Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

50S ribosomal protein L13

Gene

rplM

Organism
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
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 the 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

BioCyciDRAD243230:GH46-180-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
50S ribosomal protein L13
Gene namesi
Name:rplM
Ordered Locus Names:DR_0174
OrganismiDeinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Taxonomic identifieri243230 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciDeinococcalesDeinococcaceaeDeinococcus
Proteomesi
  • UP000002524 Componenti: Chromosome I

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 17417450S ribosomal protein L13PRO_0000133733Add
BLAST

Proteomic databases

PRIDEiQ9RXY1.

Interactioni

Subunit structurei

Part of the 50S ribosomal subunit. Contacts proteins L3 and L20.6 Publications

Protein-protein interaction databases

STRINGi243230.DR_0174.

Structurei

Secondary structure

1
174
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi41 – 455Combined sources
Beta strandi47 – 504Combined sources
Helixi51 – 6313Combined sources
Beta strandi72 – 743Combined sources
Beta strandi79 – 835Combined sources
Helixi85 – 873Combined sources
Helixi94 – 974Combined sources
Beta strandi99 – 1024Combined sources
Beta strandi111 – 1144Combined sources
Helixi115 – 1217Combined sources
Helixi124 – 13310Combined sources
Helixi139 – 1457Combined sources
Beta strandi148 – 1503Combined sources
Beta strandi154 – 1563Combined sources
Helixi159 – 1613Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GS2model-H30-171[»]
1NKWX-ray3.10H1-174[»]
1NWXX-ray3.50H1-174[»]
1NWYX-ray3.30H1-174[»]
1SM1X-ray3.42H1-174[»]
1XBPX-ray3.50H1-174[»]
2ZJPX-ray3.70G1-174[»]
2ZJQX-ray3.30G1-174[»]
2ZJRX-ray2.91G1-174[»]
3CF5X-ray3.30G1-174[»]
3DLLX-ray3.50G1-174[»]
3PIOX-ray3.25G1-174[»]
3PIPX-ray3.45G1-174[»]
4IO9X-ray3.20G1-174[»]
4IOAX-ray3.20G1-174[»]
4IOCX-ray3.60G1-174[»]
4U67X-ray3.65G1-174[»]
4V49X-ray8.70H29-171[»]
4V4AX-ray9.50H29-171[»]
4V4GX-ray11.50K29-171[»]
4WFNX-ray3.54G1-174[»]
5DM6X-ray2.90G30-171[»]
5DM7X-ray3.00G30-171[»]
ProteinModelPortaliQ9RXY1.
SMRiQ9RXY1. Positions 29-171.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9RXY1.

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein L13P family.Curated

Phylogenomic databases

eggNOGiENOG4108UM5. Bacteria.
COG0102. LUCA.
HOGENOMiHOG000225286.
InParanoidiQ9RXY1.
KOiK02871.
OMAiGMLPHNR.
OrthoDBiEOG628FBD.

Family and domain databases

Gene3Di3.90.1180.10. 1 hit.
HAMAPiMF_01366. Ribosomal_L13.
InterProiIPR005822. Ribosomal_L13.
IPR005823. Ribosomal_L13_bac-type.
IPR023563. Ribosomal_L13_CS.
[Graphical view]
PANTHERiPTHR11545. PTHR11545. 1 hit.
PfamiPF00572. Ribosomal_L13. 1 hit.
[Graphical view]
PIRSFiPIRSF002181. Ribosomal_L13. 1 hit.
SUPFAMiSSF52161. SSF52161. 1 hit.
TIGRFAMsiTIGR01066. rplM_bact. 1 hit.
PROSITEiPS00783. RIBOSOMAL_L13. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9RXY1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAFPDTDVSP PRGGPSSPAK SPLLRSFKVK TYIPKNDEQN WVVVDASGVP
60 70 80 90 100
LGRLATLIAS RIRGKHRPDF TPNMIQGDFV VVINAAQVAL TGKKLDDKVY
110 120 130 140 150
TRYTGYQGGL KTETAREALS KHPERVIEHA VFGMLPKGRQ GRAMHTRLKV
160 170
YAGETHPHSA QKPQVLKTQP LEVK
Length:174
Mass (Da):19,190
Last modified:May 1, 2000 - v1
Checksum:i9F7B977882CB715E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000513 Genomic DNA. Translation: AAF09760.1.
PIRiE75552.
RefSeqiNP_293898.2. NC_001263.1.

Genome annotation databases

EnsemblBacteriaiAAF09760; AAF09760; DR_0174.
GeneIDi1799575.
KEGGidra:DR_0174.
PATRICi21627831. VBIDeiRad64572_0338.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000513 Genomic DNA. Translation: AAF09760.1.
PIRiE75552.
RefSeqiNP_293898.2. NC_001263.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GS2model-H30-171[»]
1NKWX-ray3.10H1-174[»]
1NWXX-ray3.50H1-174[»]
1NWYX-ray3.30H1-174[»]
1SM1X-ray3.42H1-174[»]
1XBPX-ray3.50H1-174[»]
2ZJPX-ray3.70G1-174[»]
2ZJQX-ray3.30G1-174[»]
2ZJRX-ray2.91G1-174[»]
3CF5X-ray3.30G1-174[»]
3DLLX-ray3.50G1-174[»]
3PIOX-ray3.25G1-174[»]
3PIPX-ray3.45G1-174[»]
4IO9X-ray3.20G1-174[»]
4IOAX-ray3.20G1-174[»]
4IOCX-ray3.60G1-174[»]
4U67X-ray3.65G1-174[»]
4V49X-ray8.70H29-171[»]
4V4AX-ray9.50H29-171[»]
4V4GX-ray11.50K29-171[»]
4WFNX-ray3.54G1-174[»]
5DM6X-ray2.90G30-171[»]
5DM7X-ray3.00G30-171[»]
ProteinModelPortaliQ9RXY1.
SMRiQ9RXY1. Positions 29-171.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243230.DR_0174.

Proteomic databases

PRIDEiQ9RXY1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF09760; AAF09760; DR_0174.
GeneIDi1799575.
KEGGidra:DR_0174.
PATRICi21627831. VBIDeiRad64572_0338.

Phylogenomic databases

eggNOGiENOG4108UM5. Bacteria.
COG0102. LUCA.
HOGENOMiHOG000225286.
InParanoidiQ9RXY1.
KOiK02871.
OMAiGMLPHNR.
OrthoDBiEOG628FBD.

Enzyme and pathway databases

BioCyciDRAD243230:GH46-180-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9RXY1.

Family and domain databases

Gene3Di3.90.1180.10. 1 hit.
HAMAPiMF_01366. Ribosomal_L13.
InterProiIPR005822. Ribosomal_L13.
IPR005823. Ribosomal_L13_bac-type.
IPR023563. Ribosomal_L13_CS.
[Graphical view]
PANTHERiPTHR11545. PTHR11545. 1 hit.
PfamiPF00572. Ribosomal_L13. 1 hit.
[Graphical view]
PIRSFiPIRSF002181. Ribosomal_L13. 1 hit.
SUPFAMiSSF52161. SSF52161. 1 hit.
TIGRFAMsiTIGR01066. rplM_bact. 1 hit.
PROSITEiPS00783. RIBOSOMAL_L13. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  2. "High resolution structure of the large ribosomal subunit from a mesophilic eubacterium."
    Harms J., Schluenzen F., Zarivach R., Bashan A., Gat S., Agmon I., Bartels H., Franceschi F., Yonath A.
    Cell 107:679-688(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT, PROTEIN SEQUENCE OF 1-5, CONTACTS WITH 23S RRNA.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  3. "Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria."
    Schluenzen F., Zarivach R., Harms J., Bashan A., Tocilj A., Albrecht R., Yonath A., Franceschi F.
    Nature 413:814-821(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH FIVE ANTIBIOTICS.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  4. "Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression."
    Bashan A., Agmon I., Zarivach R., Schluenzen F., Harms J., Berisio R., Bartels H., Franceschi F., Auerbach T., Hansen H.A., Kossoy E., Kessler M., Yonath A.
    Mol. Cell 11:91-102(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH TRNA MIMICS.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  5. "Structural basis for the antibiotic activity of ketolides and azalides."
    Schluenzen F., Harms J.M., Franceschi F., Hansen H.A., Bartels H., Zarivach R., Yonath A.
    Structure 11:329-338(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH MODIFIED MACROLIDE ANTIBIOTICS.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  6. "Structural insight into the role of the ribosomal tunnel in cellular regulation."
    Berisio R., Schluenzen F., Harms J., Bashan A., Auerbach T., Baram D., Yonath A.
    Nat. Struct. Biol. 10:366-370(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH TROLEANDOMYCIN.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  7. "Alterations at the peptidyl transferase centre of the ribosome induced by the synergistic action of the streptogramins dalfopristin and quinupristin."
    Harms J.M., Schluenzen F., Fucini P., Bartels H., Yonath A.
    BMC Biol. 2:4-4(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH THE STREPTOGRAMINS QUINUPRISTIN AND DALFOPRISTIN.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  8. "Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin."
    Schluenzen F., Pyetan E., Fucini P., Yonath A., Harms J.M.
    Mol. Microbiol. 54:1287-1294(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH TIAMULIN.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.

Entry informationi

Entry nameiRL13_DEIRA
AccessioniPrimary (citable) accession number: Q9RXY1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2004
Last sequence update: May 1, 2000
Last modified: July 6, 2016
This is version 111 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, 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

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 one 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.