AiPD: Autoinhibited Protein Database

P62277

Gene name	RPS13
Protein name	40S ribosomal protein S13
Names	Small ribosomal subunit protein uS15
Species	Homo sapiens (Human)
KEGG Pathway	hsa:6207
EC number
Protein Class

Descriptions

The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.

Autoinhibitory domains (AIDs)

1-48 (Predicted disordered autoinhibitory region) PR

Target domain
Relief mechanism
Assay	cis-regPred

AID

1-48 (Predicted disordered autoinhibitory region)

Target domain

Relief mechanism

Assay

cis-regPred

Accessory elements

No accessory elements

References

Yeon JH et al. (2016) "Systems-wide Identification of cis-Regulatory Elements in Proteins", Cell Systems, 2, 89-100

Autoinhibited structure

Activated structure

98 structures for P62277

Entry ID	Method	Resolution	Chain	Position	Source
4UG0	EM	-	SN	1-151	PDB
4V6X	EM	500 A	AN	1-151	PDB
5A2Q	EM	390 A	N	1-151	PDB
5AJ0	EM	350 A	BN	1-151	PDB
5FLX	EM	390 A	N	1-151	PDB
5LKS	EM	360 A	SN	1-151	PDB
5OA3	EM	430 A	N	1-151	PDB
5T2C	EM	360 A	AN	1-151	PDB
5VYC	X-ray	600 A	N1/N2/N3/N4/N5/N6	1-151	PDB
6FEC	EM	630 A	Z	2-151	PDB
6G18	EM	360 A	N	1-151	PDB
6G4S	EM	400 A	N	1-151	PDB
6G4W	EM	450 A	N	1-151	PDB
6G51	EM	410 A	N	1-151	PDB
6G53	EM	450 A	N	1-151	PDB
6G5H	EM	360 A	N	1-151	PDB
6G5I	EM	350 A	N	1-151	PDB
6IP5	EM	390 A	3K	1-151	PDB
6IP6	EM	450 A	3K	1-151	PDB
6IP8	EM	390 A	3K	1-151	PDB
6OLE	EM	310 A	SN	2-151	PDB
6OLF	EM	390 A	SN	2-151	PDB
6OLG	EM	340 A	BN	2-150	PDB
6OLI	EM	350 A	SN	2-151	PDB
6OLZ	EM	390 A	BN	2-150	PDB
6OM0	EM	310 A	SN	2-151	PDB
6OM7	EM	370 A	SN	2-151	PDB
6QZP	EM	290 A	SN	2-151	PDB
6XA1	EM	280 A	SN	2-151	PDB
6Y0G	EM	320 A	SN	1-151	PDB
6Y2L	EM	300 A	SN	1-151	PDB
6Y57	EM	350 A	SN	1-151	PDB
6YBD	EM	330 A	I	1-151	PDB
6YBW	EM	310 A	I	1-151	PDB
6Z6L	EM	300 A	SN	1-151	PDB
6Z6M	EM	310 A	SN	1-151	PDB
6Z6N	EM	290 A	SN	1-151	PDB
6ZLW	EM	260 A	N	1-151	PDB
6ZM7	EM	270 A	SN	1-151	PDB
6ZME	EM	300 A	SN	1-151	PDB
6ZMI	EM	260 A	SN	1-151	PDB
6ZMO	EM	310 A	SN	1-151	PDB
6ZMT	EM	300 A	N	1-151	PDB
6ZMW	EM	370 A	I	1-151	PDB
6ZN5	EM	320 A	N	2-150	PDB
6ZOJ	EM	280 A	N	1-151	PDB
6ZOK	EM	280 A	N	1-151	PDB
6ZON	EM	300 A	m	1-151	PDB
6ZP4	EM	290 A	m	1-151	PDB
6ZUO	EM	310 A	N	1-151	PDB
6ZV6	EM	290 A	N	1-151	PDB
6ZVH	EM	290 A	N	2-151	PDB
6ZVJ	EM	380 A	m	2-150	PDB
6ZXD	EM	320 A	N	1-151	PDB
6ZXE	EM	300 A	N	1-151	PDB
6ZXF	EM	370 A	N	1-151	PDB
6ZXG	EM	260 A	N	1-151	PDB
6ZXH	EM	270 A	N	1-151	PDB
7A09	EM	350 A	m	1-151	PDB
7JQB	EM	270 A	P	1-151	PDB
7JQC	EM	330 A	P	1-151	PDB
7K5I	EM	290 A	N	1-151	PDB
7MQ8	EM	360 A	NF	1-151	PDB
7MQ9	EM	387 A	NF	1-151	PDB
7MQA	EM	270 A	NF	1-151	PDB
7QP6	EM	470 A	I	1-151	PDB
7QP7	EM	370 A	I	1-151	PDB
7R4X	EM	215 A	N	1-151	PDB
7TQL	EM	340 A	N	2-142	PDB
7WTS	EM	320 A	N	1-151	PDB
7WTT	EM	310 A	N	1-151	PDB
7WTU	EM	300 A	N	1-151	PDB
7WTV	EM	350 A	N	1-151	PDB
7WTW	EM	320 A	N	1-151	PDB
7WTX	EM	310 A	N	1-151	PDB
7WTZ	EM	300 A	N	1-151	PDB
7WU0	EM	330 A	N	1-151	PDB
7XNX	EM	270 A	SN	1-151	PDB
7XNY	EM	250 A	SN	1-151	PDB
8G5Y	EM	229 A	SN	1-151	PDB
8G5Z	EM	264 A	SN	2-151	PDB
8G60	EM	254 A	SN	1-151	PDB
8G61	EM	294 A	SN	1-151	PDB
8G6J	EM	280 A	SN	1-151	PDB
8GLP	EM	167 A	SN	1-151	PDB
8IFD	EM	259 A	3K	1-151	PDB
8IFE	EM	257 A	3K	1-151	PDB
8JDJ	EM	250 A	9	1-151	PDB
8JDK	EM	226 A	9	1-151	PDB
8JDL	EM	242 A	9	1-151	PDB
8JDM	EM	267 A	9	1-151	PDB
8OZ0	EM	350 A	V	1-151	PDB
8PPK	EM	298 A	N	1-151	PDB
8PPL	EM	265 A	AN	1-151	PDB
8T4S	EM	260 A	N	1-151	PDB
8Y0W	EM	340 A	SN	1-151	PDB
8Y0X	EM	330 A	SN	1-151	PDB
AF-P62277-F1	Predicted				AlphaFoldDB

62 variants for P62277

Variant ID(s)	Position	Change	Description	Diseaes Association	Provenance
rs772923853 CA5900330	2	G>V		No	ClinGen ExAC gnomAD
rs142912098 CA5900326	4	M>V		No	ClinGen ESP ExAC gnomAD
rs1226354096 CA379754075	6	A>T		No	ClinGen gnomAD
CA5900324 rs779432616	7	P>L		No	ClinGen ExAC gnomAD
COSM1728978 rs1324934975 CA379754067	7	P>S	Variant assessed as Somatic; 0.0 impact. liver [NCI-TCGA, Cosmic]	No	ClinGen cosmic curated NCI-TCGA gnomAD
CA5900283 rs778376279	13	Q>L		No	ClinGen ExAC TOPMed gnomAD
CA379754017 rs778376279	13	Q>R		No	ClinGen ExAC TOPMed gnomAD
rs1402086120 CA379754006	15	A>S		No	ClinGen gnomAD
rs748494500 CA379753994	17	P>S		No	ClinGen ExAC gnomAD
CA5900281 rs748494500	17	P>T		No	ClinGen ExAC gnomAD
CA5900278 rs751239686	21	S>N		No	ClinGen ExAC gnomAD
TCGA novel	25	W>*	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
TCGA novel	26	L>F	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs138459373 CA5900254	30	S>F		No	ClinGen ESP ExAC TOPMed gnomAD
CA5900251 rs755816876 COSM277116	37	I>M	Variant assessed as Somatic; 0.0 impact. large_intestine [NCI-TCGA, Cosmic]	No	ClinGen cosmic curated ExAC NCI-TCGA TOPMed gnomAD
CA5900250 rs752567885	38	Y>S		No	ClinGen ExAC gnomAD
rs763317432 CA5900248	42	K>R		No	ClinGen ExAC gnomAD
rs776948195 CA5900244	48	S>A		No	ClinGen ExAC gnomAD
rs769233177	50	I>=	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	NCI-TCGA
CA5900176 rs763234097	60	V>I		No	ClinGen ExAC gnomAD
CA379753044 rs1412673737	64	R>H	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen NCI-TCGA gnomAD
CA379753007 rs1265316997	67	T>I		No	ClinGen gnomAD
CA379752972 rs1481985886	70	K>T	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen NCI-TCGA TOPMed gnomAD
CA379752955 rs1270778701	71	I>T		No	ClinGen gnomAD
rs1223507656 CA379752900	75	L>F		No	ClinGen gnomAD
rs529137798 CA218394155	76	K>T		No	ClinGen Ensembl
CA5900174 rs150106605	78	K>R		No	ClinGen ESP ExAC TOPMed gnomAD
rs1351451134 CA379752830	82	P>S		No	ClinGen gnomAD
rs1347855704 CA379752809	85	P>R		No	ClinGen gnomAD
CA218394144 rs11550523	85	P>S		No	ClinGen gnomAD
CA379752812 rs11550523	85	P>T		No	ClinGen gnomAD
CA379752781 rs1324037191	89	Y>C		No	ClinGen TOPMed
CA379752726 rs1303854060	97	A>P		No	ClinGen TOPMed
CA379752725 rs1303854060	97	A>S		No	ClinGen TOPMed
CA5900168 rs1804354	100	K>R		No	ClinGen ESP ExAC TOPMed
CA218394125 rs1804354	100	K>T		No	ClinGen ESP ExAC TOPMed
CA5900166 rs375823183	103	E>D		No	ClinGen ESP ExAC TOPMed gnomAD
TCGA novel	103	E>Q	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1338696736 CA379752666	106	R>K		No	ClinGen gnomAD
rs1431350852 CA379752630	109	K>T		No	ClinGen TOPMed
CA5900150 rs140723889	111	A>G		No	ClinGen ESP ExAC TOPMed gnomAD
rs140723889 CA379752613	111	A>V		No	ClinGen ESP ExAC TOPMed gnomAD
CA5900149 rs773968841	114	R>C	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA gnomAD
CA5900148 rs770068384	114	R>H		No	ClinGen ExAC TOPMed gnomAD
rs781386201 CA5900146	118	I>T		No	ClinGen ExAC gnomAD
rs3200417 CA218393935	118	I>V		No	ClinGen Ensembl
CA5900145 rs755107100	120	S>T		No	ClinGen ExAC gnomAD
rs747066249 CA5900144	121	R>Q		No	ClinGen ExAC gnomAD
CA379752550 rs1422783324	121	R>W		No	ClinGen gnomAD
CA379752540 rs1304062922	122	I>T		No	ClinGen TOPMed
rs11550526 CA218393897	123	H>P		No	ClinGen Ensembl
rs1189883890 CA379752525	124	R>C		No	ClinGen gnomAD
rs1247502479 CA379752497	127	R>L		No	ClinGen TOPMed gnomAD
rs1247502479 CA379752499	127	R>Q		No	ClinGen TOPMed gnomAD
rs1252470037 CA379752488	128	Y>F		No	ClinGen gnomAD
CA5900142 rs758787169	129	Y>C		No	ClinGen ExAC gnomAD
rs1232516705 CA379752478	130	K>Q		No	ClinGen TOPMed
rs765457975 CA5900140	131	T>A		No	ClinGen ExAC gnomAD
rs757695121 CA5900139	133	R>Q		No	ClinGen ExAC TOPMed gnomAD
rs534946935 CA5900138	138	N>S		No	ClinGen 1000Genomes ExAC gnomAD
CA379752364 rs1464028574	142	E>*		No	ClinGen gnomAD
CA218393336 rs865949086	151	A>T	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen NCI-TCGA gnomAD

No associated diseases with P62277

1 regional properties for P62277

Type	Name	Position	InterPro Accession
domain	Ribosomal protein S13/S15, N-terminal	1 - 60	IPR012606

Functions

		Description
EC Number
Subcellular Localization	Cytoplasm Nucleus, nucleolus
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category	No pathway information available

12 GO annotations of cellular component

Name	Definition
cytoplasm	The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
cytosolic ribosome	A ribosome located in the cytosol.
cytosolic small ribosomal subunit	The small subunit of a ribosome located in the cytosol.
extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
focal adhesion	A cell-substrate junction that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments. In insects focal adhesion has also been referred to as hemi-adherens junction (HAJ).
membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
postsynaptic density	An electron dense network of proteins within and adjacent to the postsynaptic membrane of an asymmetric, neuron-neuron synapse. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

5 GO annotations of molecular function

Name	Definition
mRNA 5'-UTR binding	Binding to an mRNA molecule at its 5' untranslated region.
mRNA binding	Binding to messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
RNA binding	Binding to an RNA molecule or a portion thereof.
small ribosomal subunit rRNA binding	Binding to small ribosomal subunit RNA (SSU rRNA), a constituent of the small ribosomal subunit. In S. cerevisiae, this is the 18S rRNA.
structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.

3 GO annotations of biological process

Name	Definition
cytoplasmic translation	The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.
negative regulation of RNA splicing	Any process that stops, prevents, or reduces the frequency, rate or extent of RNA splicing.
translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.

1 homologous proteins in AiPD

UniProt AC	Gene Name	Protein Name	Species	Evidence Code
P05756	RPS13	40S ribosomal protein S13	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	PR

10	20	30	40	50	60
MGRMHAPGKG	LSQSALPYRR	SVPTWLKLTS	DDVKEQIYKL	AKKGLTPSQI	GVILRDSHGV
70	80	90	100	110	120
AQVRFVTGNK	ILRILKSKGL	APDLPEDLYH	LIKKAVAVRK	HLERNRKDKD	AKFRLILIES
130	140	150
RIHRLARYYK	TKRVLPPNWK	YESSTASALV	A