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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: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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

GO - Biological processi

Complete GO annotation...

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 Componenti: Chromosome I

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

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.UniRule annotation2 Publications

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 – 135Combined sources
Helixi19 – 3113Combined sources
Beta strandi36 – 394Combined sources
Helixi41 – 433Combined sources
Beta strandi45 – 484Combined sources
Helixi50 – 6213Combined sources
Helixi75 – 8410Combined sources
Turni85 – 906Combined sources
Helixi92 – 998Combined sources
Beta strandi101 – 1033Combined sources
Beta strandi109 – 1113Combined sources
Turni117 – 1193Combined sources
Turni123 – 1253Combined sources
Beta strandi128 – 1314Combined sources
Helixi132 – 1398Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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[»]
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[»]
4V4RX-ray5.90N1-145[»]
4V4SX-ray6.76N1-145[»]
4V9FX-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.
OMAiSKHLGAK.

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

        10         20         30         40         50
MSVAEFDADV IVDARDCIMG RVASQVAEQA LDGETVAVVN AERAVITGRE
60 70 80 90 100
EQIVEKYEKR VDIGNDNGYF YPKRPDGIFK RTIRGMLPHK KQRGREAFES
110 120 130 140
VRVYLGNPYD EDGEVLDGTS LDRLSNIKFV TLGEISETLG ANKTW
Length:145
Mass (Da):16,228
Last modified:December 1, 1992 - v1
Checksum:i069CE666662AE3BC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M76567 Genomic DNA. Translation: AAA73097.1.
AY596297 Genomic DNA. Translation: AAV45145.1.
PIRiB41715.
RefSeqiWP_004593558.1. NC_006396.1.
YP_134851.1. NC_006396.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M76567 Genomic DNA. Translation: AAA73097.1.
AY596297 Genomic DNA. Translation: AAV45145.1.
PIRiB41715.
RefSeqiWP_004593558.1. NC_006396.1.
YP_134851.1. NC_006396.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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[»]
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[»]
4V4RX-ray5.90N1-145[»]
4V4SX-ray6.76N1-145[»]
4V9FX-ray2.40J1-145[»]
ProteinModelPortaliP29198.
SMRiP29198. Positions 4-145.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272569.rrnAC0065.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiCOG0102.
HOGENOMiHOG000225287.
KOiK02871.
OMAiSKHLGAK.

Enzyme and pathway databases

BioCyciHMAR272569:GJDH-61-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP29198.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: June 24, 2015
This is version 110 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.