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Protein

50S ribosomal protein L4

Gene

rplD

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).By similarity
Forms part of the polypeptide exit tunnel.By similarity
This protein can be incorporated into E.coli ribosomes in vivo, which resulted in decreased peptidyltransferase (Ptase) activity of the hybrid ribosomes. The hybrid 50S subunits associate less well with 30S subunits to form the ribosome.

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
Alternative name(s):
L1e
Gene namesi
Name:rplD
Ordered Locus Names:TTHA1691
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
Proteomesi
  • UP000000532 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi55G → A: Increases Ptase activity of hybrid ribosomes to a value greater than that of pure E.coli ribosomes. Increases binding of a tRNA analog to the P site. 1 Publication1
Mutagenesisi55G → S: No effect on Ptase activity of hybrid ribosomes. No change in binding of a tRNA analog to the A or P site. 1 Publication1
Mutagenesisi56E → A: Further decreases Ptase activity in E.coli hybrid ribosomes. Significantly decreases binding of a tRNA analog to the A or P site. 1 Publication1
Mutagenesisi56E → Q: Restores Ptase activity of hybrid ribosomes to that of pure E.coli ribosomes. Significantly increases binding of a tRNA analog to the P site. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001293001 – 21050S ribosomal protein L4Add BLAST210

Post-translational modificationi

The N-terminus is blocked.

Interactioni

Subunit structurei

Part of the 50S ribosomal subunit.

Protein-protein interaction databases

STRINGi300852.TTHA1691.

Structurei

Secondary structure

1210
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi10 – 12Combined sources3
Turni22 – 25Combined sources4
Helixi30 – 43Combined sources14
Turni54 – 56Combined sources3
Beta strandi57 – 59Combined sources3
Beta strandi83 – 86Combined sources4
Helixi103 – 120Combined sources18
Beta strandi123 – 125Combined sources3
Helixi136 – 145Combined sources10
Beta strandi150 – 152Combined sources3
Beta strandi154 – 157Combined sources4
Helixi161 – 166Combined sources6
Beta strandi167 – 170Combined sources4
Beta strandi173 – 176Combined sources4
Helixi178 – 180Combined sources3
Helixi183 – 188Combined sources6
Beta strandi189 – 194Combined sources6
Helixi196 – 204Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TWVmodel-D1-210[»]
1VVJX-ray3.44RF/YF1-210[»]
1VY4X-ray2.60BF/DF1-210[»]
1VY5X-ray2.55BF/DF1-210[»]
1VY6X-ray2.90BF/DF1-210[»]
1VY7X-ray2.80BF/DF1-210[»]
4L47X-ray3.22RF/YF1-210[»]
4L71X-ray3.90RF/YF1-210[»]
4LELX-ray3.90RF/YF1-210[»]
4LFZX-ray3.92RF/YF1-210[»]
4LNTX-ray2.94RF/YF1-210[»]
4LSKX-ray3.48RF/YF1-210[»]
4LT8X-ray3.14RF/YF1-210[»]
4P6FX-ray3.60RF/YF1-210[»]
4P70X-ray3.68RF/YF1-210[»]
4TUAX-ray3.60RF/YF1-210[»]
4TUBX-ray3.60RF/YF1-210[»]
4TUCX-ray3.60RF/YF1-210[»]
4TUDX-ray3.60RF/YF1-210[»]
4TUEX-ray3.50RF/YF1-210[»]
4V42X-ray5.50BF1-210[»]
4V4PX-ray5.50BF1-210[»]
4V4XX-ray5.00BF1-210[»]
4V4YX-ray5.50BF1-210[»]
4V4ZX-ray4.51BF1-210[»]
4V51X-ray2.80BF/DF1-210[»]
4V5AX-ray3.50BF/DF1-210[»]
4V5CX-ray3.30BF/DF1-210[»]
4V5DX-ray3.50BF/DF1-210[»]
4V5EX-ray3.45BF/DF1-210[»]
4V5FX-ray3.60BF/DF1-210[»]
4V5GX-ray3.60BF/DF1-210[»]
4V5JX-ray3.10BF/DF1-210[»]
4V5KX-ray3.20BF/DF1-210[»]
4V5LX-ray3.10BF1-210[»]
4V5Melectron microscopy7.80BF1-210[»]
4V5Nelectron microscopy7.60BF1-210[»]
4V5PX-ray3.10BF/DF1-210[»]
4V5QX-ray3.10BF/DF1-210[»]
4V5RX-ray3.10BF/DF1-210[»]
4V5SX-ray3.10BF/DF1-210[»]
4V68electron microscopy6.40BF1-208[»]
4V6AX-ray3.10BF/DF1-210[»]
4V6FX-ray3.10AF/DF1-210[»]
4V6GX-ray3.50BF/DF1-210[»]
4V7JX-ray3.30AF/BF1-210[»]
4V7KX-ray3.60AF/BF1-210[»]
4V7LX-ray3.00BF/DF1-210[»]
4V7MX-ray3.45BF/DF1-210[»]
4V7WX-ray3.00BF/DF1-210[»]
4V7XX-ray3.00BF/DF1-210[»]
4V7YX-ray3.00BF/DF1-210[»]
4V7ZX-ray3.10BF/DF1-210[»]
4V87X-ray3.10AF/DF1-208[»]
4V8AX-ray3.20AF/BF6-210[»]
4V8BX-ray3.00BF/DF1-210[»]
4V8CX-ray3.30AF/BF1-210[»]
4V8DX-ray3.00BF/DF1-210[»]
4V8EX-ray3.30AF/CF1-210[»]
4V8FX-ray3.30AF/DF1-210[»]
4V8GX-ray3.00BF/DF1-210[»]
4V8HX-ray3.10BF/DF1-210[»]
4V8IX-ray2.70BF/DF1-210[»]
4V8JX-ray3.90BF/DF1-210[»]
4V8NX-ray3.10BF/DF1-210[»]
4V8OX-ray3.80BF1-210[»]
4V8QX-ray3.10AF1-210[»]
4V8UX-ray3.70BF/DF1-210[»]
4V8XX-ray3.35BF/DF1-210[»]
4V90X-ray2.95BF1-210[»]
4V95X-ray3.20BF/DF1-210[»]
4V97X-ray3.52BF/DF1-210[»]
4V9AX-ray3.30BF/DF1-210[»]
4V9BX-ray3.10BF/DF1-210[»]
4V9HX-ray2.86BF1-210[»]
4V9IX-ray3.30BF/DF1-207[»]
4V9RX-ray3.00BF/DF1-210[»]
4V9SX-ray3.10BF/DF1-210[»]
4W2EX-ray2.90F6-210[»]
4W2FX-ray2.40BF/DF1-210[»]
4W2GX-ray2.55BF/DF1-210[»]
4W2HX-ray2.70BF/DF1-210[»]
4W2IX-ray2.70BF/DF1-210[»]
4W4GX-ray3.30RF/YF1-210[»]
4WPOX-ray2.80AF/CF1-210[»]
4WQ1X-ray3.10316-207[»]
391-210[»]
4WQFX-ray2.80AF/CF1-210[»]
4WQRX-ray3.1531/391-210[»]
4WQUX-ray2.80AF/CF1-210[»]
4WQYX-ray2.80AF/CF1-210[»]
4WR6X-ray3.0531/391-210[»]
4WRAX-ray3.0531/391-210[»]
4WROX-ray3.05311-210[»]
4WSDX-ray2.9531/391-210[»]
4WSMX-ray3.3031/391-210[»]
4WT1X-ray3.0531/391-210[»]
4WT8X-ray3.40CD/DD1-207[»]
4WU1X-ray3.2031/391-210[»]
4WZDX-ray3.1031/391-210[»]
4WZOX-ray3.3031/391-210[»]
4Y4OX-ray2.301F/2F1-210[»]
4Y4PX-ray2.501F/2F1-210[»]
4YPBX-ray3.40RF/YF1-210[»]
4YZVX-ray3.10RF/YF1-210[»]
4Z3SX-ray2.651F/2F1-210[»]
4Z8CX-ray2.901F/2F1-210[»]
4ZERX-ray3.101F/2F6-208[»]
4ZSNX-ray3.60RF/YF1-210[»]
5A9Zelectron microscopy4.70AF3-210[»]
5AA0electron microscopy5.00AF3-210[»]
5CZPX-ray3.30RF/YF1-210[»]
5D8BX-ray3.63C/YA7-210[»]
5DFEX-ray3.10RF/YF1-210[»]
5DOXX-ray3.101F/2F1-210[»]
5DOYX-ray2.601F/2F1-210[»]
5E7KX-ray3.2031/391-210[»]
5E81X-ray2.9531/391-210[»]
5EL4X-ray3.1531/391-210[»]
5EL5X-ray3.1531/391-210[»]
5EL6X-ray3.1031/391-210[»]
5EL7X-ray3.1531/391-210[»]
5F8KX-ray2.801F/2F6-208[»]
5FDUX-ray2.901F/2F6-208[»]
5FDVX-ray2.801F/2F6-208[»]
5HAUX-ray3.001F/2F1-210[»]
5HCPX-ray2.891F/2F1-210[»]
5HCQX-ray2.801F/2F1-210[»]
5HCRX-ray2.801F/2F1-210[»]
5HD1X-ray2.701F/2F1-210[»]
5IB7X-ray2.9931/391-210[»]
5IB8X-ray3.1331/391-210[»]
5IBBX-ray2.9631/391-210[»]
5IMQelectron microscopy3.80c1-210[»]
5IMRelectron microscopy-c1-210[»]
5J30X-ray3.20RF/YF1-210[»]
5J3CX-ray3.04RF/YF1-210[»]
5J4BX-ray2.601F/2F1-210[»]
5J4CX-ray2.801F/2F1-210[»]
5J8BX-ray2.60F1-210[»]
ProteinModelPortaliQ5SHN9.
SMRiQ5SHN9.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SHN9.

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein L4P family.Curated

Phylogenomic databases

eggNOGiENOG4106U5A. Bacteria.
COG0088. LUCA.
HOGENOMiHOG000248767.
KOiK02926.
OMAiAHNIVIS.

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.

Q5SHN9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKEVAVYQIP VLSPSGRREL AADLPAEINP HLLWEVVRWQ LAKRRRGTAS
60 70 80 90 100
TKTRGEVAYS GRKIWPQKHT GRARHGDIGA PIFVGGGVVF GPKPRDYSYT
110 120 130 140 150
LPKKVRKKGL AMAVADRARE GKLLLVEAFA GVNGKTKEFL AWAKEAGLDG
160 170 180 190 200
SESVLLVTGN ELVRRAARNL PWVVTLAPEG LNVYDIVRTE RLVMDLDAWE
210
VFQNRIGGEA
Length:210
Mass (Da):23,235
Last modified:December 21, 2004 - v1
Checksum:iBFB99AC179C110B4
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti19 – 20EL → DV in AAA97862 (PubMed:8566766).Curated2

Mass spectrometryi

Molecular mass is 22724 Da from positions 1 - 210. Determined by MALDI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U36480 Genomic DNA. Translation: AAA97862.1.
AP008226 Genomic DNA. Translation: BAD71514.1.
RefSeqiYP_144957.2. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD71514; BAD71514; BAD71514.
GeneIDi3167923.
KEGGittj:TTHA1691.
PATRICi23958337. VBITheThe93045_1661.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U36480 Genomic DNA. Translation: AAA97862.1.
AP008226 Genomic DNA. Translation: BAD71514.1.
RefSeqiYP_144957.2. NC_006461.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TWVmodel-D1-210[»]
1VVJX-ray3.44RF/YF1-210[»]
1VY4X-ray2.60BF/DF1-210[»]
1VY5X-ray2.55BF/DF1-210[»]
1VY6X-ray2.90BF/DF1-210[»]
1VY7X-ray2.80BF/DF1-210[»]
4L47X-ray3.22RF/YF1-210[»]
4L71X-ray3.90RF/YF1-210[»]
4LELX-ray3.90RF/YF1-210[»]
4LFZX-ray3.92RF/YF1-210[»]
4LNTX-ray2.94RF/YF1-210[»]
4LSKX-ray3.48RF/YF1-210[»]
4LT8X-ray3.14RF/YF1-210[»]
4P6FX-ray3.60RF/YF1-210[»]
4P70X-ray3.68RF/YF1-210[»]
4TUAX-ray3.60RF/YF1-210[»]
4TUBX-ray3.60RF/YF1-210[»]
4TUCX-ray3.60RF/YF1-210[»]
4TUDX-ray3.60RF/YF1-210[»]
4TUEX-ray3.50RF/YF1-210[»]
4V42X-ray5.50BF1-210[»]
4V4PX-ray5.50BF1-210[»]
4V4XX-ray5.00BF1-210[»]
4V4YX-ray5.50BF1-210[»]
4V4ZX-ray4.51BF1-210[»]
4V51X-ray2.80BF/DF1-210[»]
4V5AX-ray3.50BF/DF1-210[»]
4V5CX-ray3.30BF/DF1-210[»]
4V5DX-ray3.50BF/DF1-210[»]
4V5EX-ray3.45BF/DF1-210[»]
4V5FX-ray3.60BF/DF1-210[»]
4V5GX-ray3.60BF/DF1-210[»]
4V5JX-ray3.10BF/DF1-210[»]
4V5KX-ray3.20BF/DF1-210[»]
4V5LX-ray3.10BF1-210[»]
4V5Melectron microscopy7.80BF1-210[»]
4V5Nelectron microscopy7.60BF1-210[»]
4V5PX-ray3.10BF/DF1-210[»]
4V5QX-ray3.10BF/DF1-210[»]
4V5RX-ray3.10BF/DF1-210[»]
4V5SX-ray3.10BF/DF1-210[»]
4V68electron microscopy6.40BF1-208[»]
4V6AX-ray3.10BF/DF1-210[»]
4V6FX-ray3.10AF/DF1-210[»]
4V6GX-ray3.50BF/DF1-210[»]
4V7JX-ray3.30AF/BF1-210[»]
4V7KX-ray3.60AF/BF1-210[»]
4V7LX-ray3.00BF/DF1-210[»]
4V7MX-ray3.45BF/DF1-210[»]
4V7WX-ray3.00BF/DF1-210[»]
4V7XX-ray3.00BF/DF1-210[»]
4V7YX-ray3.00BF/DF1-210[»]
4V7ZX-ray3.10BF/DF1-210[»]
4V87X-ray3.10AF/DF1-208[»]
4V8AX-ray3.20AF/BF6-210[»]
4V8BX-ray3.00BF/DF1-210[»]
4V8CX-ray3.30AF/BF1-210[»]
4V8DX-ray3.00BF/DF1-210[»]
4V8EX-ray3.30AF/CF1-210[»]
4V8FX-ray3.30AF/DF1-210[»]
4V8GX-ray3.00BF/DF1-210[»]
4V8HX-ray3.10BF/DF1-210[»]
4V8IX-ray2.70BF/DF1-210[»]
4V8JX-ray3.90BF/DF1-210[»]
4V8NX-ray3.10BF/DF1-210[»]
4V8OX-ray3.80BF1-210[»]
4V8QX-ray3.10AF1-210[»]
4V8UX-ray3.70BF/DF1-210[»]
4V8XX-ray3.35BF/DF1-210[»]
4V90X-ray2.95BF1-210[»]
4V95X-ray3.20BF/DF1-210[»]
4V97X-ray3.52BF/DF1-210[»]
4V9AX-ray3.30BF/DF1-210[»]
4V9BX-ray3.10BF/DF1-210[»]
4V9HX-ray2.86BF1-210[»]
4V9IX-ray3.30BF/DF1-207[»]
4V9RX-ray3.00BF/DF1-210[»]
4V9SX-ray3.10BF/DF1-210[»]
4W2EX-ray2.90F6-210[»]
4W2FX-ray2.40BF/DF1-210[»]
4W2GX-ray2.55BF/DF1-210[»]
4W2HX-ray2.70BF/DF1-210[»]
4W2IX-ray2.70BF/DF1-210[»]
4W4GX-ray3.30RF/YF1-210[»]
4WPOX-ray2.80AF/CF1-210[»]
4WQ1X-ray3.10316-207[»]
391-210[»]
4WQFX-ray2.80AF/CF1-210[»]
4WQRX-ray3.1531/391-210[»]
4WQUX-ray2.80AF/CF1-210[»]
4WQYX-ray2.80AF/CF1-210[»]
4WR6X-ray3.0531/391-210[»]
4WRAX-ray3.0531/391-210[»]
4WROX-ray3.05311-210[»]
4WSDX-ray2.9531/391-210[»]
4WSMX-ray3.3031/391-210[»]
4WT1X-ray3.0531/391-210[»]
4WT8X-ray3.40CD/DD1-207[»]
4WU1X-ray3.2031/391-210[»]
4WZDX-ray3.1031/391-210[»]
4WZOX-ray3.3031/391-210[»]
4Y4OX-ray2.301F/2F1-210[»]
4Y4PX-ray2.501F/2F1-210[»]
4YPBX-ray3.40RF/YF1-210[»]
4YZVX-ray3.10RF/YF1-210[»]
4Z3SX-ray2.651F/2F1-210[»]
4Z8CX-ray2.901F/2F1-210[»]
4ZERX-ray3.101F/2F6-208[»]
4ZSNX-ray3.60RF/YF1-210[»]
5A9Zelectron microscopy4.70AF3-210[»]
5AA0electron microscopy5.00AF3-210[»]
5CZPX-ray3.30RF/YF1-210[»]
5D8BX-ray3.63C/YA7-210[»]
5DFEX-ray3.10RF/YF1-210[»]
5DOXX-ray3.101F/2F1-210[»]
5DOYX-ray2.601F/2F1-210[»]
5E7KX-ray3.2031/391-210[»]
5E81X-ray2.9531/391-210[»]
5EL4X-ray3.1531/391-210[»]
5EL5X-ray3.1531/391-210[»]
5EL6X-ray3.1031/391-210[»]
5EL7X-ray3.1531/391-210[»]
5F8KX-ray2.801F/2F6-208[»]
5FDUX-ray2.901F/2F6-208[»]
5FDVX-ray2.801F/2F6-208[»]
5HAUX-ray3.001F/2F1-210[»]
5HCPX-ray2.891F/2F1-210[»]
5HCQX-ray2.801F/2F1-210[»]
5HCRX-ray2.801F/2F1-210[»]
5HD1X-ray2.701F/2F1-210[»]
5IB7X-ray2.9931/391-210[»]
5IB8X-ray3.1331/391-210[»]
5IBBX-ray2.9631/391-210[»]
5IMQelectron microscopy3.80c1-210[»]
5IMRelectron microscopy-c1-210[»]
5J30X-ray3.20RF/YF1-210[»]
5J3CX-ray3.04RF/YF1-210[»]
5J4BX-ray2.601F/2F1-210[»]
5J4CX-ray2.801F/2F1-210[»]
5J8BX-ray2.60F1-210[»]
ProteinModelPortaliQ5SHN9.
SMRiQ5SHN9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi300852.TTHA1691.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD71514; BAD71514; BAD71514.
GeneIDi3167923.
KEGGittj:TTHA1691.
PATRICi23958337. VBITheThe93045_1661.

Phylogenomic databases

eggNOGiENOG4106U5A. Bacteria.
COG0088. LUCA.
HOGENOMiHOG000248767.
KOiK02926.
OMAiAHNIVIS.

Miscellaneous databases

EvolutionaryTraceiQ5SHN9.

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_THET8
AccessioniPrimary (citable) accession number: Q5SHN9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: December 21, 2004
Last modified: November 30, 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.