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O14593

- RFXK_HUMAN

UniProt

O14593 - RFXK_HUMAN

Protein

DNA-binding protein RFXANK

Gene

RFXANK

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 139 (01 Oct 2014)
      Sequence version 2 (15 Jul 1999)
      Previous versions | rss
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    Functioni

    Activates transcription from class II MHC promoters. Activation requires the activity of the MHC class II transactivator (MHC2TA). May regulate other genes in the cell. RFX binds the X1 box of MHC-II promoters. Isoform RFX-B-delta5 is not involved in the positive regulation of MHC class II genes.

    GO - Molecular functioni

    1. DNA binding Source: ProtInc
    2. sequence-specific DNA binding transcription factor activity Source: ProtInc
    3. transcription cofactor activity Source: ProtInc

    GO - Biological processi

    1. positive regulation of transcription from RNA polymerase II promoter Source: Ensembl
    2. Ras protein signal transduction Source: Ensembl
    3. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Activator

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA-binding protein RFXANK
    Alternative name(s):
    Ankyrin repeat family A protein 1
    Regulatory factor X subunit B
    Short name:
    RFX-B
    Regulatory factor X-associated ankyrin-containing protein
    Gene namesi
    Name:RFXANK
    Synonyms:ANKRA1, RFXB
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 19

    Organism-specific databases

    HGNCiHGNC:9987. RFXANK.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: HPA
    2. intercellular bridge Source: HPA
    3. nucleus Source: HPA

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Involvement in diseasei

    Bare lymphocyte syndrome 2 (BLS2) [MIM:209920]: A severe combined immunodeficiency disease with early onset. It is characterized by a profound defect in constitutive and interferon-gamma induced MHC II expression, absence of cellular and humoral T-cell response to antigen challenge, hypogammaglobulinemia and impaired antibody production. The consequence include extreme susceptibility to viral, bacterial and fungal infections.3 Publications
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti195 – 1951L → P in BLS2. 1 Publication
    VAR_009941

    Keywords - Diseasei

    Disease mutation, SCID

    Organism-specific databases

    MIMi209920. phenotype.
    Orphaneti572. Immunodeficiency by defective expression of HLA class 2.
    PharmGKBiPA34357.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 260260DNA-binding protein RFXANKPRO_0000067049Add
    BLAST

    Proteomic databases

    MaxQBiO14593.
    PaxDbiO14593.
    PRIDEiO14593.

    PTM databases

    PhosphoSiteiO14593.

    Expressioni

    Tissue specificityi

    Ubiquitous.

    Gene expression databases

    ArrayExpressiO14593.
    BgeeiO14593.
    CleanExiHS_RFXANK.
    GenevestigatoriO14593.

    Organism-specific databases

    HPAiHPA049157.
    HPA053330.

    Interactioni

    Subunit structurei

    The RFX heterotetrameric complex consists of 2 molecules of RFX5 and one each of RFXAP and RFX-B/RFXANK; with each subunit representing a separate complementation group. RFX forms cooperative DNA binding complexes with X2BP and CBF/NF-Y. RFX associates with MHC2TA to form an active transcriptional complex.2 Publications

    Protein-protein interaction databases

    BioGridi114180. 18 interactions.
    STRINGi9606.ENSP00000305071.

    Structurei

    Secondary structure

    1
    260
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi94 – 996
    Helixi103 – 1108
    Helixi115 – 1184
    Helixi127 – 1337
    Helixi137 – 14610
    Helixi160 – 1667
    Helixi170 – 1778
    Turni178 – 1803
    Helixi193 – 1997
    Helixi203 – 2119
    Helixi226 – 2338
    Helixi236 – 24914

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3UXGX-ray1.85A90-260[»]
    3V30X-ray1.57A90-260[»]
    ProteinModelPortaliO14593.
    SMRiO14593. Positions 8-252.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Repeati89 – 11830ANK 1Add
    BLAST
    Repeati123 – 15230ANK 2Add
    BLAST
    Repeati156 – 18530ANK 3Add
    BLAST
    Repeati189 – 21830ANK 4Add
    BLAST
    Repeati222 – 25130ANK 5Add
    BLAST

    Domaini

    The third ankyrin repeat is required for association with the two other RFX subunits; RFX5 and RFXAP. The three central ANK repeats mediate binding to the PxLPxI/L motif of RFX5.

    Sequence similaritiesi

    Contains 5 ANK repeats.PROSITE-ProRule annotation

    Keywords - Domaini

    ANK repeat, Repeat

    Phylogenomic databases

    eggNOGiCOG0666.
    HOGENOMiHOG000294108.
    HOVERGENiHBG017718.
    InParanoidiO14593.
    KOiK08062.
    OMAiMEPTQPA.
    PhylomeDBiO14593.
    TreeFamiTF333112.

    Family and domain databases

    Gene3Di1.25.40.20. 2 hits.
    InterProiIPR002110. Ankyrin_rpt.
    IPR020683. Ankyrin_rpt-contain_dom.
    IPR017362. DNA-bd_RFXANK.
    [Graphical view]
    PfamiPF00023. Ank. 3 hits.
    [Graphical view]
    PIRSFiPIRSF038034. DNA-binding_RFXANK. 1 hit.
    SMARTiSM00248. ANK. 4 hits.
    [Graphical view]
    SUPFAMiSSF48403. SSF48403. 1 hit.
    PROSITEiPS50297. ANK_REP_REGION. 1 hit.
    PS50088. ANK_REPEAT. 3 hits.
    [Graphical view]

    Sequences (3)i

    Sequence statusi: Complete.

    This entry describes 3 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: O14593-1) [UniParc]FASTAAdd to Basket

    Also known as: Long

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MELTQPAEDL IQTQQTPASE LGDPEDPGEE AADGSDTVVL SLFPCTPEPV    50
    NPEPDASVSS PQAGSSLKHS TTLTNRQRGN EVSALPATLD SLSIHQLAAQ 100
    GELDQLKEHL RKGDNLVNKP DERGFTPLIW ASAFGEIETV RFLLEWGADP 150
    HILAKERESA LSLASTGGYT DIVGLLLERD VDINIYDWNG GTPLLYAVRG 200
    NHVKCVEALL ARGADLTTEA DSGYTPMDLA VALGYRKVQQ VIENHILKLF 250
    QSNLVPADPE 260
    Length:260
    Mass (Da):28,102
    Last modified:July 15, 1999 - v2
    Checksum:i6280B490F54816D2
    GO
    Isoform 2 (identifier: O14593-2) [UniParc]FASTAAdd to Basket

    Also known as: RFX-B-delta5

    The sequence of this isoform differs from the canonical sequence as follows:
         63-63: Missing.
         91-113: SLSIHQLAAQGELDQLKEHLRKG → C
         159-172: Missing.

    Show »
    Length:223
    Mass (Da):24,243
    Checksum:iD0CC4523D656840B
    GO
    Isoform 3 (identifier: O14593-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         91-113: SLSIHQLAAQGELDQLKEHLRKG → C

    Note: No experimental confirmation available.

    Show »
    Length:238
    Mass (Da):25,652
    Checksum:iCD46F8F674173B9E
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti48 – 481E → D.
    Corresponds to variant rs34282046 [ dbSNP | Ensembl ].
    VAR_048311
    Natural varianti195 – 1951L → P in BLS2. 1 Publication
    VAR_009941
    Natural varianti251 – 2511Q → E.
    Corresponds to variant rs1802498 [ dbSNP | Ensembl ].
    VAR_014472

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei63 – 631Missing in isoform 2. 1 PublicationVSP_000283
    Alternative sequencei91 – 11323SLSIH…HLRKG → C in isoform 2 and isoform 3. 2 PublicationsVSP_000284Add
    BLAST
    Alternative sequencei159 – 17214Missing in isoform 2. 1 PublicationVSP_054618Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF094760 mRNA. Translation: AAC69883.1.
    AF105427 mRNA. Translation: AAD17972.1.
    AF105428 mRNA. Translation: AAD17973.1.
    AF077196 mRNA. Translation: AAD26991.1.
    CR542199 mRNA. Translation: CAG46996.1.
    AC002126 Genomic DNA. No translation available.
    AC003110 Genomic DNA. Translation: AAB86654.1.
    CH471106 Genomic DNA. Translation: EAW84795.1.
    BC114558 mRNA. Translation: AAI14559.1.
    BC114563 mRNA. Translation: AAI14564.1.
    CCDSiCCDS12395.1. [O14593-1]
    CCDS62611.1. [O14593-3]
    RefSeqiNP_001265656.1. NM_001278727.1. [O14593-3]
    NP_001265657.1. NM_001278728.1.
    NP_003712.1. NM_003721.3. [O14593-1]
    NP_604389.1. NM_134440.2.
    XP_005260191.1. XM_005260134.2. [O14593-1]
    XP_005260192.1. XM_005260135.1. [O14593-1]
    UniGeneiHs.153629.
    Hs.296776.

    Genome annotation databases

    EnsembliENST00000303088; ENSP00000305071; ENSG00000064490. [O14593-1]
    ENST00000407360; ENSP00000384572; ENSG00000064490. [O14593-1]
    ENST00000456252; ENSP00000409138; ENSG00000064490. [O14593-3]
    GeneIDi8625.
    KEGGihsa:8625.
    UCSCiuc002nls.3. human. [O14593-1]
    uc002nlt.3. human. [O14593-2]

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Web resourcesi

    RFXANKbase

    RFXANK mutation db

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF094760 mRNA. Translation: AAC69883.1 .
    AF105427 mRNA. Translation: AAD17972.1 .
    AF105428 mRNA. Translation: AAD17973.1 .
    AF077196 mRNA. Translation: AAD26991.1 .
    CR542199 mRNA. Translation: CAG46996.1 .
    AC002126 Genomic DNA. No translation available.
    AC003110 Genomic DNA. Translation: AAB86654.1 .
    CH471106 Genomic DNA. Translation: EAW84795.1 .
    BC114558 mRNA. Translation: AAI14559.1 .
    BC114563 mRNA. Translation: AAI14564.1 .
    CCDSi CCDS12395.1. [O14593-1 ]
    CCDS62611.1. [O14593-3 ]
    RefSeqi NP_001265656.1. NM_001278727.1. [O14593-3 ]
    NP_001265657.1. NM_001278728.1.
    NP_003712.1. NM_003721.3. [O14593-1 ]
    NP_604389.1. NM_134440.2.
    XP_005260191.1. XM_005260134.2. [O14593-1 ]
    XP_005260192.1. XM_005260135.1. [O14593-1 ]
    UniGenei Hs.153629.
    Hs.296776.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3UXG X-ray 1.85 A 90-260 [» ]
    3V30 X-ray 1.57 A 90-260 [» ]
    ProteinModelPortali O14593.
    SMRi O14593. Positions 8-252.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 114180. 18 interactions.
    STRINGi 9606.ENSP00000305071.

    PTM databases

    PhosphoSitei O14593.

    Proteomic databases

    MaxQBi O14593.
    PaxDbi O14593.
    PRIDEi O14593.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000303088 ; ENSP00000305071 ; ENSG00000064490 . [O14593-1 ]
    ENST00000407360 ; ENSP00000384572 ; ENSG00000064490 . [O14593-1 ]
    ENST00000456252 ; ENSP00000409138 ; ENSG00000064490 . [O14593-3 ]
    GeneIDi 8625.
    KEGGi hsa:8625.
    UCSCi uc002nls.3. human. [O14593-1 ]
    uc002nlt.3. human. [O14593-2 ]

    Organism-specific databases

    CTDi 8625.
    GeneCardsi GC19P019303.
    HGNCi HGNC:9987. RFXANK.
    HPAi HPA049157.
    HPA053330.
    MIMi 209920. phenotype.
    603200. gene.
    neXtProti NX_O14593.
    Orphaneti 572. Immunodeficiency by defective expression of HLA class 2.
    PharmGKBi PA34357.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG0666.
    HOGENOMi HOG000294108.
    HOVERGENi HBG017718.
    InParanoidi O14593.
    KOi K08062.
    OMAi MEPTQPA.
    PhylomeDBi O14593.
    TreeFami TF333112.

    Miscellaneous databases

    GeneWikii RFXANK.
    GenomeRNAii 8625.
    NextBioi 32333.
    PROi O14593.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi O14593.
    Bgeei O14593.
    CleanExi HS_RFXANK.
    Genevestigatori O14593.

    Family and domain databases

    Gene3Di 1.25.40.20. 2 hits.
    InterProi IPR002110. Ankyrin_rpt.
    IPR020683. Ankyrin_rpt-contain_dom.
    IPR017362. DNA-bd_RFXANK.
    [Graphical view ]
    Pfami PF00023. Ank. 3 hits.
    [Graphical view ]
    PIRSFi PIRSF038034. DNA-binding_RFXANK. 1 hit.
    SMARTi SM00248. ANK. 4 hits.
    [Graphical view ]
    SUPFAMi SSF48403. SSF48403. 1 hit.
    PROSITEi PS50297. ANK_REP_REGION. 1 hit.
    PS50088. ANK_REPEAT. 3 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "A gene encoding a novel RFX-associated transactivator is mutated in the majority of MHC class II deficiency patients."
      Masternak K., Barras E., Zufferey M., Conrad B., Corthals G., Aebersold R., Sanchez J.-C., Hochstrasser D.F., Mach B., Reith W.
      Nat. Genet. 20:273-277(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), IDENTIFICATION BY MASS SPECTROMETRY, INVOLVEMENT IN BLS2.
      Tissue: B-cell.
    2. "RFX-B is the gene responsible for the most common cause of the bare lymphocyte syndrome, an MHC class II immunodeficiency."
      Nagarajan U.M., Louis-Plence P., DeSandro A., Nilsen R., Bushey A., Boss J.M.
      Immunity 10:153-162(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), PROTEIN SEQUENCE OF 79-95; 180-198; 100-210 AND 238-248, INVOLVEMENT IN BLS2.
      Tissue: Lymphoblast.
    3. "Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells."
      Zhang Q.-H., Ye M., Wu X.-Y., Ren S.-X., Zhao M., Zhao C.-J., Fu G., Shen Y., Fan H.-Y., Lu G., Zhong M., Xu X.-R., Han Z.-G., Zhang J.-W., Tao J., Huang Q.-H., Zhou J., Hu G.-X.
      , Gu J., Chen S.-J., Chen Z.
      Genome Res. 10:1546-1560(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
      Tissue: Umbilical cord blood.
    4. "Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
      Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
      Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    5. "The DNA sequence and biology of human chromosome 19."
      Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V.
      , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M.
      Nature 428:529-535(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    7. "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] (ISOFORMS 1 AND 3).
    8. "Solution structure of the heterotrimeric complex between the interaction domains of RFX5 and RFXAP from the RFX gene regulatory complex."
      Laird K.M., Briggs L.L., Boss J.M., Summers M.F., Garvie C.W.
      J. Mol. Biol. 403:40-51(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT.
    9. Cited for: X-RAY CRYSTALLOGRAPHY (1.57 ANGSTROMS) OF 90-260 IN COMPLEX WITH RFX5 PEPTIDE.
    10. "Novel mutations within the RFX-B gene and partial rescue of MHC and related genes through exogenous class II transactivator in RFX-B-deficient cells."
      Nagarajan U.M., Peijnenburg A., Gobin S.J., Boss J.M., van den Elsen P.J.
      J. Immunol. 164:3666-3674(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT BLS2 PRO-195.

    Entry informationi

    Entry nameiRFXK_HUMAN
    AccessioniPrimary (citable) accession number: O14593
    Secondary accession number(s): O95839, Q24JQ1, Q6FGA8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1999
    Last sequence update: July 15, 1999
    Last modified: October 1, 2014
    This is version 139 of the entry and version 2 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 19
      Human chromosome 19: 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. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3