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Protein

50S ribosomal protein L4

Gene

rplD

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: 4 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.
This protein is located close to the polypeptide exit tunnel, and interacts with the modified macrolide azithromycin, which blocks the tunnel.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Keywords - Ligandi

RNA-binding, rRNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
50S ribosomal protein L4
Gene namesi
Name:rplD
Ordered Locus Names:DR_0312
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)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved
ChainiPRO_00001292142 – 20550S ribosomal protein L4Add BLAST204

Interactioni

Subunit structurei

Part of the 50S ribosomal subunit. Contacts proteins L15 and L34.6 Publications

Protein-protein interaction databases

STRINGi243230.DR_0312.

Structurei

Secondary structure

1205
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 8Combined sources3
Turni19 – 21Combined sources3
Helixi24 – 36Combined sources13
Turni48 – 50Combined sources3
Beta strandi61 – 66Combined sources6
Beta strandi72 – 74Combined sources3
Beta strandi77 – 80Combined sources4
Helixi97 – 112Combined sources16
Turni113 – 115Combined sources3
Beta strandi117 – 122Combined sources6
Turni123 – 125Combined sources3
Turni126 – 128Combined sources3
Helixi130 – 139Combined sources10
Beta strandi144 – 146Combined sources3
Beta strandi148 – 153Combined sources6
Helixi155 – 161Combined sources7
Turni164 – 166Combined sources3
Beta strandi167 – 171Combined sources5
Helixi177 – 182Combined sources6
Beta strandi183 – 190Combined sources8
Turni191 – 197Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1J5AX-ray3.50K1-205[»]
1JZXX-ray3.10K1-205[»]
1JZYX-ray3.50K1-205[»]
1JZZX-ray3.80K1-205[»]
1K01X-ray3.50K1-205[»]
1NKWX-ray3.10C1-205[»]
1NWXX-ray3.50C2-205[»]
1NWYX-ray3.30C2-205[»]
1SM1X-ray3.42C1-205[»]
1XBPX-ray3.50C2-205[»]
2ZJPX-ray3.70C1-205[»]
2ZJQX-ray3.30C1-205[»]
2ZJRX-ray2.91C1-205[»]
3CF5X-ray3.30C1-205[»]
3DLLX-ray3.50C1-205[»]
3PIOX-ray3.25C1-205[»]
3PIPX-ray3.45C1-205[»]
4IO9X-ray3.20C1-205[»]
4IOAX-ray3.20C1-205[»]
4IOCX-ray3.60C1-205[»]
4U67X-ray3.65C1-205[»]
4V49X-ray8.70C2-198[»]
4V4AX-ray9.50C2-198[»]
4WFNX-ray3.54C1-205[»]
5DM6X-ray2.90C2-198[»]
5DM7X-ray3.00C2-198[»]
ProteinModelPortaliQ9RXK1.
SMRiQ9RXK1.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9RXK1.

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein L4P family.Curated

Phylogenomic databases

eggNOGiENOG4106U5A. Bacteria.
COG0088. LUCA.
HOGENOMiHOG000248767.
InParanoidiQ9RXK1.
KOiK02926.
OMAiYAQRTPK.
OrthoDBiPOG091H027V.

Family and domain databases

Gene3Di3.40.1370.10. 1 hit.
HAMAPiMF_01328_B. Ribosomal_L4_B. 1 hit.
InterProiIPR002136. Ribosomal_L4/L1e.
IPR023574. Ribosomal_L4_dom.
IPR013005. Ribosomal_uL4/L1e.
[Graphical view]
PANTHERiPTHR10746. PTHR10746. 1 hit.
PfamiPF00573. Ribosomal_L4. 1 hit.
[Graphical view]
SUPFAMiSSF52166. SSF52166. 1 hit.
TIGRFAMsiTIGR03953. rplD_bact. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9RXK1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQINVIGQN GGRTIELPLP EVNSGVLHEV VTWQLASRRR GTASTRTRAQ
60 70 80 90 100
VSKTGRKMYG QKGTGNARHG DRSVPTFVGG GVAFGPKPRS YDYTLPRQVR
110 120 130 140 150
QLGLAMAIAS RQEGGKLVAV DGFDIADAKT KNFISWAKQN GLDGTEKVLL
160 170 180 190 200
VTDDENTRRA ARNVSWVSVL PVAGVNVYDI LRHDRLVIDA AALEIVEEEA

GEEQQ
Length:205
Mass (Da):22,278
Last modified:January 23, 2007 - v3
Checksum:i760A6C160912477B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000513 Genomic DNA. Translation: AAF09893.1.
PIRiH75533.
RefSeqiNP_294035.1. NC_001263.1.
WP_010886957.1. NZ_CP015081.1.

Genome annotation databases

EnsemblBacteriaiAAF09893; AAF09893; DR_0312.
GeneIDi1799571.
KEGGidra:DR_0312.
PATRICi21628122. VBIDeiRad64572_0478.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000513 Genomic DNA. Translation: AAF09893.1.
PIRiH75533.
RefSeqiNP_294035.1. NC_001263.1.
WP_010886957.1. NZ_CP015081.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1J5AX-ray3.50K1-205[»]
1JZXX-ray3.10K1-205[»]
1JZYX-ray3.50K1-205[»]
1JZZX-ray3.80K1-205[»]
1K01X-ray3.50K1-205[»]
1NKWX-ray3.10C1-205[»]
1NWXX-ray3.50C2-205[»]
1NWYX-ray3.30C2-205[»]
1SM1X-ray3.42C1-205[»]
1XBPX-ray3.50C2-205[»]
2ZJPX-ray3.70C1-205[»]
2ZJQX-ray3.30C1-205[»]
2ZJRX-ray2.91C1-205[»]
3CF5X-ray3.30C1-205[»]
3DLLX-ray3.50C1-205[»]
3PIOX-ray3.25C1-205[»]
3PIPX-ray3.45C1-205[»]
4IO9X-ray3.20C1-205[»]
4IOAX-ray3.20C1-205[»]
4IOCX-ray3.60C1-205[»]
4U67X-ray3.65C1-205[»]
4V49X-ray8.70C2-198[»]
4V4AX-ray9.50C2-198[»]
4WFNX-ray3.54C1-205[»]
5DM6X-ray2.90C2-198[»]
5DM7X-ray3.00C2-198[»]
ProteinModelPortaliQ9RXK1.
SMRiQ9RXK1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243230.DR_0312.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF09893; AAF09893; DR_0312.
GeneIDi1799571.
KEGGidra:DR_0312.
PATRICi21628122. VBIDeiRad64572_0478.

Phylogenomic databases

eggNOGiENOG4106U5A. Bacteria.
COG0088. LUCA.
HOGENOMiHOG000248767.
InParanoidiQ9RXK1.
KOiK02926.
OMAiYAQRTPK.
OrthoDBiPOG091H027V.

Miscellaneous databases

EvolutionaryTraceiQ9RXK1.

Family and domain databases

Gene3Di3.40.1370.10. 1 hit.
HAMAPiMF_01328_B. Ribosomal_L4_B. 1 hit.
InterProiIPR002136. Ribosomal_L4/L1e.
IPR023574. Ribosomal_L4_dom.
IPR013005. Ribosomal_uL4/L1e.
[Graphical view]
PANTHERiPTHR10746. PTHR10746. 1 hit.
PfamiPF00573. Ribosomal_L4. 1 hit.
[Graphical view]
SUPFAMiSSF52166. SSF52166. 1 hit.
TIGRFAMsiTIGR03953. rplD_bact. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRL4_DEIRA
AccessioniPrimary (citable) accession number: Q9RXK1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2004
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 105 of the entry and version 3 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.