P55769 (NH2L1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
NHP2-like protein 1

Alternative name(s):
High mobility group-like nuclear protein 2 homolog 1
OTK27
SNU13 homolog
Short name=hSNU13
U4/U6.U5 tri-snRNP 15.5 kDa protein

Gene names

Name:

NHP2L1

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	128 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 to the 5'-stem-loop of U4 snRNA and may play a role in the late stage of spliceosome assembly. The protein undergoes a conformational change upon RNA-binding. Ref.2 Ref.14
Subunit structure	Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, WDR57, SNRNP40, DDX23, CD2BP2, PPIH, NHP2L1, EFTUD2, SART1 and USP39. Interacts with RAD17 and PRPF31. Ref.8 Ref.10
Subcellular location	Nucleus › nucleolus. Note: Concentrated in the dense fibrillar component of the nucleolus. Ref.7 Ref.8 Ref.9
Tissue specificity	Ubiquitous.
Sequence similarities	Belongs to the ribosomal protein L7Ae family.

Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Nucleus Spliceosome
Coding sequence diversity	Polymorphism
Ligand	RNA-binding
Molecular function	Ribonucleoprotein
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	mRNA splicing, via spliceosome Traceable author statement. Source: Reactome ribosome biogenesis Inferred from electronic annotation. Source: InterPro
Cellular_component	box C/D snoRNP complex Non-traceable author statement PubMed 17636026. Source: BHF-UCL nucleoplasm Traceable author statement. Source: Reactome spliceosomal complex Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	RNA binding Traceable author statement Ref.8. Source: ProtInc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
gag	P04591	2	EBI-712228,EBI-6179727	From a different organism.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.7

Chain

2 – 128

127

NHP2-like protein 1

PRO_0000136778

Amino acid modifications

Modified residue

2

1

N-acetylthreonine Ref.7

Natural variations

Natural variant

19

1

T → N.
Corresponds to variant rs1802521 [ dbSNP | Ensembl ].

VAR_034155

Experimental info

Mutagenesis

38

1

G → K: Abolishes completely RNA-binding. Ref.2

Mutagenesis

57

1

A → F: Abolishes completely RNA-binding. Ref.2

Mutagenesis

80

1

Y → A: Abolishes 50% of RNA-binding. Ref.2

Mutagenesis

96 – 128

33

Missing: Abolishes completely RNA-binding.

Secondary structure

1

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128

Helix Strand Turn

Details...

Beta strand

10 – 13

4

Helix

16 – 31

16

Beta strand

35 – 38

4

Helix

39 – 48

10

Beta strand

51 – 57

7

Helix

63 – 65

3

Helix

68 – 76

9

Beta strand

80 – 84

5

Helix

86 – 92

7

Beta strand

100 – 105

6

Helix

113 – 124

12

Sequences

	Sequence		Length	Mass (Da)
	P55769 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 78849EBB497089ED	FASTA	128	14,174
	10 20 30 40 50 60 MTEADVNPKA YPLADAHLTK KLLDLVQQSC NYKQLRKGAN EATKTLNRGI SEFIVMAADA 70 80 90 100 110 120 EPLEIILHLP LLCEDKNVPY VFVRSKQALG RACGVSRPVI ACSVTIKEGS QLKQQIQSIQ QSIERLLV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and mapping of a human novel cDNA (NHP2L1) that encodes a protein highly homologous to yeast nuclear protein NHP2." Saito H., Fujiwara T., Shin S., Okui K., Nakamura Y. Cytogenet. Cell Genet. 72:191-193(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"Functional interaction of a novel 15.5kD [U4/U6.U5] tri-snRNP protein with the 5' stem-loop of U4 snRNA." Nottrott S., Hartmuth K., Fabrizio P., Urlaub H., Vidovic I., Ficner R., Luehrmann R. EMBO J. 18:6119-6133(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 4-7 AND 92-106, FUNCTION, MUTAGENESIS OF GLY-38; ALA-57 AND TYR-80.
[3]	"Full-insert sequence of mapped XREF EST." Barrow I.K.-P., Boguski M.S., Touchman J.W., Spencer F. Submitted (AUG-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[4]	"A genome annotation-driven approach to cloning the human ORFeome." Collins J.E., Wright C.L., Edwards C.A., Davis M.P., Grinham J.A., Cole C.G., Goward M.E., Aguado B., Mallya M., Mokrab Y., Huckle E.J., Beare D.M., Dunham I. Genome Biol. 5:R84.1-R84.11(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[5]	"The DNA sequence of human chromosome 22." Dunham I., Hunt A.R., Collins J.E., Bruskiewich R., Beare D.M., Clamp M., Smink L.J., Ainscough R., Almeida J.P., Babbage A.K., Bagguley C., Bailey J., Barlow K.F., Bates K.N., Beasley O.P., Bird C.P., Blakey S.E., Bridgeman A.M. , Buck D., Burgess J., Burrill W.D., Burton J., Carder C., Carter N.P., Chen Y., Clark G., Clegg S.M., Cobley V.E., Cole C.G., Collier R.E., Connor R., Conroy D., Corby N.R., Coville G.J., Cox A.V., Davis J., Dawson E., Dhami P.D., Dockree C., Dodsworth S.J., Durbin R.M., Ellington A.G., Evans K.L., Fey J.M., Fleming K., French L., Garner A.A., Gilbert J.G.R., Goward M.E., Grafham D.V., Griffiths M.N.D., Hall C., Hall R.E., Hall-Tamlyn G., Heathcott R.W., Ho S., Holmes S., Hunt S.E., Jones M.C., Kershaw J., Kimberley A.M., King A., Laird G.K., Langford C.F., Leversha M.A., Lloyd C., Lloyd D.M., Martyn I.D., Mashreghi-Mohammadi M., Matthews L.H., Mccann O.T., Mcclay J., Mclaren S., McMurray A.A., Milne S.A., Mortimore B.J., Odell C.N., Pavitt R., Pearce A.V., Pearson D., Phillimore B.J.C.T., Phillips S.H., Plumb R.W., Ramsay H., Ramsey Y., Rogers L., Ross M.T., Scott C.E., Sehra H.K., Skuce C.D., Smalley S., Smith M.L., Soderlund C., Spragon L., Steward C.A., Sulston J.E., Swann R.M., Vaudin M., Wall M., Wallis J.M., Whiteley M.N., Willey D.L., Williams L., Williams S.A., Williamson H., Wilmer T.E., Wilming L., Wright C.L., Hubbard T., Bentley D.R., Beck S., Rogers J., Shimizu N., Minoshima S., Kawasaki K., Sasaki T., Asakawa S., Kudoh J., Shintani A., Shibuya K., Yoshizaki Y., Aoki N., Mitsuyama S., Roe B.A., Chen F., Chu L., Crabtree J., Deschamps S., Do A., Do T., Dorman A., Fang F., Fu Y., Hu P., Hua A., Kenton S., Lai H., Lao H.I., Lewis J., Lewis S., Lin S.-P., Loh P., Malaj E., Nguyen T., Pan H., Phan S., Qi S., Qian Y., Ray L., Ren Q., Shaull S., Sloan D., Song L., Wang Q., Wang Y., Wang Z., White J., Willingham D., Wu H., Yao Z., Zhan M., Zhang G., Chissoe S., Murray J., Miller N., Minx P., Fulton R., Johnson D., Bemis G., Bentley D., Bradshaw H., Bourne S., Cordes M., Du Z., Fulton L., Goela D., Graves T., Hawkins J., Hinds K., Kemp K., Latreille P., Layman D., Ozersky P., Rohlfing T., Scheet P., Walker C., Wamsley A., Wohldmann P., Pepin K., Nelson J., Korf I., Bedell J.A., Hillier L.W., Mardis E., Waterston R., Wilson R., Emanuel B.S., Shaikh T., Kurahashi H., Saitta S., Budarf M.L., McDermid H.E., Johnson A., Wong A.C.C., Morrow B.E., Edelmann L., Kim U.J., Shizuya H., Simon M.I., Dumanski J.P., Peyrard M., Kedra D., Seroussi E., Fransson I., Tapia I., Bruder C.E., O'Brien K.P., Wilkinson P., Bodenteich A., Hartman K., Hu X., Khan A.S., Lane L., Tilahun Y., Wright H. Nature 402:489-495(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Lung and Urinary bladder.
[7]	Bienvenut W.V. Submitted (AUG-2005) to UniProtKB Cited for: PROTEIN SEQUENCE OF 2-20; 22-33; 77-84 AND 114-125, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT THR-2, SUBCELLULAR LOCATION, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[8]	"HRad17 colocalizes with NHP2L1 in the nucleolus and redistributes after UV irradiation." Chang M.-S., Sasaki H., Campbell M.S., Kraeft S.-K., Sutherland R., Yang C.-Y., Liu Y., Auclair D., Hao L., Sonoda H., Ferland L.H., Chen L.B. J. Biol. Chem. 274:36544-36549(1999) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION, INTERACTION WITH RAD17.
[9]	"Functional proteomic analysis of human nucleolus." Scherl A., Coute Y., Deon C., Calle A., Kindbeiter K., Sanchez J.-C., Greco A., Hochstrasser D.F., Diaz J.-J. Mol. Biol. Cell 13:4100-4109(2002) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS]. Tissue: Cervix carcinoma.
[10]	"The network of protein-protein interactions within the human U4/U6.U5 tri-snRNP." Liu S., Rauhut R., Vornlocher H.-P., Luehrmann R. RNA 12:1418-1430(2006) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT.
[11]	"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] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]	"Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment." Vidovic I., Nottrott S., Hartmuth K., Luehrmann R., Ficner R. Mol. Cell 6:1331-1342(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS).
[13]	"Functional implications for a prototypical K-turn binding protein from structural and dynamical studies of 15.5K." Soss S.E., Flynn P.F. Biochemistry 46:14979-14986(2007) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR.
[14]	"Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP." Liu S., Li P., Dybkov O., Nottrott S., Hartmuth K., Luehrmann R., Carlomagno T., Wahl M.C. Science 316:115-120(2007) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH PRPF31 AND STEM-LOOP RNA OF U4 SNRNA, FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

D50420 mRNA. Translation: BAA23363.1.
AF155235 mRNA. Translation: AAF06959.1.
AF091076 mRNA. Translation: AAC72945.1.
CR456531 mRNA. Translation: CAG30417.1.
Z83840 Genomic DNA. Translation: CAB46207.1.
BC005358 mRNA. Translation: AAH05358.1.
BC019282 mRNA. Translation: AAH19282.1.

IPI

IPI00026167.

RefSeq

NP_001003796.1. NM_001003796.1.
NP_004999.1. NM_005008.3.

UniGene

Hs.182255.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1E7K	X-ray	2.90	A/B	1-128	[»]
2JNB	NMR	-	A	1-128	[»]
2OZB	X-ray	2.60	A/D	1-128	[»]
3SIU	X-ray	2.63	A/D	1-128	[»]
3SIV	X-ray	3.30	A/D/G/J	1-128	[»]

ProteinModelPortal

P55769.

ModBase

Search...

Protein-protein interaction databases

IntAct

P55769. 13 interactions.

MINT

MINT-1382515.

STRING

9606.ENSP00000215956.

PTM databases

PhosphoSite

P55769.

Polymorphism databases

DMDM

2500345.

2D gel databases

SWISS-2DPAGE

P55769.

Proteomic databases

PaxDb

P55769.

PeptideAtlas

P55769.

PRIDE

P55769.

Protocols and materials databases

DNASU

4809.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000215956; ENSP00000215956; ENSG00000100138.
ENST00000355257; ENSP00000347401; ENSG00000100138.
ENST00000401959; ENSP00000383949; ENSG00000100138.

GeneID

4809.

KEGG

hsa:4809.

UCSC

uc003bat.3. human.

Organism-specific databases

CTD

4809.

GeneCards

GC22M042069.

HGNC

HGNC:7819. NHP2L1.

HPA

HPA029199.

MIM

601304. gene.
601876. gene.

neXtProt

NX_P55769.

PharmGKB

PA31621.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG1358.

HOGENOM

HOG000055226.

HOVERGEN

HBG000328.

KO

K12845.

OrthoDB

EOG4M91T0.

PhylomeDB

P55769.

Enzyme and pathway databases

Reactome

REACT_1675. mRNA Processing.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpress

P55769.

Bgee

P55769.

CleanEx

HS_NHP2L1.

Genevestigator

P55769.

GermOnline

ENSG00000100138. Homo sapiens.

Family and domain databases

InterPro

IPR002415. H/ACA_rnp_Nhp2_euk.
IPR004038. Ribosomal_L7Ae/L30e/S12e/Gad45.
IPR018492. Ribosomal_L7Ae/L8/Nhp2.
IPR004037. Ribosomal_L7Ae_CS.
[Graphical view]

Pfam

PF01248. Ribosomal_L7Ae. 1 hit.
[Graphical view]

PRINTS

PR00881. L7ARS6FAMILY.
PR00883. NUCLEARHMG.

PROSITE

PS01082. RIBOSOMAL_L7AE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

NHP2L1. human.

EvolutionaryTrace

P55769.

GenomeRNAi

4809.

NextBio

18532.

SOURCE

Search...

Entry information

Entry name

NH2L1_HUMAN

Accession

Primary (citable) accession number: P55769

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 138 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.