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O14593

- RFXK_HUMAN

UniProt

O14593 - RFXK_HUMAN

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Protein
DNA-binding protein RFXANK
Gene
RFXANK, ANKRA1, RFXB
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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

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
Complete GO annotation...

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.
Note: The disease is caused by mutations affecting the gene represented in this entry.3 Publications
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 RFXANK
PRO_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.1 Publication

Protein-protein interaction databases

BioGridi114180. 18 interactions.
STRINGi9606.ENSP00000305071.

Structurei

Secondary structure

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.

Family & Domainsi

Domains and Repeats

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

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.
VSP_000283
Alternative sequencei91 – 11323SLSIH…HLRKG → C in isoform 2 and isoform 3.
VSP_000284Add
BLAST
Alternative sequencei159 – 17214Missing in isoform 2.
VSP_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]
ENST00000353145; ENSP00000262804; ENSG00000064490. [O14593-2]
ENST00000392324; ENSP00000376138; ENSG00000064490. [O14593-2]
ENST00000407360; ENSP00000384572; ENSG00000064490. [O14593-1]
ENST00000456252; ENSP00000409138; ENSG00000064490.
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 ]
ENST00000353145 ; ENSP00000262804 ; ENSG00000064490 . [O14593-2 ]
ENST00000392324 ; ENSP00000376138 ; ENSG00000064490 . [O14593-2 ]
ENST00000407360 ; ENSP00000384572 ; ENSG00000064490 . [O14593-1 ]
ENST00000456252 ; ENSP00000409138 ; ENSG00000064490 .
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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 138 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

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