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P12735

- RL4_HALMA

UniProt

P12735 - RL4_HALMA

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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

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
Complete GO annotation...

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
Complete GO annotation...

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 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MQATIYDLDG NTDGEVDLPD VFETPVRSDL IGKAVRAAQA NRKQDYGSDE
60 70 80 90 100
YAGLRTPAES FGSGRGQAHV PKQDGRARRV PQAVKGRSAH PPKTEKDRSL
110 120 130 140 150
DLNDKERQLA VRSALAATAD ADLVADRGHE FDRDEVPVVV SDDFEDLVKT
160 170 180 190 200
QEVVSLLEAL DVHADIDRAD ETKIKAGQGS ARGRKYRRPA SILFVTSDEP
210 220 230 240
STAARNLAGA DVATASEVNT EDLAPGGAPG RLTVFTESAL AEVAER
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

« Hide 'large scale' publications
  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