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P12735

- RL4_HALMA

UniProt

P12735 - RL4_HALMA

Protein

50S ribosomal protein L4

Gene

rpl4

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 117 (01 Oct 2014)
      Sequence version 4 (04 Jan 2005)
      Previous versions | rss
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    Functioni

    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.By similarity
    Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.
    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.

    GO - Molecular functioni

    1. rRNA binding Source: UniProtKB-HAMAP
    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-1466-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    50S ribosomal protein L4
    Alternative name(s):
    Hl6
    Hmal4
    Gene namesi
    Name:rpl4
    Ordered Locus Names:rrnAC1610
    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. ribosome Source: UniProtKB-KW

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 24624650S ribosomal protein L4PRO_0000129329Add
    BLAST

    Interactioni

    Subunit structurei

    Part of the 50S ribosomal subunit. Interacts weakly with proteins L18e, L24 and L37e. Has been cross-linked to L18e.2 Publications

    Protein-protein interaction databases

    STRINGi272569.rrnAC1610.

    Structurei

    Secondary structure

    1
    246
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 65
    Turni8 – 103
    Beta strandi12 – 176
    Helixi20 – 234
    Helixi28 – 4114
    Turni50 – 545
    Beta strandi63 – 664
    Beta strandi71 – 733
    Beta strandi94 – 963
    Helixi104 – 11714
    Helixi121 – 1277
    Beta strandi137 – 1404
    Helixi142 – 1465
    Helixi150 – 15910
    Helixi164 – 1685
    Helixi178 – 1825
    Beta strandi193 – 1997
    Turni202 – 2065
    Beta strandi211 – 2144
    Turni215 – 2173
    Helixi220 – 2234
    Helixi225 – 2273
    Beta strandi233 – 2364
    Helixi237 – 2426
    Helixi243 – 2453

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1FFKX-ray2.40C1-246[»]
    1JJ2X-ray2.40C1-246[»]
    1K73X-ray3.01E1-246[»]
    1K8AX-ray3.00E1-246[»]
    1K9MX-ray3.00E1-246[»]
    1KC8X-ray3.01E1-246[»]
    1KD1X-ray3.00E1-246[»]
    1KQSX-ray3.10C1-246[»]
    1M1KX-ray3.20E1-246[»]
    1M90X-ray2.80E1-246[»]
    1ML5electron microscopy14.00f1-246[»]
    1N8RX-ray3.00E1-246[»]
    1NJIX-ray3.00E1-246[»]
    1Q7YX-ray3.20E1-246[»]
    1Q81X-ray2.95E1-246[»]
    1Q82X-ray2.98E1-246[»]
    1Q86X-ray3.00E1-246[»]
    1QVFX-ray3.10C1-246[»]
    1QVGX-ray2.90C1-246[»]
    1S72X-ray2.40C1-246[»]
    1VQ4X-ray2.70C1-246[»]
    1VQ5X-ray2.60C1-246[»]
    1VQ6X-ray2.70C1-246[»]
    1VQ7X-ray2.50C1-246[»]
    1VQ8X-ray2.20C1-246[»]
    1VQ9X-ray2.40C1-246[»]
    1VQKX-ray2.30C1-246[»]
    1VQLX-ray2.30C1-246[»]
    1VQMX-ray2.30C1-246[»]
    1VQNX-ray2.40C1-246[»]
    1VQOX-ray2.20C1-246[»]
    1VQPX-ray2.25C1-246[»]
    1W2BX-ray3.50C1-246[»]
    1YHQX-ray2.40C1-246[»]
    1YI2X-ray2.65C1-246[»]
    1YIJX-ray2.60C1-246[»]
    1YITX-ray2.80C1-246[»]
    1YJ9X-ray2.90C1-246[»]
    1YJNX-ray3.00C1-246[»]
    1YJWX-ray2.90C1-246[»]
    2B66X-ray5.90F1-246[»]
    2B9NX-ray6.76F1-246[»]
    2B9PX-ray6.46F1-246[»]
    2OTJX-ray2.90C1-246[»]
    2OTLX-ray2.70C1-246[»]
    2QA4X-ray3.00C1-246[»]
    2QEXX-ray2.90C1-246[»]
    3CC2X-ray2.40C1-246[»]
    3CC4X-ray2.70C1-246[»]
    3CC7X-ray2.70C1-246[»]
    3CCEX-ray2.75C1-246[»]
    3CCJX-ray2.70C1-246[»]
    3CCLX-ray2.90C1-246[»]
    3CCMX-ray2.55C1-246[»]
    3CCQX-ray2.90C1-246[»]
    3CCRX-ray3.00C1-246[»]
    3CCSX-ray2.95C1-246[»]
    3CCUX-ray2.80C1-246[»]
    3CCVX-ray2.90C1-246[»]
    3CD6X-ray2.75C1-246[»]
    3CMAX-ray2.80C1-246[»]
    3CMEX-ray2.95C1-246[»]
    3CPWX-ray2.70C1-246[»]
    3CXCX-ray3.00C1-246[»]
    3G4SX-ray3.20C1-246[»]
    3G6EX-ray2.70C1-246[»]
    3G71X-ray2.85C1-246[»]
    3I55X-ray3.11C1-246[»]
    3I56X-ray2.90C1-246[»]
    3OW2X-ray2.70C1-246[»]
    4ADXelectron microscopy6.60C1-246[»]
    4HUBX-ray2.40C1-246[»]
    ProteinModelPortaliP12735.
    SMRiP12735. Positions 1-246.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP12735.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the ribosomal protein L4P family.Curated

    Phylogenomic databases

    eggNOGiCOG0088.
    HOGENOMiHOG000107332.
    KOiK02930.
    OMAiVADRGHE.

    Family and domain databases

    Gene3Di3.40.1370.10. 1 hit.
    HAMAPiMF_01328_A. Ribosomal_L4_A.
    InterProiIPR002136. Ribosomal_L4/L1e.
    IPR013000. Ribosomal_L4/L1e_euk/arc_CS.
    IPR023574. Ribosomal_L4_dom.
    IPR019970. Ribosomall_L4.
    [Graphical view]
    PfamiPF00573. Ribosomal_L4. 1 hit.
    [Graphical view]
    SUPFAMiSSF52166. SSF52166. 1 hit.
    TIGRFAMsiTIGR03672. rpl4p_arch. 1 hit.
    PROSITEiPS00939. RIBOSOMAL_L1E. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P12735-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQATIYDLDG NTDGEVDLPD VFETPVRSDL IGKAVRAAQA NRKQDYGSDE    50
    YAGLRTPAES FGSGRGQAHV PKQDGRARRV PQAVKGRSAH PPKTEKDRSL 100
    DLNDKERQLA VRSALAATAD ADLVADRGHE FDRDEVPVVV SDDFEDLVKT 150
    QEVVSLLEAL DVHADIDRAD ETKIKAGQGS ARGRKYRRPA SILFVTSDEP 200
    STAARNLAGA DVATASEVNT EDLAPGGAPG RLTVFTESAL AEVAER 246
    Length:246
    Mass (Da):26,420
    Last modified:January 4, 2005 - v4
    Checksum:i4BCA2FE20EE24EDF
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti154 – 1541V → K AA sequence (PubMed:3196689)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J05222 Genomic DNA. Translation: AAA86860.1.
    AY596297 Genomic DNA. Translation: AAV46527.1.
    PIRiD35063. R5HS6H.
    RefSeqiYP_136233.1. NC_006396.1.

    Genome annotation databases

    EnsemblBacteriaiAAV46527; AAV46527; rrnAC1610.
    GeneIDi3128386.
    KEGGihma:rrnAC1610.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J05222 Genomic DNA. Translation: AAA86860.1 .
    AY596297 Genomic DNA. Translation: AAV46527.1 .
    PIRi D35063. R5HS6H.
    RefSeqi YP_136233.1. 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 C 1-246 [» ]
    1JJ2 X-ray 2.40 C 1-246 [» ]
    1K73 X-ray 3.01 E 1-246 [» ]
    1K8A X-ray 3.00 E 1-246 [» ]
    1K9M X-ray 3.00 E 1-246 [» ]
    1KC8 X-ray 3.01 E 1-246 [» ]
    1KD1 X-ray 3.00 E 1-246 [» ]
    1KQS X-ray 3.10 C 1-246 [» ]
    1M1K X-ray 3.20 E 1-246 [» ]
    1M90 X-ray 2.80 E 1-246 [» ]
    1ML5 electron microscopy 14.00 f 1-246 [» ]
    1N8R X-ray 3.00 E 1-246 [» ]
    1NJI X-ray 3.00 E 1-246 [» ]
    1Q7Y X-ray 3.20 E 1-246 [» ]
    1Q81 X-ray 2.95 E 1-246 [» ]
    1Q82 X-ray 2.98 E 1-246 [» ]
    1Q86 X-ray 3.00 E 1-246 [» ]
    1QVF X-ray 3.10 C 1-246 [» ]
    1QVG X-ray 2.90 C 1-246 [» ]
    1S72 X-ray 2.40 C 1-246 [» ]
    1VQ4 X-ray 2.70 C 1-246 [» ]
    1VQ5 X-ray 2.60 C 1-246 [» ]
    1VQ6 X-ray 2.70 C 1-246 [» ]
    1VQ7 X-ray 2.50 C 1-246 [» ]
    1VQ8 X-ray 2.20 C 1-246 [» ]
    1VQ9 X-ray 2.40 C 1-246 [» ]
    1VQK X-ray 2.30 C 1-246 [» ]
    1VQL X-ray 2.30 C 1-246 [» ]
    1VQM X-ray 2.30 C 1-246 [» ]
    1VQN X-ray 2.40 C 1-246 [» ]
    1VQO X-ray 2.20 C 1-246 [» ]
    1VQP X-ray 2.25 C 1-246 [» ]
    1W2B X-ray 3.50 C 1-246 [» ]
    1YHQ X-ray 2.40 C 1-246 [» ]
    1YI2 X-ray 2.65 C 1-246 [» ]
    1YIJ X-ray 2.60 C 1-246 [» ]
    1YIT X-ray 2.80 C 1-246 [» ]
    1YJ9 X-ray 2.90 C 1-246 [» ]
    1YJN X-ray 3.00 C 1-246 [» ]
    1YJW X-ray 2.90 C 1-246 [» ]
    2B66 X-ray 5.90 F 1-246 [» ]
    2B9N X-ray 6.76 F 1-246 [» ]
    2B9P X-ray 6.46 F 1-246 [» ]
    2OTJ X-ray 2.90 C 1-246 [» ]
    2OTL X-ray 2.70 C 1-246 [» ]
    2QA4 X-ray 3.00 C 1-246 [» ]
    2QEX X-ray 2.90 C 1-246 [» ]
    3CC2 X-ray 2.40 C 1-246 [» ]
    3CC4 X-ray 2.70 C 1-246 [» ]
    3CC7 X-ray 2.70 C 1-246 [» ]
    3CCE X-ray 2.75 C 1-246 [» ]
    3CCJ X-ray 2.70 C 1-246 [» ]
    3CCL X-ray 2.90 C 1-246 [» ]
    3CCM X-ray 2.55 C 1-246 [» ]
    3CCQ X-ray 2.90 C 1-246 [» ]
    3CCR X-ray 3.00 C 1-246 [» ]
    3CCS X-ray 2.95 C 1-246 [» ]
    3CCU X-ray 2.80 C 1-246 [» ]
    3CCV X-ray 2.90 C 1-246 [» ]
    3CD6 X-ray 2.75 C 1-246 [» ]
    3CMA X-ray 2.80 C 1-246 [» ]
    3CME X-ray 2.95 C 1-246 [» ]
    3CPW X-ray 2.70 C 1-246 [» ]
    3CXC X-ray 3.00 C 1-246 [» ]
    3G4S X-ray 3.20 C 1-246 [» ]
    3G6E X-ray 2.70 C 1-246 [» ]
    3G71 X-ray 2.85 C 1-246 [» ]
    3I55 X-ray 3.11 C 1-246 [» ]
    3I56 X-ray 2.90 C 1-246 [» ]
    3OW2 X-ray 2.70 C 1-246 [» ]
    4ADX electron microscopy 6.60 C 1-246 [» ]
    4HUB X-ray 2.40 C 1-246 [» ]
    ProteinModelPortali P12735.
    SMRi P12735. Positions 1-246.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 272569.rrnAC1610.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAV46527 ; AAV46527 ; rrnAC1610 .
    GeneIDi 3128386.
    KEGGi hma:rrnAC1610.

    Phylogenomic databases

    eggNOGi COG0088.
    HOGENOMi HOG000107332.
    KOi K02930.
    OMAi VADRGHE.

    Enzyme and pathway databases

    BioCyci HMAR272569:GJDH-1466-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P12735.

    Family and domain databases

    Gene3Di 3.40.1370.10. 1 hit.
    HAMAPi MF_01328_A. Ribosomal_L4_A.
    InterProi IPR002136. Ribosomal_L4/L1e.
    IPR013000. Ribosomal_L4/L1e_euk/arc_CS.
    IPR023574. Ribosomal_L4_dom.
    IPR019970. Ribosomall_L4.
    [Graphical view ]
    Pfami PF00573. Ribosomal_L4. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52166. SSF52166. 1 hit.
    TIGRFAMsi TIGR03672. rpl4p_arch. 1 hit.
    PROSITEi PS00939. RIBOSOMAL_L1E. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Organization and nucleotide sequence of a gene cluster coding for eight ribosomal proteins in the archaebacterium Halobacterium marismortui."
      Arndt E., Kroemer W., Hatakeyama T.
      J. Biol. Chem. 265:3034-3039(1990) [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. "Extended N-terminal sequencing of proteins of archaebacterial ribosomes blotted from two-dimensional gels onto glass fiber and poly(vinylidene difluoride) membrane."
      Walsh M.J., McDougall J., Wittmann-Liebold B.
      Biochemistry 27:6867-6876(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-28 AND 153-181.
    4. "Localization of proteins HL29 and HL31 from Haloarcula marismortui within the 50 S ribosomal subunit by chemical crosslinking."
      Bergmann U., Wittmann-Liebold B.
      J. Mol. Biol. 232:693-700(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 34-47; 86-117 AND 176-200, CROSS-LINKING TO L18E.
    5. "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.
    6. "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.
    7. "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.
    8. "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.
    9. "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.
    10. Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE 50S SUBUNIT.
      Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
    11. "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.
    12. "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.
    13. "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 nameiRL4_HALMA
    AccessioniPrimary (citable) accession number: P12735
    Secondary accession number(s): Q5V1S5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1989
    Last sequence update: January 4, 2005
    Last modified: October 1, 2014
    This is version 117 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, 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