AiPD: Autoinhibited Protein Database

Q9BYD1

Gene name	MRPL13
Protein name	39S ribosomal protein L13, mitochondrial
Names	L13mt, MRP-L13, Mitochondrial large ribosomal subunit protein uL13m
Species	Homo sapiens (Human)
KEGG Pathway	hsa:28998
EC number
Protein Class

Descriptions

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

Autoinhibitory domains (AIDs)

112-178 (Predicted disordered autoinhibitory region) PR

Target domain
Relief mechanism
Assay	cis-regPred

AID

112-178 (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

61 structures for Q9BYD1

Entry ID	Method	Resolution	Chain	Position	Source
3J7Y	EM	340 A	K	1-178	PDB
3J9M	EM	350 A	K	1-178	PDB
5OOL	EM	306 A	K	1-178	PDB
5OOM	EM	303 A	K	1-178	PDB
6I9R	EM	390 A	K	1-178	PDB
6NU2	EM	390 A	K	2-178	PDB
6NU3	EM	440 A	K	1-178	PDB
6VLZ	EM	297 A	K	1-178	PDB
6VMI	EM	296 A	K	1-178	PDB
6ZM5	EM	289 A	K	2-178	PDB
6ZM6	EM	259 A	K	2-178	PDB
6ZS9	EM	400 A	XK	1-178	PDB
6ZSA	EM	400 A	XK	1-178	PDB
6ZSB	EM	450 A	XK	1-178	PDB
6ZSC	EM	350 A	XK	1-178	PDB
6ZSD	EM	370 A	XK	1-178	PDB
6ZSE	EM	500 A	XK	1-178	PDB
6ZSG	EM	400 A	XK	1-178	PDB
7A5F	EM	440 A	K3	1-178	PDB
7A5G	EM	433 A	K3	1-178	PDB
7A5H	EM	330 A	K	1-178	PDB
7A5I	EM	370 A	K3	1-178	PDB
7A5J	EM	310 A	K	1-178	PDB
7A5K	EM	370 A	K3	1-178	PDB
7L08	EM	349 A	K	1-178	PDB
7L20	EM	315 A	K	1-178	PDB
7O9K	EM	310 A	K	1-178	PDB
7O9M	EM	250 A	K	1-178	PDB
7ODR	EM	290 A	K	1-178	PDB
7ODS	EM	310 A	K	1-178	PDB
7ODT	EM	310 A	K	1-178	PDB
7OF0	EM	220 A	K	1-178	PDB
7OF2	EM	270 A	K	1-178	PDB
7OF3	EM	270 A	K	1-178	PDB
7OF4	EM	270 A	K	1-178	PDB
7OF5	EM	290 A	K	1-178	PDB
7OF6	EM	260 A	K	1-178	PDB
7OF7	EM	250 A	K	1-178	PDB
7OG4	EM	380 A	XK	1-178	PDB
7OI6	EM	570 A	K	1-178	PDB
7OI7	EM	350 A	K	1-178	PDB
7OI8	EM	350 A	K	1-178	PDB
7OI9	EM	330 A	K	1-178	PDB
7OIA	EM	320 A	K	1-178	PDB
7OIB	EM	330 A	K	1-178	PDB
7OIC	EM	310 A	K	1-178	PDB
7OID	EM	370 A	K	1-178	PDB
7OIE	EM	350 A	K	1-178	PDB
7PD3	EM	340 A	K	1-178	PDB
7PO4	EM	256 A	K	2-178	PDB
7QH6	EM	308 A	K	1-178	PDB
7QH7	EM	289 A	K	2-178	PDB
7QI4	EM	221 A	K	1-178	PDB
7QI5	EM	263 A	K	1-178	PDB
7QI6	EM	298 A	K	1-178	PDB
8ANY	EM	285 A	K	1-178	PDB
8OIR	EM	310 A	BR	1-178	PDB
8OIT	EM	290 A	BR	1-178	PDB
8PK0	EM	303 A	K	1-178	PDB
8QSJ	EM	300 A	K	1-178	PDB
AF-Q9BYD1-F1	Predicted				AlphaFoldDB

141 variants for Q9BYD1

Variant ID(s)	Position	Change	Description	Diseaes Association	Provenance
rs368733531 CA4860479	2	S>L		No	ClinGen ESP ExAC TOPMed gnomAD
CA4860478 rs763443203	3	S>G		No	ClinGen ExAC TOPMed gnomAD
rs763443203 CA4860477	3	S>R		No	ClinGen ExAC TOPMed gnomAD
rs937859308 CA184414166	5	S>C		No	ClinGen TOPMed gnomAD
CA372086512 rs937859308	5	S>F		No	ClinGen TOPMed gnomAD
CA372086514 rs1210679938	5	S>P		No	ClinGen TOPMed
rs765510557 CA4860475	6	R>G		No	ClinGen ExAC gnomAD
CA372086502 rs1423634054	7	A>E		No	ClinGen gnomAD
rs759465650 CA4860474	7	A>S		No	ClinGen ExAC TOPMed gnomAD
CA4860472 rs770939801	8	P>R		No	ClinGen ExAC gnomAD
rs1159805809 COSM603956 CA372086497	8	P>S	lung Variant assessed as Somatic; 0.0 impact. [Cosmic, NCI-TCGA]	No	ClinGen cosmic curated NCI-TCGA gnomAD
rs773318401 CA372086489	9	Q>H		No	ClinGen ExAC TOPMed gnomAD
rs746918589 CA4860471	9	Q>R		No	ClinGen ExAC TOPMed gnomAD
rs1586930563 CA371904042	10	Q>K		No	ClinGen Ensembl
CA4860433 rs748910343	11	W>L		No	ClinGen ExAC gnomAD
rs367890575 CA184412536	15	A>G		No	ClinGen ESP TOPMed gnomAD
rs769281823 CA4860431	15	A>S		No	ClinGen ExAC gnomAD
CA4860430 rs373743772	16	R>G		No	ClinGen ESP ExAC TOPMed gnomAD
CA4860429 rs778072725	16	R>I		No	ClinGen ExAC gnomAD
CA4860428 rs758975894	17	I>M		No	ClinGen ExAC
rs1202302790 CA371903883	18	W>L		No	ClinGen gnomAD
CA4860427 rs532931304	19	Y>C		No	ClinGen 1000Genomes ExAC gnomAD
CA371903846 rs1274186117	20	L>V		No	ClinGen gnomAD
rs1195521824 CA371903812	22	D>N		No	ClinGen gnomAD
rs779310705 CA371903779	23	G>A		No	ClinGen ExAC TOPMed gnomAD
CA4860426 rs779310705	23	G>E		No	ClinGen ExAC TOPMed gnomAD
CA4860425 rs202202802	26	Q>*		No	ClinGen 1000Genomes ExAC gnomAD
TCGA novel	27	P>L	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs370236025 CA4860424	28	P>S		No	ClinGen ESP ExAC gnomAD
rs766762299 CA4860423	30	K>E		No	ClinGen ExAC TOPMed gnomAD
rs1314355751 CA371903634	30	K>N		No	ClinGen TOPMed gnomAD
rs376460038 CA4860422	32	A>D		No	ClinGen ESP ExAC TOPMed gnomAD
CA4860421 rs750564947	34	M>I		No	ClinGen ExAC gnomAD
CA4860418 rs774195780	37	I>M		No	ClinGen ExAC TOPMed gnomAD
CA4860419 rs145547223	37	I>V	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ESP ExAC NCI-TCGA TOPMed gnomAD
rs1165669863 CA371903494	39	L>P		No	ClinGen gnomAD
CA4860417 rs768495585	43	H>R		No	ClinGen ExAC gnomAD
CA4860416 rs762795483	45	P>A		No	ClinGen ExAC TOPMed gnomAD
rs1563778952 CA371903405	47	Y>C		No	ClinGen Ensembl
rs775064449 CA4860415	50	L>V		No	ClinGen ExAC gnomAD
rs1170746344 CA371901132	51	S>N		No	ClinGen TOPMed
CA371901096 rs1200553295	52	D>E		No	ClinGen gnomAD
rs759165600 CA184404202	53	C>F		No	ClinGen ExAC gnomAD
rs1490413959 CA371901091	53	C>R		No	ClinGen gnomAD
CA4860395 rs759165600	53	C>Y		No	ClinGen ExAC gnomAD
CA184404190 rs897751245	56	H>R		No	ClinGen TOPMed
CA4860394 rs776183110	56	H>Y		No	ClinGen ExAC gnomAD
CA184404182 rs770466745	57	V>F		No	ClinGen ExAC TOPMed gnomAD
rs770466745 CA4860393	57	V>I		No	ClinGen ExAC TOPMed gnomAD
CA4860392 rs746556207	59	I>L		No	ClinGen ExAC TOPMed
CA371900939 rs1416244394	59	I>M		No	ClinGen gnomAD
CA4860391 rs774860506	59	I>T		No	ClinGen ExAC TOPMed gnomAD
CA184404175 rs746556207	59	I>V		No	ClinGen ExAC TOPMed
rs769320456 CA4860390	60	M>T		No	ClinGen ExAC gnomAD
rs908856781 CA184404164	62	T>I		No	ClinGen Ensembl
rs372618286 CA4860388	65	I>V		No	ClinGen ESP ExAC TOPMed gnomAD
CA371900879 rs1291994900	68	S>F		No	ClinGen gnomAD
rs1433031555 CA371900864	70	N>K		No	ClinGen gnomAD
rs746099133 CA371900848	72	W>*		No	ClinGen ExAC TOPMed gnomAD
CA4860386 rs746099133	72	W>C		No	ClinGen ExAC TOPMed gnomAD
rs1456146839 CA371900846	73	E>K		No	ClinGen gnomAD
CA4860385 rs149721671	74	Q>H		No	ClinGen ESP ExAC TOPMed gnomAD
CA371900838 rs1177621550	74	Q>K		No	ClinGen gnomAD
rs759002067 CA184404141	76	V>I		No	ClinGen Ensembl
CA371900812 rs368775668	77	Y>*	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ESP ExAC NCI-TCGA TOPMed gnomAD
rs1189076442 COSM1454576 CA371900805	78	S>F	Variant assessed as Somatic; 0.0 impact. large_intestine [NCI-TCGA, Cosmic]	No	ClinGen cosmic curated NCI-TCGA gnomAD
CA4860383 rs377312788	79	S>L		No	ClinGen ESP ExAC TOPMed gnomAD
rs1042034478 CA184404106	80	H>R		No	ClinGen TOPMed
CA371908254 rs1447124474	83	Y>C		No	ClinGen gnomAD
rs984756614 CA184428645	84	P>A		No	ClinGen TOPMed
rs770269380 CA4860370	84	P>Q		No	ClinGen ExAC gnomAD
TCGA novel	84	P>R	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA371908246 rs1333989218	85	G>S		No	ClinGen TOPMed
CA184428639 rs61753788	86	G>A		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
rs61753788 CA4860369	86	G>E		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
CA371908240 rs1204198869	86	G>R		No	ClinGen gnomAD
rs757449945 CA4860367	87	F>L		No	ClinGen ExAC gnomAD
rs1308319574 CA371908218	89	Q>R		No	ClinGen gnomAD
rs961914579 CA184428583	90	V>I		No	ClinGen gnomAD
CA184428560 rs750610879	93	A>S		No	ClinGen ExAC TOPMed gnomAD
CA4860366 rs750610879	93	A>T		No	ClinGen ExAC TOPMed gnomAD
rs777807679 CA4860365	94	Q>R		No	ClinGen ExAC TOPMed gnomAD
rs1377528807 CA371908143	101	V>E		No	ClinGen TOPMed gnomAD
CA184424800 rs998004251	103	I>F		No	ClinGen Ensembl
rs766832666 CA4860338	103	I>T		No	ClinGen ExAC gnomAD
TCGA novel	106	L>T	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs965329281 CA184424769	111	M>I		No	ClinGen gnomAD
CA371907530 rs1209384992	116	L>F		No	ClinGen gnomAD
CA4860337 rs372015707	118	R>K		No	ClinGen ESP ExAC TOPMed gnomAD
CA4860336 rs751147932	121	M>K		No	ClinGen ExAC gnomAD
rs1240419119 CA371907486	121	M>V		No	ClinGen TOPMed gnomAD
rs765724004 CA4860335	122	M>V		No	ClinGen ExAC gnomAD
CA4860334 CA371907427 rs759937576	124	R>S		No	ClinGen ExAC TOPMed gnomAD
CA184424722 rs999147181	126	H>P		No	ClinGen TOPMed
rs999147181 CA371907398	126	H>R		No	ClinGen TOPMed
rs1323806946 CA371907385	127	L>P		No	ClinGen gnomAD
CA4860332 rs771195899	128	F>L		No	ClinGen ExAC gnomAD
TCGA novel	132	Y>C	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA371906631 rs751305288	132	Y>D		No	ClinGen ExAC gnomAD
CA4860316 rs751305288	132	Y>N		No	ClinGen ExAC gnomAD
rs145317361 CA4860315	134	P>T		No	ClinGen ESP ExAC TOPMed gnomAD
rs375407917 CA4860313	137	I>T		No	ClinGen ESP ExAC TOPMed gnomAD
rs140699456 CA4860314	137	I>V		No	ClinGen ESP ExAC TOPMed gnomAD
rs1470862097 CA371906529	139	K>N		No	ClinGen gnomAD
CA371906515 rs1402669644	140	N>I		No	ClinGen gnomAD
CA184421151 rs930269932	142	V>A	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen NCI-TCGA TOPMed gnomAD
CA371906495 rs1460282498	142	V>I		No	ClinGen TOPMed
rs1477165079 CA371906447	145	L>F		No	ClinGen gnomAD
rs1239384566 CA371906422	147	Q>*		No	ClinGen TOPMed
COSM3432088 rs757521875 CA4860312	149	R>*	Variant assessed as Somatic; 0.0 impact. large_intestine [NCI-TCGA, Cosmic]	No	ClinGen cosmic curated ExAC NCI-TCGA TOPMed gnomAD
CA4860311 rs367814802	149	R>Q		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
rs773595776 CA4860310	152	P>L		No	ClinGen ExAC TOPMed gnomAD
rs767921915 CA4860309	154	R>C		No	ClinGen ExAC TOPMed gnomAD
CA4860308 rs748961366	154	R>H		No	ClinGen ExAC TOPMed gnomAD
rs767921915 CA371906357	154	R>S		No	ClinGen ExAC TOPMed gnomAD
CA371906338 rs1469145195	156	D>N		No	ClinGen TOPMed
CA371906323 rs1342509556	157	E>K		No	ClinGen gnomAD
CA371906305 rs1331941394	158	Y>H	Variant assessed as Somatic; impact. [NCI-TCGA]	No	ClinGen NCI-TCGA TOPMed
rs1430202135 CA371906277	160	Q>*		No	ClinGen gnomAD
rs774705230 CA4860307	160	Q>R		No	ClinGen ExAC TOPMed gnomAD
CA371906219 rs1294706401	163	I>T		No	ClinGen gnomAD
rs142198818 CA4860306	163	I>V		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
CA371906198 rs1340922650	165	A>S		No	ClinGen gnomAD
rs1340922650 CA371906196	165	A>T	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen NCI-TCGA gnomAD
CA371906159 rs1333279755	168	R>G		No	ClinGen gnomAD
CA184421041 rs1049493201	170	W>*		No	ClinGen Ensembl
CA4860301 rs781110831	172	P>L	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA TOPMed gnomAD
rs781110831 CA371906097	172	P>R		No	ClinGen ExAC TOPMed gnomAD
rs745611473 CA4860302	172	P>S	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA gnomAD
rs1052048791 CA184407465	173	P>R		No	ClinGen Ensembl
CA371904205 rs1289123712	173	P>T		No	ClinGen gnomAD
rs141879192 CA4860274	174	E>K		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
rs141879192 CA371904201	174	E>Q		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
rs368686814 CA4860273	175	D>H		No	ClinGen ESP ExAC gnomAD
rs368686814 CA371904194	175	D>N		No	ClinGen ESP ExAC gnomAD
rs771785157 CA4860272	176	Y>C		No	ClinGen ExAC gnomAD
TCGA novel	176	Y>H	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA4860271 rs747559903	177	R>Q		No	ClinGen ExAC TOPMed gnomAD
rs375407538 CA184407451	177	R>W		No	ClinGen ESP gnomAD
CA4860268 rs751198248	179	L>=		No	ClinGen ExAC TOPMed gnomAD
rs754552388 CA4860269	179	L>Q		No	ClinGen ExAC TOPMed gnomAD

No associated diseases with Q9BYD1

1 regional properties for Q9BYD1

Type	Name	Position	InterPro Accession
conserved_site	Ribosomal protein L13, conserved site	108 - 130	IPR023563

Functions

		Description
EC Number
Subcellular Localization	Mitochondrion
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category	No pathway information available

5 GO annotations of cellular component

Name	Definition
mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
mitochondrial large ribosomal subunit	The larger of the two subunits of a mitochondrial ribosome. Two sites on the ribosomal large subunit are involved in translation: the aminoacyl site (A site) and peptidyl site (P site).
mitochondrial ribosome	A ribosome found in the mitochondrion of a eukaryotic cell; contains a characteristic set of proteins distinct from those of cytosolic ribosomes.
mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
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.

3 GO annotations of molecular function

Name	Definition
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.
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
mitochondrial translation	The chemical reactions and pathways resulting in the formation of a protein in a mitochondrion. 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; the mitochondrion has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code.
negative regulation of translation	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
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
Q3SYS1	MRPL13	39S ribosomal protein L13, mitochondrial	Bos taurus (Bovine)	PR

10	20	30	40	50	60
MSSFSRAPQQ	WATFARIWYL	LDGKMQPPGK	LAAMASIRLQ	GLHKPVYHAL	SDCGDHVVIM
70	80	90	100	110	120
NTRHIAFSGN	KWEQKVYSSH	TGYPGGFRQV	TAAQLHLRDP	VAIVKLAIYG	MLPKNLHRRT
130	140	150	160	170
MMERLHLFPD	EYIPEDILKN	LVEELPQPRK	IPKRLDEYTQ	EEIDAFPRLW	TPPEDYRL