RL4_HALMA
ID RL4_HALMA Reviewed; 246 AA.
AC P12735; Q5V1S5;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 04-JAN-2005, sequence version 4.
DT 25-MAY-2022, entry version 151.
DE RecName: Full=50S ribosomal protein L4;
DE AltName: Full=Hl6;
DE AltName: Full=Hmal4;
GN Name=rpl4; OrderedLocusNames=rrnAC1610;
OS Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM
OS B-1809) (Halobacterium marismortui).
OC Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria; Halobacteriales;
OC Haloarculaceae; Haloarcula.
OX NCBI_TaxID=272569;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2406244; DOI=10.1016/s0021-9258(19)39729-7;
RA Arndt E., Kroemer W., Hatakeyama T.;
RT "Organization and nucleotide sequence of a gene cluster coding for eight
RT ribosomal proteins in the archaebacterium Halobacterium marismortui.";
RL J. Biol. Chem. 265:3034-3039(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809;
RX PubMed=15520287; DOI=10.1101/gr.2700304;
RA Baliga N.S., Bonneau R., Facciotti M.T., Pan M., Glusman G., Deutsch E.W.,
RA Shannon P., Chiu Y., Weng R.S., Gan R.R., Hung P., Date S.V., Marcotte E.,
RA Hood L., Ng W.V.;
RT "Genome sequence of Haloarcula marismortui: a halophilic archaeon from the
RT Dead Sea.";
RL Genome Res. 14:2221-2234(2004).
RN [3]
RP PROTEIN SEQUENCE OF 1-28 AND 153-181.
RX PubMed=3196689; DOI=10.1021/bi00418a032;
RA Walsh M.J., McDougall J., Wittmann-Liebold B.;
RT "Extended N-terminal sequencing of proteins of archaebacterial ribosomes
RT blotted from two-dimensional gels onto glass fiber and poly(vinylidene
RT difluoride) membrane.";
RL Biochemistry 27:6867-6876(1988).
RN [4]
RP PROTEIN SEQUENCE OF 34-47; 86-117 AND 176-200, AND CROSS-LINKING TO L18E.
RX PubMed=8345527; DOI=10.1006/jmbi.1993.1419;
RA Bergmann U., Wittmann-Liebold B.;
RT "Localization of proteins HL29 and HL31 from Haloarcula marismortui within
RT the 50 S ribosomal subunit by chemical crosslinking.";
RL J. Mol. Biol. 232:693-700(1993).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF THE 50S SUBUNIT.
RC STRAIN=ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809;
RX PubMed=10937989; DOI=10.1126/science.289.5481.905;
RA Ban N., Nissen P., Hansen J., Moore P.B., Steitz T.A.;
RT "The complete atomic structure of the large ribosomal subunit at 2.4 A
RT resolution.";
RL Science 289:905-920(2000).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF THE 50S SUBUNIT.
RC STRAIN=ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809;
RX PubMed=10937990; DOI=10.1126/science.289.5481.920;
RA Nissen P., Hansen J., Ban N., Moore P.B., Steitz T.A.;
RT "The structural basis of ribosome activity in peptide bond synthesis.";
RL Science 289:920-930(2000).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT.
RC STRAIN=ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809;
RX PubMed=11828326; DOI=10.1038/nsb758;
RA Schmeing T.M., Seila A.C., Hansen J.L., Freeborn B., Soukup J.K.,
RA Scaringe S.A., Strobel S.A., Moore P.B., Steitz T.A.;
RT "A pre-translocational intermediate in protein synthesis observed in
RT crystals of enzymatically active 50S subunits.";
RL Nat. Struct. Biol. 9:225-230(2002).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF THE 50S SUBUNIT.
RC STRAIN=ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809;
RX PubMed=11483524; DOI=10.1093/emboj/20.15.4214;
RA Klein D.J., Schmeing T.M., Moore P.B., Steitz T.A.;
RT "The kink-turn: a new RNA secondary structure motif.";
RL EMBO J. 20:4214-4221(2001).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH
RP FOUR MACROLIDE ANTIBIOTICS.
RC STRAIN=ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809;
RX PubMed=12150912; DOI=10.1016/s1097-2765(02)00570-1;
RA Hansen J.L., Ippolito J.A., Ban N., Nissen P., Moore P.B., Steitz T.A.;
RT "The structures of four macrolide antibiotics bound to the large ribosomal
RT subunit.";
RL Mol. Cell 10:117-128(2002).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE 50S SUBUNIT.
RC STRAIN=ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809;
RX PubMed=12185246; DOI=10.1073/pnas.172404099;
RA Hansen J.L., Schmeing T.M., Moore P.B., Steitz T.A.;
RT "Structural insights into peptide bond formation.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:11670-11675(2002).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH
RP FIVE ANTIBIOTICS AT THE PEPTIDYL TRANSFERASE CENTER.
RC STRAIN=ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809;
RX PubMed=12860128; DOI=10.1016/s0022-2836(03)00668-5;
RA Hansen J.L., Moore P.B., Steitz T.A.;
RT "Structures of five antibiotics bound at the peptidyl transferase center of
RT the large ribosomal subunit.";
RL J. Mol. Biol. 330:1061-1075(2003).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF THE 50S SUBUNIT WITH TWO DIFFERENT
RP E SITE SUBSTRATES.
RX PubMed=14561884; DOI=10.1261/rna.5120503;
RA Schmeing T.M., Moore P.B., Steitz T.A.;
RT "Structures of deacylated tRNA mimics bound to the E site of the large
RT ribosomal subunit.";
RL RNA 9:1345-1352(2003).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF THE 50S SUBUNIT.
RX PubMed=23695244; DOI=10.1107/s0907444913004745;
RA Gabdulkhakov A., Nikonov S., Garber M.;
RT "Revisiting the Haloarcula marismortui 50S ribosomal subunit model.";
RL Acta Crystallogr. D 69:997-1004(2013).
CC -!- FUNCTION: One of the primary rRNA binding proteins, this protein
CC initially binds near the 5'-end of the 23S rRNA. It is important during
CC the early stages of 50S assembly (By similarity). {ECO:0000250}.
CC -!- FUNCTION: Makes multiple contacts with different domains of the 23S
CC rRNA in the assembled 50S subunit.
CC -!- FUNCTION: Forms part of the polypeptide exit tunnel, in which it helps
CC forms a bend with protein L22. Contacts the macrolide antibiotic
CC spiramycin in the polypeptide exit tunnel.
CC -!- SUBUNIT: Part of the 50S ribosomal subunit. Interacts weakly with
CC proteins L18e, L24 and L37e. Has been cross-linked to L18e.
CC {ECO:0000269|PubMed:12150912, ECO:0000269|PubMed:12860128}.
CC -!- SIMILARITY: Belongs to the universal ribosomal protein uL4 family.
CC {ECO:0000305}.
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DR EMBL; J05222; AAA86860.1; -; Genomic_DNA.
DR EMBL; AY596297; AAV46527.1; -; Genomic_DNA.
DR PIR; D35063; R5HS6H.
DR RefSeq; WP_004957420.1; NZ_CP039138.1.
DR PDB; 1FFK; X-ray; 2.40 A; C=1-246.
DR PDB; 1JJ2; X-ray; 2.40 A; C=1-246.
DR PDB; 1K73; X-ray; 3.01 A; E=1-246.
DR PDB; 1K8A; X-ray; 3.00 A; E=1-246.
DR PDB; 1K9M; X-ray; 3.00 A; E=1-246.
DR PDB; 1KC8; X-ray; 3.01 A; E=1-246.
DR PDB; 1KD1; X-ray; 3.00 A; E=1-246.
DR PDB; 1KQS; X-ray; 3.10 A; C=1-246.
DR PDB; 1M1K; X-ray; 3.20 A; E=1-246.
DR PDB; 1M90; X-ray; 2.80 A; E=1-246.
DR PDB; 1ML5; EM; 14.00 A; f=1-246.
DR PDB; 1N8R; X-ray; 3.00 A; E=1-246.
DR PDB; 1NJI; X-ray; 3.00 A; E=1-246.
DR PDB; 1Q7Y; X-ray; 3.20 A; E=1-246.
DR PDB; 1Q81; X-ray; 2.95 A; E=1-246.
DR PDB; 1Q82; X-ray; 2.98 A; E=1-246.
DR PDB; 1Q86; X-ray; 3.00 A; E=1-246.
DR PDB; 1QVF; X-ray; 3.10 A; C=1-246.
DR PDB; 1QVG; X-ray; 2.90 A; C=1-246.
DR PDB; 1S72; X-ray; 2.40 A; C=1-246.
DR PDB; 1VQ4; X-ray; 2.70 A; C=1-246.
DR PDB; 1VQ5; X-ray; 2.60 A; C=1-246.
DR PDB; 1VQ6; X-ray; 2.70 A; C=1-246.
DR PDB; 1VQ7; X-ray; 2.50 A; C=1-246.
DR PDB; 1VQ8; X-ray; 2.20 A; C=1-246.
DR PDB; 1VQ9; X-ray; 2.40 A; C=1-246.
DR PDB; 1VQK; X-ray; 2.30 A; C=1-246.
DR PDB; 1VQL; X-ray; 2.30 A; C=1-246.
DR PDB; 1VQM; X-ray; 2.30 A; C=1-246.
DR PDB; 1VQN; X-ray; 2.40 A; C=1-246.
DR PDB; 1VQO; X-ray; 2.20 A; C=1-246.
DR PDB; 1VQP; X-ray; 2.25 A; C=1-246.
DR PDB; 1W2B; X-ray; 3.50 A; C=1-246.
DR PDB; 1YHQ; X-ray; 2.40 A; C=1-246.
DR PDB; 1YI2; X-ray; 2.65 A; C=1-246.
DR PDB; 1YIJ; X-ray; 2.60 A; C=1-246.
DR PDB; 1YIT; X-ray; 2.80 A; C=1-246.
DR PDB; 1YJ9; X-ray; 2.90 A; C=1-246.
DR PDB; 1YJN; X-ray; 3.00 A; C=1-246.
DR PDB; 1YJW; X-ray; 2.90 A; C=1-246.
DR PDB; 2OTJ; X-ray; 2.90 A; C=1-246.
DR PDB; 2OTL; X-ray; 2.70 A; C=1-246.
DR PDB; 2QA4; X-ray; 3.00 A; C=1-246.
DR PDB; 2QEX; X-ray; 2.90 A; C=1-246.
DR PDB; 3CC2; X-ray; 2.40 A; C=1-246.
DR PDB; 3CC4; X-ray; 2.70 A; C=1-246.
DR PDB; 3CC7; X-ray; 2.70 A; C=1-246.
DR PDB; 3CCE; X-ray; 2.75 A; C=1-246.
DR PDB; 3CCJ; X-ray; 2.70 A; C=1-246.
DR PDB; 3CCL; X-ray; 2.90 A; C=1-246.
DR PDB; 3CCM; X-ray; 2.55 A; C=1-246.
DR PDB; 3CCQ; X-ray; 2.90 A; C=1-246.
DR PDB; 3CCR; X-ray; 3.00 A; C=1-246.
DR PDB; 3CCS; X-ray; 2.95 A; C=1-246.
DR PDB; 3CCU; X-ray; 2.80 A; C=1-246.
DR PDB; 3CCV; X-ray; 2.90 A; C=1-246.
DR PDB; 3CD6; X-ray; 2.75 A; C=1-246.
DR PDB; 3CMA; X-ray; 2.80 A; C=1-246.
DR PDB; 3CME; X-ray; 2.95 A; C=1-246.
DR PDB; 3CPW; X-ray; 2.70 A; C=1-246.
DR PDB; 3CXC; X-ray; 3.00 A; C=1-246.
DR PDB; 3G4S; X-ray; 3.20 A; C=1-246.
DR PDB; 3G6E; X-ray; 2.70 A; C=1-246.
DR PDB; 3G71; X-ray; 2.85 A; C=1-246.
DR PDB; 3I55; X-ray; 3.11 A; C=1-246.
DR PDB; 3I56; X-ray; 2.90 A; C=1-246.
DR PDB; 3OW2; X-ray; 2.70 A; C=1-246.
DR PDB; 4ADX; EM; 6.60 A; C=1-246.
DR PDB; 4V42; X-ray; 5.50 A; BF=1-246.
DR PDB; 4V4R; X-ray; 5.90 A; F=1-246.
DR PDB; 4V4S; X-ray; 6.76 A; F=1-246.
DR PDB; 4V4T; X-ray; 6.46 A; F=1-246.
DR PDB; 4V9F; X-ray; 2.40 A; C=1-246.
DR PDBsum; 1FFK; -.
DR PDBsum; 1JJ2; -.
DR PDBsum; 1K73; -.
DR PDBsum; 1K8A; -.
DR PDBsum; 1K9M; -.
DR PDBsum; 1KC8; -.
DR PDBsum; 1KD1; -.
DR PDBsum; 1KQS; -.
DR PDBsum; 1M1K; -.
DR PDBsum; 1M90; -.
DR PDBsum; 1ML5; -.
DR PDBsum; 1N8R; -.
DR PDBsum; 1NJI; -.
DR PDBsum; 1Q7Y; -.
DR PDBsum; 1Q81; -.
DR PDBsum; 1Q82; -.
DR PDBsum; 1Q86; -.
DR PDBsum; 1QVF; -.
DR PDBsum; 1QVG; -.
DR PDBsum; 1S72; -.
DR PDBsum; 1VQ4; -.
DR PDBsum; 1VQ5; -.
DR PDBsum; 1VQ6; -.
DR PDBsum; 1VQ7; -.
DR PDBsum; 1VQ8; -.
DR PDBsum; 1VQ9; -.
DR PDBsum; 1VQK; -.
DR PDBsum; 1VQL; -.
DR PDBsum; 1VQM; -.
DR PDBsum; 1VQN; -.
DR PDBsum; 1VQO; -.
DR PDBsum; 1VQP; -.
DR PDBsum; 1W2B; -.
DR PDBsum; 1YHQ; -.
DR PDBsum; 1YI2; -.
DR PDBsum; 1YIJ; -.
DR PDBsum; 1YIT; -.
DR PDBsum; 1YJ9; -.
DR PDBsum; 1YJN; -.
DR PDBsum; 1YJW; -.
DR PDBsum; 2OTJ; -.
DR PDBsum; 2OTL; -.
DR PDBsum; 2QA4; -.
DR PDBsum; 2QEX; -.
DR PDBsum; 3CC2; -.
DR PDBsum; 3CC4; -.
DR PDBsum; 3CC7; -.
DR PDBsum; 3CCE; -.
DR PDBsum; 3CCJ; -.
DR PDBsum; 3CCL; -.
DR PDBsum; 3CCM; -.
DR PDBsum; 3CCQ; -.
DR PDBsum; 3CCR; -.
DR PDBsum; 3CCS; -.
DR PDBsum; 3CCU; -.
DR PDBsum; 3CCV; -.
DR PDBsum; 3CD6; -.
DR PDBsum; 3CMA; -.
DR PDBsum; 3CME; -.
DR PDBsum; 3CPW; -.
DR PDBsum; 3CXC; -.
DR PDBsum; 3G4S; -.
DR PDBsum; 3G6E; -.
DR PDBsum; 3G71; -.
DR PDBsum; 3I55; -.
DR PDBsum; 3I56; -.
DR PDBsum; 3OW2; -.
DR PDBsum; 4ADX; -.
DR PDBsum; 4V42; -.
DR PDBsum; 4V4R; -.
DR PDBsum; 4V4S; -.
DR PDBsum; 4V4T; -.
DR PDBsum; 4V9F; -.
DR AlphaFoldDB; P12735; -.
DR SMR; P12735; -.
DR IntAct; P12735; 3.
DR STRING; 272569.rrnAC1610; -.
DR EnsemblBacteria; AAV46527; AAV46527; rrnAC1610.
DR GeneID; 40152576; -.
DR GeneID; 64821816; -.
DR KEGG; hma:rrnAC1610; -.
DR PATRIC; fig|272569.17.peg.2300; -.
DR eggNOG; arCOG04071; Archaea.
DR HOGENOM; CLU_026535_0_0_2; -.
DR OMA; WHQKVNV; -.
DR EvolutionaryTrace; P12735; -.
DR Proteomes; UP000001169; Chromosome I.
DR GO; GO:0005840; C:ribosome; IEA:UniProtKB-KW.
DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003735; F:structural constituent of ribosome; IEA:InterPro.
DR GO; GO:0006412; P:translation; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.1370.10; -; 1.
DR HAMAP; MF_01328_A; Ribosomal_L4_A; 1.
DR InterPro; IPR002136; Ribosomal_L4/L1e.
DR InterPro; IPR013000; Ribosomal_L4/L1e_euk/arc_CS.
DR InterPro; IPR023574; Ribosomal_L4_dom_sf.
DR InterPro; IPR045240; Ribosomal_L4_euk/arch.
DR InterPro; IPR019970; Ribosomall_L4-archaea.
DR PANTHER; PTHR19431; PTHR19431; 1.
DR Pfam; PF00573; Ribosomal_L4; 1.
DR SUPFAM; SSF52166; SSF52166; 1.
DR TIGRFAMs; TIGR03672; rpl4p_arch; 1.
DR PROSITE; PS00939; RIBOSOMAL_L1E; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Reference proteome;
KW Ribonucleoprotein; Ribosomal protein; RNA-binding; rRNA-binding.
FT CHAIN 1..246
FT /note="50S ribosomal protein L4"
FT /id="PRO_0000129329"
FT REGION 37..103
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 89..103
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 154
FT /note="V -> K (in Ref. 3; AA sequence)"
FT /evidence="ECO:0000305"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:1VQ8"
FT TURN 8..10
FT /evidence="ECO:0007829|PDB:3CME"
FT STRAND 12..17
FT /evidence="ECO:0007829|PDB:1VQ8"
FT HELIX 20..23
FT /evidence="ECO:0007829|PDB:1VQ8"
FT HELIX 28..41
FT /evidence="ECO:0007829|PDB:1VQ8"
FT TURN 50..54
FT /evidence="ECO:0007829|PDB:1VQ8"
FT STRAND 63..66
FT /evidence="ECO:0007829|PDB:1VQ8"
FT STRAND 71..73
FT /evidence="ECO:0007829|PDB:3CCU"
FT STRAND 94..96
FT /evidence="ECO:0007829|PDB:3G71"
FT HELIX 104..117
FT /evidence="ECO:0007829|PDB:1VQ8"
FT HELIX 121..127
FT /evidence="ECO:0007829|PDB:1VQ8"
FT STRAND 137..140
FT /evidence="ECO:0007829|PDB:1VQ8"
FT HELIX 142..146
FT /evidence="ECO:0007829|PDB:1VQ8"
FT HELIX 150..159
FT /evidence="ECO:0007829|PDB:1VQ8"
FT HELIX 164..168
FT /evidence="ECO:0007829|PDB:1VQ8"
FT HELIX 178..182
FT /evidence="ECO:0007829|PDB:1VQ8"
FT STRAND 193..199
FT /evidence="ECO:0007829|PDB:1VQ8"
FT TURN 202..206
FT /evidence="ECO:0007829|PDB:1VQ8"
FT STRAND 211..214
FT /evidence="ECO:0007829|PDB:1VQ8"
FT TURN 215..217
FT /evidence="ECO:0007829|PDB:1VQ8"
FT HELIX 220..223
FT /evidence="ECO:0007829|PDB:1VQ8"
FT HELIX 225..227
FT /evidence="ECO:0007829|PDB:1VQ8"
FT STRAND 233..236
FT /evidence="ECO:0007829|PDB:1VQ8"
FT HELIX 237..242
FT /evidence="ECO:0007829|PDB:1VQ8"
FT HELIX 243..245
FT /evidence="ECO:0007829|PDB:1VQ8"
SQ SEQUENCE 246 AA; 26420 MW; 4BCA2FE20EE24EDF CRC64;
MQATIYDLDG NTDGEVDLPD VFETPVRSDL IGKAVRAAQA NRKQDYGSDE YAGLRTPAES
FGSGRGQAHV PKQDGRARRV PQAVKGRSAH PPKTEKDRSL DLNDKERQLA VRSALAATAD
ADLVADRGHE FDRDEVPVVV SDDFEDLVKT QEVVSLLEAL DVHADIDRAD ETKIKAGQGS
ARGRKYRRPA SILFVTSDEP STAARNLAGA DVATASEVNT EDLAPGGAPG RLTVFTESAL
AEVAER
