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Protein

60S ribosomal protein L3

Gene

RPL3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded message by selecting cognate aminoacyl-transfer RNA (tRNA) molecules. The large subunit (LSU) contains the ribosomal catalytic site termed the peptidyl transferase center (PTC), which catalyzes the formation of peptide bonds, thereby polymerizing the amino acids delivered by tRNAs into a polypeptide chain. The nascent polypeptides leave the ribosome through a tunnel in the LSU and interact with protein factors that function in enzymatic processing, targeting, and the membrane insertion of nascent chains at the exit of the ribosomal tunnel. uL3 plays a role in coordinating processes of accommodating the aminoacyl-tRNA in the PTC.1 Publication

Miscellaneous

Present with 450 molecules/cell in log phase SD medium.1 Publication

GO - Molecular functioni

  • structural constituent of ribosome Source: SGD

GO - Biological processi

  • cytoplasmic translation Source: SGD
  • ribosomal large subunit assembly Source: SGD

Keywordsi

Molecular functionRibonucleoprotein, Ribosomal protein

Enzyme and pathway databases

BioCyciYEAST:G3O-33603-MONOMER.
ReactomeiR-SCE-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-SCE-1799339. SRP-dependent cotranslational protein targeting to membrane.
R-SCE-72689. Formation of a pool of free 40S subunits.
R-SCE-72706. GTP hydrolysis and joining of the 60S ribosomal subunit.
R-SCE-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-SCE-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Names & Taxonomyi

Protein namesi
Recommended name:
60S ribosomal protein L31 Publication
Alternative name(s):
Large ribosomal subunit protein uL31 Publication
Maintenance of killer protein 8
RP1
Trichodermin resistance protein
YL1
Gene namesi
Name:RPL31 Publication
Synonyms:MAK8, TCM1
Ordered Locus Names:YOR063W
ORF Names:YOR29-14
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOR063W.
SGDiS000005589. RPL3.

Subcellular locationi

GO - Cellular componenti

  • cytosolic large ribosomal subunit Source: SGD

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

A mutant confers resistance to trichodermin, a trichotecene toxin produced by plant-pathogenic fungi.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved2 Publications
ChainiPRO_00000772512 – 38760S ribosomal protein L3Add BLAST386

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei24PhosphoserineCombined sources1
Cross-linki39Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei103PhosphothreonineCombined sources1
Cross-linki136Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei156PhosphoserineCombined sources1
Modified residuei243Pros-methylhistidine1 Publication1
Modified residuei297PhosphoserineCombined sources1

Keywords - PTMi

Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP14126.
PRIDEiP14126.

PTM databases

iPTMnetiP14126.

Interactioni

Subunit structurei

Component of the small ribosomal subunit (SSU). Mature yeast ribosomes consist of a small (40S) and a large (60S) subunit. The 40S small subunit contains 1 molecule of ribosomal RNA (18S rRNA) and 33 different proteins (encoded by 57 genes). The large 60S subunit contains 3 rRNA molecules (25S, 5.8S and 5S rRNA) and 46 different proteins (encoded by 81 genes). uL3 forms together with ES39L one of the contact sites for the signal recognition particle that targets ribosomes to the endoplasmic reticulum membrane (PubMed:9559554, PubMed:22096102).1 Publication1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
SRV2P175553EBI-15364,EBI-4024

Protein-protein interaction databases

BioGridi34462. 277 interactors.
DIPiDIP-6264N.
IntActiP14126. 109 interactors.
MINTiMINT-604187.

Structurei

Secondary structure

1387
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi14 – 16Combined sources3
Beta strandi23 – 26Combined sources4
Beta strandi37 – 39Combined sources3
Beta strandi44 – 59Combined sources16
Turni66 – 69Combined sources4
Beta strandi70 – 80Combined sources11
Beta strandi84 – 93Combined sources10
Beta strandi100 – 106Combined sources7
Helixi112 – 115Combined sources4
Helixi116 – 118Combined sources3
Turni122 – 124Combined sources3
Turni129 – 133Combined sources5
Helixi134 – 137Combined sources4
Beta strandi139 – 141Combined sources3
Helixi142 – 153Combined sources12
Beta strandi156 – 163Combined sources8
Helixi166 – 168Combined sources3
Beta strandi178 – 182Combined sources5
Beta strandi185 – 187Combined sources3
Helixi188 – 197Combined sources10
Turni198 – 200Combined sources3
Beta strandi201 – 203Combined sources3
Helixi205 – 207Combined sources3
Beta strandi214 – 220Combined sources7
Beta strandi223 – 227Combined sources5
Helixi229 – 233Combined sources5
Beta strandi246 – 248Combined sources3
Beta strandi255 – 259Combined sources5
Beta strandi268 – 271Combined sources4
Beta strandi274 – 286Combined sources13
Turni291 – 294Combined sources4
Turni297 – 299Combined sources3
Turni312 – 314Combined sources3
Beta strandi321 – 326Combined sources6
Beta strandi335 – 340Combined sources6
Turni349 – 351Combined sources3
Beta strandi356 – 359Combined sources4
Turni364 – 367Combined sources4
Helixi373 – 380Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1K5Ymodel-C8-366[»]
3J6Xelectron microscopy6.10L31-387[»]
3J6Yelectron microscopy6.10L31-387[»]
3J77electron microscopy6.20L31-387[»]
3J78electron microscopy6.30L31-387[»]
3JCTelectron microscopy3.08B1-387[»]
4U3MX-ray3.00L3/l32-387[»]
4U3NX-ray3.20L3/l32-387[»]
4U3UX-ray2.90L3/l32-387[»]
4U4NX-ray3.10L3/l32-387[»]
4U4OX-ray3.60L3/l32-387[»]
4U4QX-ray3.00L3/l32-387[»]
4U4RX-ray2.80L3/l32-387[»]
4U4UX-ray3.00L3/l32-387[»]
4U4YX-ray3.20L3/l32-387[»]
4U4ZX-ray3.10L3/l32-387[»]
4U50X-ray3.20L3/l32-387[»]
4U51X-ray3.20L3/l32-387[»]
4U52X-ray3.00L3/l32-387[»]
4U53X-ray3.30L3/l32-387[»]
4U55X-ray3.20L3/l32-387[»]
4U56X-ray3.45L3/l32-387[»]
4U6FX-ray3.10L3/l32-387[»]
4V4Belectron microscopy11.70BC2-387[»]
4V6Ielectron microscopy8.80BC1-387[»]
4V7Felectron microscopy8.70C1-387[»]
4V7RX-ray4.00BC/DC1-387[»]
4V88X-ray3.00BB/DB1-387[»]
4V8Telectron microscopy8.10B1-387[»]
4V8Yelectron microscopy4.30BB2-387[»]
4V8Zelectron microscopy6.60BB2-387[»]
4V91electron microscopy3.70B1-387[»]
5APNelectron microscopy3.91B1-387[»]
5APOelectron microscopy3.41B1-387[»]
5DATX-ray3.15L3/l32-387[»]
5DC3X-ray3.25L3/l32-387[»]
5DGEX-ray3.45L3/l32-387[»]
5DGFX-ray3.30L3/l32-387[»]
5DGVX-ray3.10L3/l32-387[»]
5FCIX-ray3.40L3/l32-387[»]
5FCJX-ray3.10L3/l32-387[»]
5FL8electron microscopy9.50B1-387[»]
5GAKelectron microscopy3.88F1-387[»]
5H4Pelectron microscopy3.07B1-387[»]
5I4LX-ray3.10L3/l32-387[»]
5JCSelectron microscopy9.50B1-387[»]
5JUOelectron microscopy4.00G1-387[»]
5JUPelectron microscopy3.50G1-387[»]
5JUSelectron microscopy4.20G1-387[»]
5JUTelectron microscopy4.00G1-387[»]
5JUUelectron microscopy4.00G1-387[»]
5LYBX-ray3.25L3/l32-387[»]
5M1Jelectron microscopy3.30B52-387[»]
5MC6electron microscopy3.80BA1-387[»]
5T62electron microscopy3.30E1-387[»]
5T6Relectron microscopy4.50E1-387[»]
5TGAX-ray3.30L3/l32-387[»]
5TGMX-ray3.50L3/l32-387[»]
ProteinModelPortaliP14126.
SMRiP14126.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP14126.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000017606.
HOGENOMiHOG000107319.
InParanoidiP14126.
KOiK02925.
OMAiVPRIRSW.
OrthoDBiEOG092C2SEF.

Family and domain databases

InterProiView protein in InterPro
IPR000597. Ribosomal_L3.
IPR019926. Ribosomal_L3_CS.
IPR009000. Transl_B-barrel.
PfamiView protein in Pfam
PF00297. Ribosomal_L3. 1 hit.
SUPFAMiSSF50447. SSF50447. 1 hit.
PROSITEiView protein in PROSITE
PS00474. RIBOSOMAL_L3. 1 hit.

Sequencei

Sequence statusi: Complete.

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

P14126-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSHRKYEAPR HGHLGFLPRK RAASIRARVK AFPKDDRSKP VALTSFLGYK
60 70 80 90 100
AGMTTIVRDL DRPGSKFHKR EVVEAVTVVD TPPVVVVGVV GYVETPRGLR
110 120 130 140 150
SLTTVWAEHL SDEVKRRFYK NWYKSKKKAF TKYSAKYAQD GAGIERELAR
160 170 180 190 200
IKKYASVVRV LVHTQIRKTP LAQKKAHLAE IQLNGGSISE KVDWAREHFE
210 220 230 240 250
KTVAVDSVFE QNEMIDAIAV TKGHGFEGVT HRWGTKKLPR KTHRGLRKVA
260 270 280 290 300
CIGAWHPAHV MWSVARAGQR GYHSRTSINH KIYRVGKGDD EANGATSFDR
310 320 330 340 350
TKKTITPMGG FVHYGEIKND FIMVKGCIPG NRKRIVTLRK SLYTNTSRKA
360 370 380
LEEVSLKWID TASKFGKGRF QTPAEKHAFM GTLKKDL
Length:387
Mass (Da):43,758
Last modified:January 23, 2007 - v4
Checksum:i986769A218E9698A
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti255W → C in AAA88732 (PubMed:6305925).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J01351 Genomic DNA. Translation: AAA88732.1.
Z74971 Genomic DNA. Translation: CAA99256.1.
Z70678 Genomic DNA. Translation: CAA94548.1.
BK006948 Genomic DNA. Translation: DAA10842.1.
PIRiS66946. R5BY4E.
RefSeqiNP_014706.1. NM_001183482.1.

Genome annotation databases

EnsemblFungiiYOR063W; YOR063W; YOR063W.
GeneIDi854229.
KEGGisce:YOR063W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J01351 Genomic DNA. Translation: AAA88732.1.
Z74971 Genomic DNA. Translation: CAA99256.1.
Z70678 Genomic DNA. Translation: CAA94548.1.
BK006948 Genomic DNA. Translation: DAA10842.1.
PIRiS66946. R5BY4E.
RefSeqiNP_014706.1. NM_001183482.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1K5Ymodel-C8-366[»]
3J6Xelectron microscopy6.10L31-387[»]
3J6Yelectron microscopy6.10L31-387[»]
3J77electron microscopy6.20L31-387[»]
3J78electron microscopy6.30L31-387[»]
3JCTelectron microscopy3.08B1-387[»]
4U3MX-ray3.00L3/l32-387[»]
4U3NX-ray3.20L3/l32-387[»]
4U3UX-ray2.90L3/l32-387[»]
4U4NX-ray3.10L3/l32-387[»]
4U4OX-ray3.60L3/l32-387[»]
4U4QX-ray3.00L3/l32-387[»]
4U4RX-ray2.80L3/l32-387[»]
4U4UX-ray3.00L3/l32-387[»]
4U4YX-ray3.20L3/l32-387[»]
4U4ZX-ray3.10L3/l32-387[»]
4U50X-ray3.20L3/l32-387[»]
4U51X-ray3.20L3/l32-387[»]
4U52X-ray3.00L3/l32-387[»]
4U53X-ray3.30L3/l32-387[»]
4U55X-ray3.20L3/l32-387[»]
4U56X-ray3.45L3/l32-387[»]
4U6FX-ray3.10L3/l32-387[»]
4V4Belectron microscopy11.70BC2-387[»]
4V6Ielectron microscopy8.80BC1-387[»]
4V7Felectron microscopy8.70C1-387[»]
4V7RX-ray4.00BC/DC1-387[»]
4V88X-ray3.00BB/DB1-387[»]
4V8Telectron microscopy8.10B1-387[»]
4V8Yelectron microscopy4.30BB2-387[»]
4V8Zelectron microscopy6.60BB2-387[»]
4V91electron microscopy3.70B1-387[»]
5APNelectron microscopy3.91B1-387[»]
5APOelectron microscopy3.41B1-387[»]
5DATX-ray3.15L3/l32-387[»]
5DC3X-ray3.25L3/l32-387[»]
5DGEX-ray3.45L3/l32-387[»]
5DGFX-ray3.30L3/l32-387[»]
5DGVX-ray3.10L3/l32-387[»]
5FCIX-ray3.40L3/l32-387[»]
5FCJX-ray3.10L3/l32-387[»]
5FL8electron microscopy9.50B1-387[»]
5GAKelectron microscopy3.88F1-387[»]
5H4Pelectron microscopy3.07B1-387[»]
5I4LX-ray3.10L3/l32-387[»]
5JCSelectron microscopy9.50B1-387[»]
5JUOelectron microscopy4.00G1-387[»]
5JUPelectron microscopy3.50G1-387[»]
5JUSelectron microscopy4.20G1-387[»]
5JUTelectron microscopy4.00G1-387[»]
5JUUelectron microscopy4.00G1-387[»]
5LYBX-ray3.25L3/l32-387[»]
5M1Jelectron microscopy3.30B52-387[»]
5MC6electron microscopy3.80BA1-387[»]
5T62electron microscopy3.30E1-387[»]
5T6Relectron microscopy4.50E1-387[»]
5TGAX-ray3.30L3/l32-387[»]
5TGMX-ray3.50L3/l32-387[»]
ProteinModelPortaliP14126.
SMRiP14126.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34462. 277 interactors.
DIPiDIP-6264N.
IntActiP14126. 109 interactors.
MINTiMINT-604187.

PTM databases

iPTMnetiP14126.

Proteomic databases

MaxQBiP14126.
PRIDEiP14126.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOR063W; YOR063W; YOR063W.
GeneIDi854229.
KEGGisce:YOR063W.

Organism-specific databases

EuPathDBiFungiDB:YOR063W.
SGDiS000005589. RPL3.

Phylogenomic databases

GeneTreeiENSGT00390000017606.
HOGENOMiHOG000107319.
InParanoidiP14126.
KOiK02925.
OMAiVPRIRSW.
OrthoDBiEOG092C2SEF.

Enzyme and pathway databases

BioCyciYEAST:G3O-33603-MONOMER.
ReactomeiR-SCE-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-SCE-1799339. SRP-dependent cotranslational protein targeting to membrane.
R-SCE-72689. Formation of a pool of free 40S subunits.
R-SCE-72706. GTP hydrolysis and joining of the 60S ribosomal subunit.
R-SCE-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-SCE-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Miscellaneous databases

EvolutionaryTraceiP14126.
PROiPR:P14126.

Family and domain databases

InterProiView protein in InterPro
IPR000597. Ribosomal_L3.
IPR019926. Ribosomal_L3_CS.
IPR009000. Transl_B-barrel.
PfamiView protein in Pfam
PF00297. Ribosomal_L3. 1 hit.
SUPFAMiSSF50447. SSF50447. 1 hit.
PROSITEiView protein in PROSITE
PS00474. RIBOSOMAL_L3. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRL3_YEAST
AccessioniPrimary (citable) accession number: P14126
Secondary accession number(s): D6W2C6, Q08459
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 23, 2007
Last modified: April 12, 2017
This is version 174 of the entry and version 4 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal 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
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

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.