIDE ANTIBIOTICS.
      Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
    8. Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE 50S SUBUNIT.
      Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
    9. "Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit."
      Hansen J.L., Moore P.B., Steitz T.A.
      J. Mol. Biol. 330:1061-1075(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH FIVE ANTIBIOTICS AT THE PEPTIDYL TRANSFERASE CENTER.
      Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
    10. "Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit."
      Schmeing T.M., Moore P.B., Steitz T.A.
      RNA 9:1345-1352(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF THE 50S SUBUNIT WITH TWO DIFFERENT E SITE SUBSTRATES.
    11. "Revisiting the Haloarcula marismortui 50S ribosomal subunit model."
      Gabdulkhakov A., Nikonov S., Garber M.
      Acta Crystallogr. D 69:997-1004(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF THE 50S SUBUNIT.

    Entry informationi

    Entry nameiRL13_HALMA
    AccessioniPrimary (citable) accession number: P29198
    Secondary accession number(s): Q5V5Q7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 1, 1992
    Last sequence update: December 1, 1992
    Last modified: October 1, 2014
    This is version 104 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. Ribosomal proteins
      Ribosomal proteins families and list of entries
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3