AiPD: Autoinhibited Protein Database

P08579

Gene name	SNRPB2
Protein name	U2 small nuclear ribonucleoprotein B''
Names	Leukocyte common antigen, L-CA, T200, U2 snRNP B''
Species	Homo sapiens (Human)
KEGG Pathway	hsa:6629
EC number
Protein Class

Descriptions

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

Autoinhibitory domains (AIDs)

72-171 (Predicted disordered autoinhibitory region) PR

Target domain
Relief mechanism
Assay	cis-regPred

AID

72-171 (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

31 structures for P08579

Entry ID	Method	Resolution	Chain	Position	Source
1A9N	X-ray	238 A	B/D	1-96	PDB
5MQF	EM	590 A	X	1-225	PDB
5O9Z	EM	450 A	1	1-225	PDB
5XJC	EM	360 A	p	1-225	PDB
5YZG	EM	410 A	p	1-225	PDB
5Z56	EM	510 A	p	1-225	PDB
5Z57	EM	650 A	p	1-225	PDB
5Z58	EM	490 A	p	1-225	PDB
6AH0	EM	570 A	p	1-225	PDB
6AHD	EM	380 A	p	1-225	PDB
6FF7	EM	450 A	X	1-225	PDB
6ICZ	EM	300 A	p	1-225	PDB
6ID0	EM	290 A	p	1-225	PDB
6ID1	EM	286 A	p	1-225	PDB
6QDV	EM	330 A	Y	3-94	PDB
6QX9	EM	328 A	2B	1-225	PDB
6Y53	EM	710 A	b	1-225	PDB
6Y5Q	EM	710 A	b	1-225	PDB
7A5P	EM	500 A	X	1-225	PDB
7ABG	EM	780 A	B	1-225	PDB
7ABI	EM	800 A	B	1-225	PDB
7EVO	EM	250 A	G	1-225	PDB
7VPX	EM	300 A	G	1-225	PDB
7W59	EM	360 A	p	1-225	PDB
7W5A	EM	360 A	p	1-225	PDB
7W5B	EM	430 A	p	1-225	PDB
8C6J	EM	280 A	Y	1-225	PDB
8CH6	EM	590 A	s	1-225	PDB
8HK1	EM	270 A	G	1-225	PDB
8QO9	EM	529 A	2B	1-225	PDB
AF-P08579-F1	Predicted				AlphaFoldDB

119 variants for P08579

Variant ID(s)	Position	Change	Description	Diseaes Association	Provenance
TCGA novel	2	D>N	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA9771048 rs756678488	3	I>V		No	ClinGen ExAC TOPMed gnomAD
rs780379983 CA9771049	4	R>S		No	ClinGen ExAC gnomAD
rs550195499 CA312227651	5	P>L		No	ClinGen 1000Genomes
rs749672995 CA9771050	6	N>D		No	ClinGen ExAC gnomAD
CA408310972 rs1440365305	7	H>Q		No	ClinGen gnomAD
rs1287802668 CA408310978	8	T>I		No	ClinGen gnomAD
rs1287802668 CA408310976	8	T>K		No	ClinGen gnomAD
rs769071088 CA9771051	9	I>V		No	ClinGen ExAC gnomAD
CA312227654 rs892030383	10	Y>C		No	ClinGen TOPMed gnomAD
CA408310988 rs892030383	10	Y>S		No	ClinGen TOPMed gnomAD
rs939073941 CA312227659	12	N>S		No	ClinGen Ensembl
CA408311019 rs1333831606	14	M>R		No	ClinGen gnomAD
CA9771053 rs747858296	15	N>D		No	ClinGen ExAC TOPMed gnomAD
CA9771054 rs138493707	17	K>R		No	ClinGen ESP ExAC gnomAD
VAR_035487	19	K>Q	a colorectal cancer sample; somatic mutation [UniProt]	No	UniProt
CA312227678 COSM4141340 rs6111264	22	E>K	ovary [Cosmic]	No	ClinGen cosmic curated TOPMed
CA408311076 rs6111264	22	E>Q		No	ClinGen TOPMed
rs1194521885 CA408311097	23	L>*		No	ClinGen gnomAD
CA9771071 rs748490519	26	S>T		No	ClinGen ExAC gnomAD
TCGA novel	27	L>I	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs564815966 CA312228162	27	L>P		No	ClinGen 1000Genomes gnomAD
CA9771074 rs746541036	36	H>N		No	ClinGen ExAC gnomAD
rs146906743 CA9771075	36	H>R		No	ClinGen ESP ExAC TOPMed gnomAD
CA9771077 rs757434273	38	V>A	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA TOPMed gnomAD
CA408311211 rs1227350186	40	I>T		No	ClinGen gnomAD
rs200193714 CA312228200	41	V>E		No	ClinGen 1000Genomes
rs1485916042 CA408311251	46	M>I		No	ClinGen gnomAD
CA312228208 rs907418701	46	M>V		No	ClinGen TOPMed gnomAD
CA408311267 rs1206186045	48	M>T		No	ClinGen gnomAD
rs1048573148 CA312228245	49	R>K		No	ClinGen TOPMed gnomAD
TCGA novel	51	Q>H	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1439238892 CA408311291	52	A>T		No	ClinGen TOPMed
rs1555817698 CA9771082	55	I>M		No	ClinGen Ensembl
rs767798003 CA9771084	57	K>E		No	ClinGen ExAC gnomAD
rs773244742 CA408311340	59	L>V		No	ClinGen ExAC gnomAD
CA9771086 rs760943329	61	S>L	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA gnomAD
CA408311363 rs1377086435	63	T>A		No	ClinGen gnomAD
rs1454397307 CA408311370	64	N>Y		No	ClinGen gnomAD
CA312228284 rs888630608	70	Q>*		No	ClinGen Ensembl
CA408311455 rs1326326275 COSM1024761	76	G>D	Variant assessed as Somatic; 0.0 impact. endometrium [NCI-TCGA, Cosmic]	No	ClinGen cosmic curated NCI-TCGA gnomAD
rs1490927374 CA408311453	76	G>R		No	ClinGen TOPMed
CA408311463 rs1293494985	77	K>I		No	ClinGen TOPMed
CA9771090 rs139323338	79	M>V		No	ClinGen ESP ExAC TOPMed gnomAD
rs765852324 CA9771108	80	R>*		No	ClinGen ExAC gnomAD
rs753187978 CA9771109	80	R>Q		No	ClinGen ExAC gnomAD
rs1481078123 CA408312459	83	Y>C		No	ClinGen gnomAD
rs1249635444 CA408312466	84	A>T		No	ClinGen gnomAD
CA408312510 rs1308465688	86	T>R		No	ClinGen TOPMed
CA9771113 rs756892682	88	S>L	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA gnomAD
TCGA novel	89	D>A	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1370082966 CA408312600	91	I>M		No	ClinGen TOPMed
CA312232489 rs868508953	91	I>V		No	ClinGen Ensembl
CA9771116 rs755558697	94	M>V		No	ClinGen ExAC
CA9771118 rs377685264	95	R>C		No	ClinGen ESP ExAC gnomAD
rs377685264 CA9771117	95	R>G		No	ClinGen ESP ExAC gnomAD
CA9771119 rs768613886	95	R>H		No	ClinGen ExAC TOPMed gnomAD
rs756378077 CA9771120	96	G>D*		No	ClinGen ExAC
CA9771122 rs747933050	99	A>G		No	ClinGen ExAC gnomAD
CA408312692 rs1463193280	99	A>T		No	ClinGen gnomAD
CA408312697 rs1349309885	100	D>N		No	ClinGen gnomAD
CA408312722 rs1288488834	103	K>E		No	ClinGen TOPMed
TCGA novel	106	E>*	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs865801799 CA312232560	106	E>K		No	ClinGen Ensembl
TCGA novel	106	E>R	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs776935953 CA9771125	107	K>R		No	ClinGen ExAC gnomAD
rs1227114666 CA408312760	108	K>E		No	ClinGen gnomAD
TCGA novel	110	A>P	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA408312775 rs1312457795	110	A>S		No	ClinGen gnomAD
rs957693215 CA312232571	111	K>R		No	ClinGen TOPMed
CA9771128 rs781579916	113	V>M		No	ClinGen ExAC TOPMed gnomAD
rs1482870427 CA408312808	115	Q>*		No	ClinGen gnomAD
rs1454234729 CA408312823	117	A>T		No	ClinGen TOPMed
CA9771129 rs775689768	117	A>V		No	ClinGen ExAC gnomAD
CA9771130 rs763411300	118	T>A		No	ClinGen ExAC TOPMed gnomAD
rs764622835 CA9771131	119	T>I		No	ClinGen ExAC gnomAD
rs1181275593 CA408312843	121	N>D		No	ClinGen TOPMed gnomAD
rs1419946069 CA408312867	124	P>A		No	ClinGen gnomAD
rs1434111312 CA408312871	124	P>L		No	ClinGen TOPMed
rs751894701 CA408312879	125	G>A		No	ClinGen ExAC TOPMed gnomAD
CA9771132 rs751894701	125	G>V		No	ClinGen ExAC TOPMed gnomAD
rs1434967377 CA408312887	126	Q>R		No	ClinGen gnomAD
rs770109949 CA9771148	127	G>R		No	ClinGen ExAC gnomAD
CA408313350 rs1346258356	128	T>P		No	ClinGen gnomAD
rs1332205689 CA408313396	135	Q>*		No	ClinGen Ensembl
CA408313402 rs763041649	135	Q>H		No	ClinGen ExAC TOPMed gnomAD
CA408313428 rs1441897373	139	T>I		No	ClinGen gnomAD
rs769059926 CA9771151	142	P>A		No	ClinGen ExAC gnomAD
rs774858280 CA9771152	142	P>L		No	ClinGen ExAC gnomAD
rs1375697919 CA408313472	144	V>A		No	ClinGen gnomAD
TCGA novel	144	V>F	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA9771169 rs1555818566	145	P>A		No	ClinGen Ensembl
rs1226477962 CA408313483	146	D>V		No	ClinGen TOPMed gnomAD
CA408313508 rs1413695757	150	N>Y		No	ClinGen TOPMed
rs143329029 CA9771171	151	Y>C		No	ClinGen ESP ExAC TOPMed gnomAD
CA408313525 rs1335427089	152	I>T		No	ClinGen gnomAD
CA408313608 rs1234100519	164	E>K		No	ClinGen gnomAD
rs1411817766 CA408313661	171	F>I		No	ClinGen gnomAD
CA408313667 rs1183826435	171	F>L		No	ClinGen TOPMed
rs1299570230 CA408313730	178	K>R		No	ClinGen gnomAD
TCGA novel	181	R>C	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1280407960 CA408313750	181	R>H		No	ClinGen gnomAD
rs1381650776 CA408313763	183	V>G		No	ClinGen TOPMed
rs372236210 CA312188877	189	I>V		No	ClinGen ESP TOPMed gnomAD
rs1568755850 CA408313855	196	N>H		No	ClinGen Ensembl
rs1454189462 CA408313861	196	N>T		No	ClinGen TOPMed
CA9771207 rs764757509	197	D>H		No	ClinGen ExAC gnomAD
rs375598794 CA408313926	201	G>*		No	ClinGen ESP ExAC gnomAD
rs375598794 CA9771208	201	G>R		No	ClinGen ESP ExAC gnomAD
rs751616704 CA9771211	208	Q>*		No	ClinGen ExAC gnomAD
rs1467681562 CA408314069	211	K>R		No	ClinGen gnomAD
TCGA novel	212	I>T	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA408314080 rs1170924591	212	I>V		No	ClinGen gnomAD
CA9771212 rs757251293	214	P>L		No	ClinGen ExAC TOPMed gnomAD
TCGA novel	216	H>M	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA9771214 rs750149251	216	H>R		No	ClinGen ExAC gnomAD
rs1460464097 CA408314189	220	I>V		No	ClinGen TOPMed
rs1374698100 CA408314222	222	Y>C		No	ClinGen TOPMed
CA408314250 rs1170950913	224	K>R		No	ClinGen TOPMed

No associated diseases with P08579

No regional properties for P08579

Type	Name	Position	InterPro Accession
No domain, repeats, and functional sites for P08579

Functions

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

11 GO annotations of cellular component

Name	Definition
catalytic step 2 spliceosome	A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
cytoplasmic ribonucleoprotein granule	A ribonucleoprotein granule located in the cytoplasm.
fibrillar center	A structure found most metazoan nucleoli, but not usually found in lower eukaryotes; surrounded by the dense fibrillar component; the zone of transcription from multiple copies of the pre-rRNA genes is in the border region between these two structures.
nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
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.
spliceosomal complex	Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.
U1 snRNP	A ribonucleoprotein complex that contains small nuclear RNA U1, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U1 snRNP, most of which remain associated with the U1 snRNA both while the U1 snRNP is free or assembled into a series of spliceosomal complexes.
U2 snRNP	A ribonucleoprotein complex that contains small nuclear RNA U2, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U2 snRNP, most of which remain associated with the U2 snRNA both while the U2 snRNP is free or assembled into a series of spliceosomal complexes.
U2-type catalytic step 2 spliceosome	A spliceosomal complex that contains the U2, U5 and U6 snRNPs bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the U2, U5 and U6 snRNPs.
U2-type precatalytic spliceosome	A spliceosomal complex that is formed by the recruitment of the preassembled U4/U6.U5 tri-snRNP to the prespliceosome. Although all 5 snRNPs are present, the precatalytic spliceosome is catalytically inactive. The precatalytic spliceosome includes many proteins in addition to those found in the U1, U2 and U4/U6.U5 snRNPs.

1 GO annotations of molecular function

Name	Definition
U1 snRNA binding	Binding to a U1 small nuclear RNA (U1 snRNA).

2 GO annotations of biological process

Name	Definition
mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
U2-type prespliceosome assembly	The aggregation, arrangement and bonding together of a set of components to form an U2-type prespliceosome.

2 homologous proteins in AiPD

UniProt AC	Gene Name	Protein Name	Species	Evidence Code
P09012	SNRPA	U1 small nuclear ribonucleoprotein A	Homo sapiens (Human)	PR
Q6ZRY4	RBPMS2	RNA-binding protein with multiple splicing 2	Homo sapiens (Human)	PR

10	20	30	40	50	60
MDIRPNHTIY	INNMNDKIKK	EELKRSLYAL	FSQFGHVVDI	VALKTMKMRG	QAFVIFKELG
70	80	90	100	110	120
SSTNALRQLQ	GFPFYGKPMR	IQYAKTDSDI	ISKMRGTFAD	KEKKKEKKKA	KTVEQTATTT
130	140	150	160	170	180
NKKPGQGTPN	SANTQGNSTP	NPQVPDYPPN	YILFLNNLPE	ETNEMMLSML	FNQFPGFKEV
190	200	210	220
RLVPGRHDIA	FVEFENDGQA	GAARDALQGF	KITPSHAMKI	TYAKK