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P48382 (RFX5_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 128. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA-binding protein RFX5
Alternative name(s):
Regulatory factor X 5
Gene names
Name:RFX5
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length616 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding between RFX and NF-Y. RFX binds the X1 box of MHC-II promoters.

Subunit structure

Homodimer. 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 CIITA to form an active transcriptional complex. Ref.10

Subcellular location

Nucleus.

Tissue specificity

Ubiquitous.

Domain

The N-terminus is required for dimer formation, association with RFXANK and RFXAP, assembly of the RFX complex, and for binding of this complex to its X box target site in the MHC-II promoter. The C-terminus mediates cooperative binding between the RFX complex and NF-Y. Ref.10

Post-translational modification

Phosphorylated.

Involvement in disease

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. Ref.12

Sequence similarities

Belongs to the RFX family.

Contains 1 RFX-type winged-helix DNA-binding domain.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

HDAC2Q927694EBI-923266,EBI-301821

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.9
Chain2 – 616615DNA-binding protein RFX5
PRO_0000215292

Regions

DNA binding92 – 16877RFX-type winged-helix
Region25 – 9066N-terminal domain
Region62 – 665Leucine-rich region; critical for dimer formation and for interaction with RFXAP

Amino acid modifications

Modified residue21N-acetylalanine Ref.9
Modified residue1851Phosphoserine Ref.8

Natural variations

Natural variant1491R → Q in BLS2. Ref.12
VAR_015550
Natural variant1971R → Q.
Corresponds to variant rs2233851 [ dbSNP | Ensembl ].
VAR_034448
Natural variant4091P → R.
Corresponds to variant rs2233854 [ dbSNP | Ensembl ].
VAR_034449
Natural variant4991P → S.
Corresponds to variant rs2233855 [ dbSNP | Ensembl ].
VAR_034450

Secondary structure

............. 616
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P48382 [UniParc].

Last modified February 1, 1996. Version 1.
Checksum: 5EBB33C677BB717F

FASTA61665,323
        10         20         30         40         50         60 
MAEDEPDAKS PKTGGRAPPG GAEAGEPTTL LQRLRGTISK AVQNKVEGIL QDVQKFSDND 

        70         80         90        100        110        120 
KLYLYLQLPS GPTTGDKSSE PSTLSNEEYM YAYRWIRNHL EEHTDTCLPK QSVYDAYRKY 

       130        140        150        160        170        180 
CESLACCRPL STANFGKIIR EIFPDIKARR LGGRGQSKYC YSGIRRKTLV SMPPLPGLDL 

       190        200        210        220        230        240 
KGSESPEMGP EVTPAPRDEL VEAACALTCD WAERILKRSF SSIVEVARFL LQQHLISARS 

       250        260        270        280        290        300 
AHAHVLKAMG LAEEDEHAPR ERSSKPKNGL ENPEGGAHKK PERLAQPPKD LEARTGAGPL 

       310        320        330        340        350        360 
ARGERKKSVV ESSAPGANNL QVNALVARLP LLLPRAPRSL IPPIPVSPPI LAPRLSSGAL 

       370        380        390        400        410        420 
KVATLPLSSR AGAPPAAVPI INMILPTVPA LPGPGPGPGR APPGGLTQPR GTENREVGIG 

       430        440        450        460        470        480 
GDQGPHDKGV KRTAEVPVSE ASGQAPPAKA AKQDIEDTAS DAKRKRGRPR KKSGGSGERN 

       490        500        510        520        530        540 
STPLKSAAAM ESAQSSRLPW ETWGSGGEGN SAGGAERPGP MGEAEKGAVL AQGQGDGTVS 

       550        560        570        580        590        600 
KGGRGPGSQH TKEAEDKIPL VPSKVSVIKG SRSQKEAFPL AKGEVDTAPQ GNKDLKEHVL 

       610 
QSSLSQEHKD PKATPP 

« Hide

References

« Hide 'large scale' references
[1]"A novel DNA-binding regulatory factor is mutated in primary MHC class II deficiency (bare lymphocyte syndrome)."
Steimle V., Durand B., Barras E., Zufferey M., Hadam M.R., Mach B., Reith W.
Genes Dev. 9:1021-1032(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"The DNA sequence and biological annotation of human chromosome 1."
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. expand/collapse author list , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"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: Uterus.
[5]"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: PARTIAL PROTEIN SEQUENCE.
Tissue: Lymphoblast.
[6]Erratum
Nagarajan U.M., Louis-Plence P., DeSandro A., Nilsen R., Bushey A., Boss J.M.
Immunity 10:399-399(1999)
[7]"A functionally essential domain of RFX5 mediates activation of major histocompatibility complex class II promoters by promoting cooperative binding between RFX and NF-Y."
Villard J., Peretti M., Masternak K., Barras E., Caretti G., Mantovani R., Reith W.
Mol. Cell. Biol. 20:3364-3376(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION.
[8]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-185, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[9]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
[10]"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: STRUCTURE BY NMR OF 24-90, SUBUNIT, DOMAIN N-TERMINAL.
[11]"Sequence-specific recognition of a PxLPxI/L motif by an ankyrin repeat tumbler lock."
Xu C., Jin J., Bian C., Lam R., Tian R., Weist R., You L., Nie J., Bochkarev A., Tempel W., Tan C.S., Wasney G.A., Vedadi M., Gish G.D., Arrowsmith C.H., Pawson T., Yang X.J., Min J.
Sci. Signal. 5:RA39-RA39(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.57 ANGSTROMS) OF 167-183 IN COMPLEX WITH RFXANK.
[12]"Mutations in the bare lymphocyte syndrome define critical steps in the assembly of the regulatory factor X complex."
Nekrep N., Jabrane-Ferrat N., Peterlin B.M.
Mol. Cell. Biol. 20:4455-4461(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT BLS2 GLN-149.
+Additional computationally mapped references.

Web resources

RFX5base

RFX5 mutation db

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X85786 mRNA. Translation: CAA59771.1.
AL391069 Genomic DNA. Translation: CAH70327.1.
CH471121 Genomic DNA. Translation: EAW53446.1.
CH471121 Genomic DNA. Translation: EAW53447.1.
CH471121 Genomic DNA. Translation: EAW53448.1.
BC017471 mRNA. Translation: AAH17471.1.
CCDSCCDS994.1.
PIRI38155.
RefSeqNP_000440.1. NM_000449.3.
NP_001020774.1. NM_001025603.1.
XP_005245462.1. XM_005245405.1.
XP_005245463.1. XM_005245406.1.
UniGeneHs.632472.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2KW3NMR-A/B24-90[»]
3V30X-ray1.57B167-183[»]
ProteinModelPortalP48382.
SMRP48382. Positions 24-90, 94-167.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid111925. 16 interactions.
IntActP48382. 4 interactions.
MINTMINT-7944772.
STRING9606.ENSP00000290524.

PTM databases

PhosphoSiteP48382.

Polymorphism databases

DMDM1350587.

Proteomic databases

MaxQBP48382.
PaxDbP48382.
PRIDEP48382.

Protocols and materials databases

DNASU5993.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000290524; ENSP00000290524; ENSG00000143390.
ENST00000368870; ENSP00000357864; ENSG00000143390.
ENST00000452671; ENSP00000389130; ENSG00000143390.
GeneID5993.
KEGGhsa:5993.
UCSCuc001exv.1. human.

Organism-specific databases

CTD5993.
GeneCardsGC01M151313.
HGNCHGNC:9986. RFX5.
HPAHPA018519.
MIM209920. phenotype.
601863. gene.
neXtProtNX_P48382.
Orphanet572. Immunodeficiency by defective expression of HLA class 2.
PharmGKBPA34356.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG315073.
HOGENOMHOG000037928.
HOVERGENHBG014939.
InParanoidP48382.
KOK08061.
OMATCDWAER.
OrthoDBEOG7MD4P8.
PhylomeDBP48382.
TreeFamTF321340.

Gene expression databases

ArrayExpressP48382.
BgeeP48382.
CleanExHS_RFX5.
GenevestigatorP48382.

Family and domain databases

Gene3D1.10.10.10. 1 hit.
InterProIPR003150. DNA-bd_RFX.
IPR029298. RFX5_C.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamPF14621. RFX5_DNA_bdg. 1 hit.
PF02257. RFX_DNA_binding. 1 hit.
[Graphical view]
PROSITEPS51526. RFX_DBD. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP48382.
GeneWikiRFX5.
GenomeRNAi5993.
NextBio23349.
PROP48382.
SOURCESearch...

Entry information

Entry nameRFX5_HUMAN
AccessionPrimary (citable) accession number: P48382
Secondary accession number(s): D3DV19, Q5VWC3
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: July 9, 2014
This is version 128 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM