AiPD: Autoinhibited Protein Database

P46781

Gene name	RPS9
Protein name	40S ribosomal protein S9
Names	Small ribosomal subunit protein uS4
Species	Homo sapiens (Human)
KEGG Pathway	hsa:6203
EC number
Protein Class

Descriptions

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

Autoinhibitory domains (AIDs)

1-57 (Predicted disordered autoinhibitory region) PR

Target domain
Relief mechanism
Assay	cis-regPred

AID

1-57 (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

95 structures for P46781

Entry ID	Method	Resolution	Chain	Position	Source
4UG0	EM	-	SJ	1-194	PDB
4V6X	EM	500 A	AJ	1-194	PDB
5A2Q	EM	390 A	J	1-194	PDB
5AJ0	EM	350 A	BJ	1-194	PDB
5FLX	EM	390 A	J	1-194	PDB
5LKS	EM	360 A	SJ	1-194	PDB
5OA3	EM	430 A	J	1-194	PDB
5T2C	EM	360 A	AL	1-194	PDB
5VYC	X-ray	600 A	J1/J2/J3/J4/J5/J6	1-194	PDB
6FEC	EM	630 A	K	7-188	PDB
6G18	EM	360 A	J	1-194	PDB
6G4S	EM	400 A	J	1-194	PDB
6G4W	EM	450 A	J	1-194	PDB
6G51	EM	410 A	J	1-194	PDB
6G53	EM	450 A	J	1-194	PDB
6G5H	EM	360 A	J	1-194	PDB
6G5I	EM	350 A	J	1-194	PDB
6IP5	EM	390 A	3I	1-194	PDB
6IP6	EM	450 A	3I	1-194	PDB
6IP8	EM	390 A	3I	1-194	PDB
6OLE	EM	310 A	SJ	2-186	PDB
6OLF	EM	390 A	SJ	2-186	PDB
6OLG	EM	340 A	BJ	2-180	PDB
6OLI	EM	350 A	SJ	2-186	PDB
6OLZ	EM	390 A	BJ	2-180	PDB
6OM0	EM	310 A	SJ	2-186	PDB
6OM7	EM	370 A	SJ	2-186	PDB
6QZP	EM	290 A	SJ	2-186	PDB
6XA1	EM	280 A	SJ	2-181	PDB
6Y0G	EM	320 A	SJ	1-194	PDB
6Y2L	EM	300 A	SJ	1-194	PDB
6Y57	EM	350 A	SJ	1-194	PDB
6YBW	EM	310 A	D	1-194	PDB
6Z6L	EM	300 A	SJ	1-194	PDB
6Z6M	EM	310 A	SJ	1-194	PDB
6Z6N	EM	290 A	SJ	1-194	PDB
6ZLW	EM	260 A	J	1-194	PDB
6ZM7	EM	270 A	SJ	1-194	PDB
6ZME	EM	300 A	SJ	1-194	PDB
6ZMI	EM	260 A	SJ	1-194	PDB
6ZMO	EM	310 A	SJ	1-194	PDB
6ZMT	EM	300 A	J	1-194	PDB
6ZMW	EM	370 A	D	1-194	PDB
6ZN5	EM	320 A	J	2-181	PDB
6ZOJ	EM	280 A	J	1-194	PDB
6ZOK	EM	280 A	J	1-194	PDB
6ZON	EM	300 A	c	1-194	PDB
6ZP4	EM	290 A	c	1-194	PDB
6ZUO	EM	310 A	J	1-194	PDB
6ZV6	EM	290 A	J	1-194	PDB
6ZVH	EM	290 A	J	2-186	PDB
6ZVJ	EM	380 A	c	2-181	PDB
6ZXD	EM	320 A	J	1-194	PDB
6ZXE	EM	300 A	J	1-194	PDB
6ZXF	EM	370 A	J	1-194	PDB
6ZXG	EM	260 A	J	1-194	PDB
6ZXH	EM	270 A	J	1-194	PDB
7A09	EM	350 A	c	1-194	PDB
7K5I	EM	290 A	J	1-194	PDB
7MQ8	EM	360 A	L9	1-194	PDB
7MQ9	EM	387 A	L9	1-194	PDB
7MQA	EM	270 A	L9	1-194	PDB
7QP6	EM	470 A	D	1-194	PDB
7QP7	EM	370 A	D	1-194	PDB
7R4X	EM	215 A	J	1-194	PDB
7TQL	EM	340 A	J	2-181	PDB
7WTS	EM	320 A	J	1-194	PDB
7WTT	EM	310 A	J	1-194	PDB
7WTU	EM	300 A	J	1-194	PDB
7WTV	EM	350 A	J	1-194	PDB
7WTW	EM	320 A	J	1-194	PDB
7WTX	EM	310 A	J	1-194	PDB
7WTZ	EM	300 A	J	1-194	PDB
7WU0	EM	330 A	J	1-194	PDB
7XNX	EM	270 A	SJ	1-194	PDB
7XNY	EM	250 A	SJ	1-194	PDB
8G5Y	EM	229 A	SJ	1-194	PDB
8G5Z	EM	264 A	SJ	2-186	PDB
8G60	EM	254 A	SJ	1-194	PDB
8G61	EM	294 A	SJ	1-194	PDB
8G6J	EM	280 A	SJ	1-194	PDB
8GLP	EM	167 A	SJ	1-194	PDB
8IFD	EM	259 A	3I	1-194	PDB
8IFE	EM	257 A	3I	1-194	PDB
8JDJ	EM	250 A	6	1-194	PDB
8JDK	EM	226 A	6	1-194	PDB
8JDL	EM	242 A	6	1-194	PDB
8JDM	EM	267 A	6	1-194	PDB
8OZ0	EM	350 A	Z	1-194	PDB
8PPK	EM	298 A	J	1-194	PDB
8PPL	EM	265 A	AJ	1-194	PDB
8T4S	EM	260 A	J	1-194	PDB
8Y0W	EM	340 A	SJ	1-194	PDB
8Y0X	EM	330 A	SJ	1-194	PDB
AF-P46781-F1	Predicted				AlphaFoldDB

114 variants for P46781

Variant ID(s)	Position	Change	Description	Diseaes Association	Provenance
CA309386548 rs780013236	4	A>S	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ExAC TOPMed gnomAD ClinGen NCI-TCGA
rs1294927878 CA407770419	4	A>V		No	TOPMed ClinGen
CA309386550 rs987673847	6	S>R		No	TOPMed ClinGen
rs1450755130 CA407770511	7	W>C		No	gnomAD ClinGen
CA407770485 rs1405760317	7	W>R		No	gnomAD ClinGen
TCGA novel	18	R>T	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1355751609 CA407770863	24	R>H		No	gnomAD ClinGen
rs928989934 CA309386573	25	L>R		No	TOPMed ClinGen
rs1001491105 CA309386574	27	Q>L		No	Ensembl ClinGen
CA407771003 rs1180659268	31	L>V		No	TOPMed ClinGen
rs771384115	32	I>=	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	NCI-TCGA
CA407771222 rs1371925089	35	Y>F		No	TOPMed ClinGen
rs1433041489 CA407771302	40	K>R		No	TOPMed ClinGen
CA309386920 rs765192871	45	R>K		No	ExAC gnomAD ClinGen
CA309386918 rs765192871	45	R>M		No	ExAC gnomAD ClinGen
rs918485306 CA309386922	46	V>I		No	TOPMed gnomAD ClinGen
rs1331805342 CA407771428	47	K>R		No	gnomAD ClinGen
TCGA novel	48	F>L	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1400527503 CA407771447	48	F>Y		No	TOPMed ClinGen
CA407771472 rs1346531635	49	T>I	Variant assessed as Somatic; impact. [NCI-TCGA]	No	TOPMed gnomAD ClinGen NCI-TCGA
TCGA novel	51	A>T	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs758488045 CA309386926	57	A>S		No	ExAC TOPMed gnomAD ClinGen
rs11544025 CA309386929	58	R>W		No	Ensembl ClinGen
rs1271083534 CA407771607	59	E>Q		No	gnomAD ClinGen
rs751577461 CA309386941	60	L>R		No	ExAC gnomAD ClinGen
CA309386943 rs781238845	63	L>V		No	ExAC gnomAD ClinGen
CA407771662 rs1568886369	64	D>H		No	Ensembl ClinGen
TCGA novel	64	D>N	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs552278556 CA309386945	66	K>R		No	ClinGen 1000Genomes ExAC gnomAD
CA407771720 rs1194484585	67	D>E		No	gnomAD ClinGen
rs1245325930 CA407771753	70	R>L		No	gnomAD ClinGen
TCGA novel	71	L>M	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1183173104 CA407771761	71	L>P		No	gnomAD ClinGen
rs755561765 CA309389571	76	A>S		No	ExAC gnomAD ClinGen
CA309389579 rs547751032	80	R>Q		No	1000Genomes ClinGen
CA309389576 rs770300853	80	R>W		No	ExAC TOPMed gnomAD ClinGen
rs377074811 CA309389581	82	V>I		No	ESP ClinGen
rs1289126782 CA407773079	83	R>C		No	TOPMed ClinGen
CA309389583 rs780838584	83	R>L		No	ExAC gnomAD ClinGen
CA407773086 rs1395546924	84	I>F		No	TOPMed gnomAD ClinGen
TCGA novel	86	V>G	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs745457807 CA309389586	87	L>M		No	ExAC gnomAD ClinGen
TCGA novel	88	D>N	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1600768957 CA407773197	92	M>L		No	Ensembl ClinGen
rs1484895413 CA407773228	94	L>Q		No	TOPMed gnomAD ClinGen
TCGA novel	98	L>M	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1269588876 CA407773337	102	I>T		No	gnomAD ClinGen
TCGA novel	103	E>Q	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs762622828 CA309389593	104	D>H		No	ExAC gnomAD ClinGen
CA309389595 rs11544035	105	F>S		No	Ensembl ClinGen
TCGA novel	107	E>D	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA407773394 rs13579	109	R>C		No	gnomAD ClinGen
rs768668988 CA309389598	109	R>H		No	ExAC gnomAD ClinGen
rs768668988 CA407773396	109	R>L		No	ExAC gnomAD ClinGen
CA309389596 rs13579	109	R>S		No	gnomAD ClinGen
rs1426081582 CA407773478	122	S>T		No	gnomAD ClinGen
rs1170252609 CA407773486	123	I>V		No	ClinGen gnomAD
rs761031429 CA309389609	127	R>C		No	ExAC TOPMed gnomAD ClinGen
rs754299712 CA309389613	128	V>M	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ExAC gnomAD ClinGen NCI-TCGA
rs779499933 CA309389621	131	R>C		No	ExAC TOPMed gnomAD ClinGen
rs1452077232 CA407773564	131	R>H		No	TOPMed ClinGen
CA309389623 rs753088540	133	R>C	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ExAC gnomAD ClinGen NCI-TCGA
CA309389626 rs756797802	133	R>H		No	ExAC TOPMed gnomAD ClinGen
TCGA novel	133	R>P	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1224877696 CA407773597	135	I>F		No	gnomAD ClinGen
VAR_036543	137	V>F	a breast cancer sample; somatic mutation [UniProt]	No	UniProt
CA407773921 rs1262241117	137	V>I		No	gnomAD ClinGen
CA309390094 rs866946296	138	R>H		No	Ensembl ClinGen
CA407773980 rs1206475241	141	V>M		No	gnomAD ClinGen
CA407774020 rs1261735656	144	I>M		No	TOPMed gnomAD ClinGen
rs765869315 CA309390100	144	I>V		No	ExAC gnomAD ClinGen
rs1481695245 CA407774026	145	P>L		No	gnomAD ClinGen
rs1451177349 CA407774042	148	I>V		No	Ensembl ClinGen
CA309390104 rs953867805	150	R>C		No	TOPMed ClinGen
CA407774056 rs549353125	150	R>H		No	1000Genomes ExAC gnomAD ClinGen
CA309390106 rs549353125	150	R>L		No	ClinGen 1000Genomes ExAC gnomAD
rs11544022 CA309390110	154	Q>R		No	Ensembl ClinGen
CA309390112 rs11544021	156	H>L		No	Ensembl ClinGen
CA407774104 rs4838	157	I>M		No	1000Genomes ESP ExAC TOPMed gnomAD ClinGen
rs374081180 CA309390114	157	I>V		No	ESP ExAC TOPMed gnomAD ClinGen
CA407774105 rs1204919937	158	D>N		No	TOPMed ClinGen
CA309390120 rs11544023	160	S>F	Variant assessed as Somatic; impact. [NCI-TCGA]	No	ClinGen Ensembl NCI-TCGA
CA407774133 rs1325824131	162	R>C		No	Ensembl ClinGen
rs1385939319 CA407774135	162	R>H		No	gnomAD ClinGen
TCGA novel	167	G>C	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1275516508 CA407774216	168	G>A		No	TOPMed ClinGen
TCGA novel	169	R>missing	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA309390127 rs770765525	169	R>C		No	Ensembl ClinGen
rs1568906846 CA407774238	170	P>L		No	Ensembl ClinGen
rs15938 CA309390131	171	G>C		No	Ensembl ClinGen
CA309390133 rs776634735	172	R>C		No	ExAC gnomAD ClinGen
rs1306161430 CA407774271	173	V>L		No	TOPMed ClinGen
rs1279844269 CA407774300	175	R>W		No	ClinGen gnomAD
rs3208871 CA309390141	177	N>T		No	Ensembl ClinGen
CA407774341 rs1409106159	178	A>S		No	TOPMed ClinGen
TCGA novel	178	A>V	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA407774360 rs1213891190	179	K>R		No	ClinGen gnomAD
rs763318299 CA309390151	181	G>V		No	ExAC gnomAD ClinGen
CA407774410 rs1802698	183	G>C		No	TOPMed ClinGen
rs916771810 CA309390156	183	G>D		No	Ensembl ClinGen
CA309390155 rs1802698	183	G>S		No	TOPMed ClinGen
CA407774467 rs1234929879	187	A>V		No	TOPMed gnomAD ClinGen
CA309390162 rs1065597	188	G>E		No	TOPMed ClinGen
rs1184408370 CA407774473	188	G>R		No	ClinGen gnomAD
CA309390170 rs142681896	190	D>E	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ESP ExAC TOPMed ClinGen NCI-TCGA
CA407774515 rs1334112497	190	D>G		No	gnomAD ClinGen
rs1439282774 CA407774506	190	D>N		No	gnomAD ClinGen
TCGA novel	190	D>Y	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs753325379 CA309390178	191	E>D	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ExAC TOPMed gnomAD ClinGen NCI-TCGA
CA309390174 rs1059792	191	E>K		No	ClinGen TOPMed
CA309390176 rs1059792	191	E>Q		No	TOPMed ClinGen
rs3206325 CA309390180	192	E>G		No	Ensembl ClinGen
CA407774569 rs754474712	193	E>D		No	ExAC TOPMed gnomAD ClinGen
CA309390182 rs1065313	193	E>G		No	Ensembl ClinGen

No associated diseases with P46781

3 regional properties for P46781

Type	Name	Position	InterPro Accession
domain	Ribosomal protein S4/S9, N-terminal	3 - 107	IPR001912
domain	RNA-binding S4 domain	108 - 179	IPR002942
conserved_site	Ribosomal protein S4, conserved site	106 - 130	IPR018079

Functions

		Description
EC Number
Subcellular Localization	Cytoplasm Nucleus, nucleolus	Localized in cytoplasmic mRNP granules containing untranslated mRNAs
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category	No pathway information available

14 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.
ribonucleoprotein complex	A macromolecular complex that contains both RNA and protein molecules.
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.
small ribosomal subunit	The smaller of the two subunits of a ribosome.
synapse	The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

4 GO annotations of molecular function

Name	Definition
RNA binding	Binding to an RNA molecule or a portion thereof.
rRNA binding	Binding to a ribosomal RNA.
structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
translation regulator activity	Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.

4 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.
positive regulation of cell population proliferation	Any process that activates or increases the rate or extent of cell proliferation.
positive regulation of translational fidelity	Any process that increases the ability of the translational apparatus to interpret the genetic code.
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.

7 homologous proteins in AiPD

UniProt AC	Gene Name	Protein Name	Species	Evidence Code
A6QLG5	RPS9	40S ribosomal protein S9	Bos taurus (Bovine)	PR
P0A7V8	rpsD	30S ribosomal protein S4	Escherichia coli (strain K12)	PR
P55935	RpS9	40S ribosomal protein S9	Drosophila melanogaster (Fruit fly)	PR
Q6ZWN5	Rps9	40S ribosomal protein S9	Mus musculus (Mouse)	PR
P29314	Rps9	40S ribosomal protein S9	Rattus norvegicus (Rat)	PR
Q20228	rps-9	40S ribosomal protein S9	Caenorhabditis elegans	PR
Q9FLF0	RPS9C	40S ribosomal protein S9-2	Arabidopsis thaliana (Mouse-ear cress)	PR

10	20	30	40	50	60
MPVARSWVCR	KTYVTPRRPF	EKSRLDQELK	LIGEYGLRNK	REVWRVKFTL	AKIRKAAREL
70	80	90	100	110	120
LTLDEKDPRR	LFEGNALLRR	LVRIGVLDEG	KMKLDYILGL	KIEDFLERRL	QTQVFKLGLA
130	140	150	160	170	180
KSIHHARVLI	RQRHIRVRKQ	VVNIPSFIVR	LDSQKHIDFS	LRSPYGGGRP	GRVKRKNAKK
190
GQGGAGAGDD	EEED