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P55769

- NH2L1_HUMAN

UniProt

P55769 - NH2L1_HUMAN

Protein

NHP2-like protein 1

Gene

NHP2L1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
  1. Functioni

    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.2 Publications

    GO - Molecular functioni

    1. poly(A) RNA binding Source: UniProtKB
    2. protein binding Source: IntAct
    3. RNA binding Source: ProtInc

    GO - Biological processi

    1. gene expression Source: Reactome
    2. mRNA splicing, via spliceosome Source: Reactome
    3. ribosome biogenesis Source: InterPro
    4. RNA splicing Source: Reactome

    Keywords - Molecular functioni

    Ribonucleoprotein

    Keywords - Biological processi

    mRNA processing, mRNA splicing

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    ReactomeiREACT_1753. mRNA Splicing - Minor Pathway.
    REACT_467. mRNA Splicing - Major Pathway.

    Names & Taxonomyi

    Protein namesi
    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
    Cleaved into the following chain:
    Gene namesi
    Name:NHP2L1
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 22

    Organism-specific databases

    HGNCiHGNC:7819. NHP2L1.

    Subcellular locationi

    Nucleusnucleolus 3 Publications
    Note: Concentrated in the dense fibrillar component of the nucleolus.

    GO - Cellular componenti

    1. box C/D snoRNP complex Source: BHF-UCL
    2. nucleolus Source: ProtInc
    3. nucleoplasm Source: Reactome
    4. nucleus Source: ProtInc
    5. spliceosomal complex Source: UniProtKB-KW

    Keywords - Cellular componenti

    Nucleus, Spliceosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi38 – 381G → K: Abolishes completely RNA-binding. 1 Publication
    Mutagenesisi57 – 571A → F: Abolishes completely RNA-binding. 1 Publication
    Mutagenesisi80 – 801Y → A: Abolishes 50% of RNA-binding. 1 Publication
    Mutagenesisi96 – 12833Missing: Abolishes completely RNA-binding. Add
    BLAST

    Organism-specific databases

    PharmGKBiPA31621.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 128128NHP2-like protein 1PRO_0000423260Add
    BLAST
    Initiator methioninei1 – 11Removed; alternate1 Publication
    Chaini2 – 128127NHP2-like protein 1, N-terminally processedPRO_0000136778Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1 – 11N-acetylmethionine1 Publication
    Modified residuei2 – 21N-acetylthreonine; in NHP2-like protein 1, N-terminally processed2 Publications
    Modified residuei21 – 211N6-acetyllysineBy similarity

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiP55769.
    PaxDbiP55769.
    PeptideAtlasiP55769.
    PRIDEiP55769.

    2D gel databases

    SWISS-2DPAGEP55769.

    PTM databases

    PhosphoSiteiP55769.

    Expressioni

    Tissue specificityi

    Ubiquitous.

    Gene expression databases

    ArrayExpressiP55769.
    BgeeiP55769.
    CleanExiHS_NHP2L1.
    GenevestigatoriP55769.

    Organism-specific databases

    HPAiHPA029199.

    Interactioni

    Subunit structurei

    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 PRPF31.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    gagP045912EBI-712228,EBI-6179727From a different organism.
    NUFIP1Q9UHK02EBI-712228,EBI-2563549

    Protein-protein interaction databases

    BioGridi110874. 114 interactions.
    IntActiP55769. 18 interactions.
    MINTiMINT-1382515.
    STRINGi9606.ENSP00000215956.

    Structurei

    Secondary structure

    1
    128
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi10 – 134
    Helixi16 – 3116
    Beta strandi35 – 384
    Helixi39 – 4810
    Beta strandi51 – 577
    Helixi63 – 653
    Helixi68 – 769
    Beta strandi80 – 845
    Helixi86 – 927
    Beta strandi100 – 1056
    Helixi113 – 12412

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1E7KX-ray2.90A/B1-128[»]
    2JNBNMR-A1-128[»]
    2OZBX-ray2.60A/D1-128[»]
    3SIUX-ray2.63A/D1-128[»]
    3SIVX-ray3.30A/D/G/J1-128[»]
    ProteinModelPortaliP55769.
    SMRiP55769. Positions 3-128.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP55769.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the ribosomal protein L7Ae family.Curated

    Phylogenomic databases

    eggNOGiCOG1358.
    HOGENOMiHOG000055226.
    HOVERGENiHBG000328.
    KOiK12845.
    OrthoDBiEOG78WKTT.
    PhylomeDBiP55769.
    TreeFamiTF300184.

    Family and domain databases

    Gene3Di3.30.1330.30. 1 hit.
    InterProiIPR002415. H/ACA_rnp_Nhp2_euk.
    IPR029064. L30e-like.
    IPR004038. Ribosomal_L7Ae/L30e/S12e/Gad45.
    IPR018492. Ribosomal_L7Ae/L8/Nhp2.
    IPR004037. Ribosomal_L7Ae_CS.
    [Graphical view]
    PfamiPF01248. Ribosomal_L7Ae. 1 hit.
    [Graphical view]
    PRINTSiPR00881. L7ARS6FAMILY.
    PR00883. NUCLEARHMG.
    SUPFAMiSSF55315. SSF55315. 1 hit.
    PROSITEiPS01082. RIBOSOMAL_L7AE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P55769-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTEADVNPKA YPLADAHLTK KLLDLVQQSC NYKQLRKGAN EATKTLNRGI    50
    SEFIVMAADA EPLEIILHLP LLCEDKNVPY VFVRSKQALG RACGVSRPVI 100
    ACSVTIKEGS QLKQQIQSIQ QSIERLLV 128
    Length:128
    Mass (Da):14,174
    Last modified:January 23, 2007 - v3
    Checksum:i78849EBB497089ED
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti19 – 191T → N.
    Corresponds to variant rs1802521 [ dbSNP | Ensembl ].
    VAR_034155

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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.
    CCDSiCCDS14022.1.
    CCDS33653.1.
    RefSeqiNP_001003796.1. NM_001003796.1.
    NP_004999.1. NM_005008.3.
    UniGeneiHs.182255.

    Genome annotation databases

    EnsembliENST00000215956; ENSP00000215956; ENSG00000100138.
    ENST00000355257; ENSP00000347401; ENSG00000100138.
    ENST00000401959; ENSP00000383949; ENSG00000100138.
    GeneIDi4809.
    KEGGihsa:4809.
    UCSCiuc003bat.4. human.

    Polymorphism databases

    DMDMi2500345.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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 .
    CCDSi CCDS14022.1.
    CCDS33653.1.
    RefSeqi NP_001003796.1. NM_001003796.1.
    NP_004999.1. NM_005008.3.
    UniGenei Hs.182255.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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 [» ]
    ProteinModelPortali P55769.
    SMRi P55769. Positions 3-128.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 110874. 114 interactions.
    IntActi P55769. 18 interactions.
    MINTi MINT-1382515.
    STRINGi 9606.ENSP00000215956.

    PTM databases

    PhosphoSitei P55769.

    Polymorphism databases

    DMDMi 2500345.

    2D gel databases

    SWISS-2DPAGE P55769.

    Proteomic databases

    MaxQBi P55769.
    PaxDbi P55769.
    PeptideAtlasi P55769.
    PRIDEi P55769.

    Protocols and materials databases

    DNASUi 4809.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000215956 ; ENSP00000215956 ; ENSG00000100138 .
    ENST00000355257 ; ENSP00000347401 ; ENSG00000100138 .
    ENST00000401959 ; ENSP00000383949 ; ENSG00000100138 .
    GeneIDi 4809.
    KEGGi hsa:4809.
    UCSCi uc003bat.4. human.

    Organism-specific databases

    CTDi 4809.
    GeneCardsi GC22M042069.
    HGNCi HGNC:7819. NHP2L1.
    HPAi HPA029199.
    MIMi 601304. gene.
    601876. gene.
    neXtProti NX_P55769.
    PharmGKBi PA31621.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG1358.
    HOGENOMi HOG000055226.
    HOVERGENi HBG000328.
    KOi K12845.
    OrthoDBi EOG78WKTT.
    PhylomeDBi P55769.
    TreeFami TF300184.

    Enzyme and pathway databases

    Reactomei REACT_1753. mRNA Splicing - Minor Pathway.
    REACT_467. mRNA Splicing - Major Pathway.

    Miscellaneous databases

    ChiTaRSi NHP2L1. human.
    EvolutionaryTracei P55769.
    GeneWikii NHP2L1.
    GenomeRNAii 4809.
    NextBioi 18532.
    PROi P55769.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi P55769.
    Bgeei P55769.
    CleanExi HS_NHP2L1.
    Genevestigatori P55769.

    Family and domain databases

    Gene3Di 3.30.1330.30. 1 hit.
    InterProi IPR002415. H/ACA_rnp_Nhp2_euk.
    IPR029064. L30e-like.
    IPR004038. Ribosomal_L7Ae/L30e/S12e/Gad45.
    IPR018492. Ribosomal_L7Ae/L8/Nhp2.
    IPR004037. Ribosomal_L7Ae_CS.
    [Graphical view ]
    Pfami PF01248. Ribosomal_L7Ae. 1 hit.
    [Graphical view ]
    PRINTSi PR00881. L7ARS6FAMILY.
    PR00883. NUCLEARHMG.
    SUPFAMi SSF55315. SSF55315. 1 hit.
    PROSITEi PS01082. RIBOSOMAL_L7AE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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. 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, IDENTIFICATION BY 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. Cited for: 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. "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] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1 AND THR-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    12. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    13. "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).
    14. "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.
    15. "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.

    Entry informationi

    Entry nameiNH2L1_HUMAN
    AccessioniPrimary (citable) accession number: P55769
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 152 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny 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.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Human chromosome 22
      Human chromosome 22: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. Ribosomal proteins
      Ribosomal proteins families and list of entries
    7. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3