P09012 (SNRPA_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
U1 small nuclear ribonucleoprotein A
Short name=U1 snRNP A
Short name=U1-A
Short name=U1A

Gene names

Name:

SNRPA

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	282 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro. Ref.5
Subunit structure	Belongs to the spliceosome where it is associated with snRNP U1. Interacts with SFPQ. Also component of a snRNP-free complex with SFPQ. Ref.5
Subcellular location	Nucleus.
Sequence similarities	Belongs to the RRM U1 A/B'' family. Contains 2 RRM (RNA recognition motif) domains.

Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Nucleus Spliceosome
Domain	Repeat
Ligand	RNA-binding
Molecular function	Ribonucleoprotein
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	nuclear mRNA splicing, via spliceosome Inferred by curator. Source: HGNC
Cellular component	nucleoplasm Traceable author statement. Source: Reactome spliceosomal complex Inferred from direct assay. Source: HGNC
Molecular function	RNA binding Inferred from direct assay Ref.9. Source: UniProtKB nucleotide binding Inferred from electronic annotation. Source: InterPro protein binding Inferred from physical interaction Ref.5. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
SFPQ	P23246	4	EBI-607085,EBI-355453

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.4

Chain

2 – 282

281

U1 small nuclear ribonucleoprotein A

PRO_0000081887

Regions

Domain

10 – 89

80

RRM 1

Domain

208 – 282

75

RRM 2

Compositional bias

140 – 206

67

Pro-rich

Amino acid modifications

Modified residue

2

1

N-acetylalanine Ref.4 Ref.7

Modified residue

60

1

N6-acetyllysine Ref.8

Modified residue

131

1

Phosphothreonine Ref.6

Experimental info

Mutagenesis

11

1

T → V: Abolishes RNA binding.

Mutagenesis

13

1

Y → F: Substantially reduces RNA binding.

Mutagenesis

15

1

N → V: Abolishes RNA binding.

Mutagenesis

16

1

N → V: Substantially reduces RNA binding.

Mutagenesis

52

1

R → Q: Abolishes RNA binding.

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

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.

.

282

Helix Strand Turn

Details...

Beta strand

10 – 16

7

Helix

23 – 34

12

Helix

35 – 37

3

Beta strand

40 – 45

6

Turn

49 – 53

5

Beta strand

55 – 61

7

Helix

62 – 71

10

Beta strand

83 – 86

4

Helix

92 – 95

4

Beta strand

208 – 213

6

Helix

221 – 229

9

Beta strand

234 – 238

5

Beta strand

246 – 253

8

Helix

254 – 263

10

Turn

264 – 266

3

Helix

269 – 271

3

Sequences

	Sequence		Length	Mass (Da)
	P09012 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 9426E83EE5A22894	FASTA	282	31,280
	10 20 30 40 50 60 MAVPETRPNH TIYINNLNEK IKKDELKKSL YAIFSQFGQI LDILVSRSLK MRGQAFVIFK 70 80 90 100 110 120 EVSSATNALR SMQGFPFYDK PMRIQYAKTD SDIIAKMKGT FVERDRKREK RKPKSQETPA 130 140 150 160 170 180 TKKAVQGGGA TPVVGAVQGP VPGMPPMTQA PRIMHHMPGQ PPYMPPPGMI PPPGLAPGQI 190 200 210 220 230 240 PPGAMPPQQL MPGQMPPAQP LSENPPNHIL FLTNLPEETN ELMLSMLFNQ FPGFKEVRLV 250 260 270 280 PGRHDIAFVE FDNEVQAGAA RDALQGFKIT QNNAMKISFA KK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structure, chromosomal localization and evolutionary conservation of the gene encoding human U1 snRNP-specific A protein." Nelissen R.L.H., Sillekens P.T.G., Beijer R.P., Geurts van Kessel A.H.M., van Venrooij W.J. Gene 102:189-196(1991) [PubMed: 1831431] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Tissue: Liver.
[2]	"cDNA cloning of the human U1 snRNA-associated A protein: extensive homology between U1 and U2 snRNP-specific proteins." Sillekens P.T.G., Habets W.J., Beijer R.P., van Venrooij W.J. EMBO J. 6:3841-3848(1987) [PubMed: 2962859] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Lung and Lymph.
[4]	Bienvenut W.V. Submitted (JAN-2004) to UniProtKB Cited for: PROTEIN SEQUENCE OF 2-19, ACETYLATION AT ALA-2, MASS SPECTROMETRY. Tissue: B-cell lymphoma.
[5]	"The snRNP-free U1A (SF-A) complex(es): identification of the largest subunit as PSF, the polypyrimidine-tract binding protein-associated splicing factor." Lutz C.S., Cooke C., O'Connor J.P., Kobayashi R., Alwine J.C. RNA 4:1493-1499(1998) [PubMed: 9848648] [Abstract] Cited for: FUNCTION IN COUPLED SPLICING, FUNCTION IN POLYADENYLATION PROCESS, INTERACTION WITH SFPQ, IDENTIFICATION IN A SNRNP-FREE COMPLEX WITH SFPQ.
[6]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-131, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[7]	"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach." Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S. Anal. Chem. 81:4493-4501(2009) [PubMed: 19413330] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, MASS SPECTROMETRY. Tissue: Embryonic kidney.
[8]	"Lysine acetylation targets protein complexes and co-regulates major cellular functions." Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T., Olsen J.V., Mann M. Science 325:834-840(2009) [PubMed: 19608861] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-60, MASS SPECTROMETRY.
[9]	"Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins." Ray D., Kazan H., Chan E.T., Pena Castillo L., Chaudhry S., Talukder S., Blencowe B.J., Morris Q., Hughes T.R. Nat. Biotechnol. 27:667-670(2009) [PubMed: 19561594] [Abstract] Cited for: RNA-BINDING.
[10]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed: 21269460] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]	"Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A." Nagai K., Oubridge C., Jessen T.-H., Li J., Evans P.R. Nature 348:515-520(1990) [PubMed: 2147232] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 1-95.
[12]	"Crystal structure at 1.92-A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin." Oubridge C., Ito N., Evans P.R., Teo C.-H., Nagai K. Nature 372:432-438(1994) [PubMed: 7984237] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.92 ANGSTROMS).
[13]	"RNA-binding domain of the A protein component of the U1 small nuclear ribonucleoprotein analyzed by NMR spectroscopy is structurally similar to ribosomal proteins." Hoffman D.W., Query C.C., Golden B.L., White S.W., Keene J.D. Proc. Natl. Acad. Sci. U.S.A. 88:2495-2499(1991) [PubMed: 1826055] [Abstract] Cited for: STRUCTURE BY NMR OF 11-94.
[14]	"NMR studies of U1 snRNA recognition by the N-terminal RNP domain of the human U1A protein." Howe P.W.A., Nagai K., Neuhaus D., Varani G. EMBO J. 13:3873-3881(1994) [PubMed: 8070414] [Abstract] Cited for: STRUCTURE BY NMR OF 1-102.
[15]	"Specificity of ribonucleoprotein interaction determined by RNA folding during complex formulation." Allain F.H.-T., Gubser C.C., Howe P.W.A., Nagai K., Neuhaus D., Varani G. Nature 380:646-650(1996) [PubMed: 8602269] [Abstract] Cited for: STRUCTURE BY NMR OF 1-102.
[16]	"Solution structure of the N-terminal RNP domain of U1A protein: the role of C-terminal residues in structure stability and RNA binding." Avis J.M., Allain F.H.-T., Howe P.W.A., Varani G., Nagai K., Neuhaus D. J. Mol. Biol. 257:398-411(1996) [PubMed: 8609632] [Abstract] Cited for: STRUCTURE BY NMR OF 1-117.
[17]	"Structural basis of the RNA-binding specificity of human U1A protein." Allain F.H.-T., Howe P.W., Neuhaus D., Varani G. EMBO J. 16:5764-5772(1997) [PubMed: 9312034] [Abstract] Cited for: STRUCTURE BY NMR OF 1-102.
[18]	"Tertiary structure of RBD2 and backbone dynamics of RBD1 and RBD2 of the human U1A protein determined by NMR spectroscopy." Lu J., Hall K.B. Biochemistry 36:10393-10405(1997) [PubMed: 9265619] [Abstract] Cited for: STRUCTURE BY NMR OF 195-282.
[19]	"Identification of molecular contacts between the U1 A small nuclear ribonucleoprotein and U1 RNA." Jessen T.-H., Oubridge C., Teo C.H., Pritchard C., Nagai K. EMBO J. 10:3447-3456(1991) [PubMed: 1833186] [Abstract] Cited for: MUTAGENESIS, DETAILED STUDIES OF RNA-BINDING.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M60784 , M60779, M60780, M60781, M60782, M60783 Genomic DNA. Translation: AAA61245.1.
X06347 mRNA. Translation: CAA29653.1.
BC000405 mRNA. Translation: AAH00405.1.
BC008290 mRNA. Translation: AAH08290.1.

IPI

IPI00012382.

PIR

JQ1528.

RefSeq

NP_004587.1. NM_004596.4.

UniGene

Hs.466775.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AUD	NMR	-	A	2-102	[»]
1CX0	X-ray	2.30	A	4-97	[»]
1DRZ	X-ray	2.30	A	2-98	[»]
1DZ5	NMR	-	A/B	2-102	[»]
1FHT	NMR	-	A	2-117	[»]
1M5K	X-ray	2.40	C/F	1-100	[»]
1M5O	X-ray	2.20	C/F	1-100	[»]
1M5P	X-ray	2.60	C/F	1-100	[»]
1M5V	X-ray	2.40	C/F	1-100	[»]
1NU4	X-ray	1.80	A/B	2-98	[»]
1OIA	X-ray	2.40	A/B	1-95	[»]
1SJ3	X-ray	2.20	P	1-100	[»]
1SJ4	X-ray	2.70	P	1-100	[»]
1SJF	X-ray	2.75	A	1-100	[»]
1U6B	X-ray	3.10	A	1-98	[»]
1URN	X-ray	1.92	A/B/C	2-98	[»]
1VBX	X-ray	2.70	A	1-100	[»]
1VBY	X-ray	2.90	A	1-100	[»]
1VBZ	X-ray	2.80	A	1-100	[»]
1VC0	X-ray	2.50	A	1-100	[»]
1VC5	X-ray	3.40	A	1-100	[»]
1VC6	X-ray	2.80	A	1-100	[»]
1VC7	X-ray	2.45	A	1-100	[»]
1ZZN	X-ray	3.37	A	2-97	[»]
2A3J	NMR	-	A	40-43	[»]
2NZ4	X-ray	2.50	A/B/C/D	5-97	[»]
2OIH	X-ray	2.40	A	2-99	[»]
2OJ3	X-ray	2.90	A	2-99	[»]
2U1A	NMR	-	A	197-282	[»]
3BO2	X-ray	3.31	A	4-98	[»]
3BO3	X-ray	3.40	A	4-98	[»]
3BO4	X-ray	3.33	A	4-98	[»]
3CUL	X-ray	2.80	A/B	1-98	[»]
3CUN	X-ray	3.00	A/B	1-98	[»]
3EGZ	X-ray	2.20	A	1-98	[»]
3G8S	X-ray	3.10	A/B/C/D	1-98	[»]
3G8T	X-ray	3.00	A/B/C/D	1-98	[»]
3G96	X-ray	3.01	A/B/C/D	1-98	[»]
3G9C	X-ray	2.90	A/B/C/D	1-98	[»]
3HHN	X-ray	2.99	B/D	2-98	[»]
3IIN	X-ray	4.18	A	4-98	[»]
3IRW	X-ray	2.70	P	1-98	[»]
3IWN	X-ray	3.20	C/D	6-96	[»]
3K0J	X-ray	3.10	A/B/C/D	2-97	[»]
3L3C	X-ray	2.85	A/B/C/D	7-96	[»]
3MUM	X-ray	2.90	P	1-98	[»]
3MUR	X-ray	3.00	P	1-98	[»]
3MUT	X-ray	3.00	P	1-98	[»]
3MUV	X-ray	3.20	P	1-98	[»]
3MXH	X-ray	2.30	P	1-98	[»]
3P49	X-ray	3.55	B	1-98	[»]
3PGW	X-ray	4.40	A/P	1-282	[»]
3R1H	X-ray	3.15	A/D	1-98	[»]
3R1L	X-ray	3.12	A/D	1-98	[»]
3UTR	model	-	B/D	1-98	[»]

ProteinModelPortal

P09012.

SMR

P09012. Positions 2-117, 195-282.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-29407N.

IntAct

P09012. 12 interactions.

MINT

MINT-125665.

STRING

P09012.

PTM databases

PhosphoSite

P09012.

Polymorphism databases

DMDM

134092.

Proteomic databases

PeptideAtlas

P09012.

PRIDE

P09012.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000243563; ENSP00000243563; ENSG00000077312.

GeneID

6626.

KEGG

hsa:6626.

UCSC

uc002ooz.1. human.

Organism-specific databases

CTD

6626.

GeneCards

GC19P041256.

H-InvDB

HIX0015143.

HGNC

HGNC:11151. SNRPA.

HPA

CAB004652.

MIM

182285. gene.

neXtProt

NX_P09012.

PharmGKB

PA35993.

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG14824.

GeneTree

ENSGT00390000007046.

HOGENOM

HBG329120.

HOVERGEN

HBG000895.

InParanoid

P09012.

OMA

MSQAPRM.

OrthoDB

EOG498V1W.

PhylomeDB

P09012.

Enzyme and pathway databases

Reactome

REACT_1675. mRNA Processing.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpress

P09012.

Bgee

P09012.

CleanEx

HS_SNRPA.

Genevestigator

P09012.

GermOnline

ENSG00000077312. Homo sapiens.

Family and domain databases

InterPro

IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
IPR024888. U1_snRNP_A/U2_snRNP_B''.
[Graphical view]

Gene3D

G3DSA:3.30.70.330. a_b_plait_nuc_bd. 2 hits.

KO

K11091.

PANTHER

PTHR10501. PTHR10501. 1 hit.

Pfam

PF00076. RRM_1. 2 hits.
[Graphical view]

SMART

SM00360. RRM. 2 hits.
[Graphical view]

PROSITE

PS50102. RRM. 2 hits.
[Graphical view]

ProtoNet

Search...

Other

NextBio

25809.

SOURCE

Search...

Entry information

Entry name

SNRPA_HUMAN

Accession

Primary (citable) accession number: P09012

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1988
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 150 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.