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Protein

MHC class II regulatory factor RFX1

Gene

RFX1

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

Functioni

Regulatory factor essential for MHC class II genes expression. Binds to the X boxes of MHC class II genes. Also binds to an inverted repeat (ENH1) required for hepatitis B virus genes expression and to the most upstream element (alpha) of the RPL30 promoter.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi438 – 51376RFX-type winged-helixPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. RNA polymerase II core promoter proximal region sequence-specific DNA binding Source: GO_Central
  2. RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity Source: ProtInc

GO - Biological processi

  1. immune response Source: ProtInc
  2. regulation of transcription from RNA polymerase II promoter Source: GOC
  3. transcription from RNA polymerase II promoter Source: GOC
Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

SignaLinkiP22670.

Names & Taxonomyi

Protein namesi
Recommended name:
MHC class II regulatory factor RFX1
Alternative name(s):
Enhancer factor C
Short name:
EF-C
Regulatory factor X 1
Short name:
RFX
Transcription factor RFX1
Gene namesi
Name:RFX1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 19

Organism-specific databases

HGNCiHGNC:9982. RFX1.

Subcellular locationi

GO - Cellular componenti

  1. intracellular membrane-bounded organelle Source: HPA
  2. nucleoplasm Source: HPA
  3. nucleus Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA34352.

Polymorphism and mutation databases

BioMutaiRFX1.
DMDMi288558824.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 979979MHC class II regulatory factor RFX1PRO_0000215286Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei978 – 9781Phosphoserine1 Publication
Modified residuei979 – 9791Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP22670.
PaxDbiP22670.
PRIDEiP22670.

PTM databases

PhosphoSiteiP22670.

Expressioni

Gene expression databases

BgeeiP22670.
CleanExiHS_RFX1.
ExpressionAtlasiP22670. baseline and differential.
GenevestigatoriP22670.

Organism-specific databases

HPAiHPA048722.

Interactioni

Subunit structurei

Binds DNA as a homodimer.1 Publication

Protein-protein interaction databases

BioGridi111921. 17 interactions.
IntActiP22670. 8 interactions.
MINTiMINT-1186898.
STRINGi9606.ENSP00000254325.

Structurei

Secondary structure

1
979
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi439 – 4457Combined sources
Beta strandi446 – 45510Combined sources
Helixi456 – 46914Combined sources
Helixi477 – 48711Combined sources
Beta strandi492 – 4987Combined sources
Beta strandi503 – 5119Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DP7X-ray1.50P438-513[»]
ProteinModelPortaliP22670.
SMRiP22670. Positions 438-513.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP22670.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni744 – 979236Necessary for dimerizationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi381 – 41131Gly-richAdd
BLAST
Compositional biasi920 – 93617Asp/Glu-rich (acidic)Add
BLAST

Sequence similaritiesi

Belongs to the RFX family.PROSITE-ProRule annotation
Contains 1 RFX-type winged-helix DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiNOG264634.
GeneTreeiENSGT00550000074532.
HOGENOMiHOG000294091.
HOVERGENiHBG002753.
InParanoidiP22670.
KOiK09173.
OMAiGGQKQYV.
OrthoDBiEOG7TF793.
PhylomeDBiP22670.
TreeFamiTF321340.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR003150. DNA-bd_RFX.
IPR007668. RFX1_trans_act.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF04589. RFX1_trans_act. 1 hit.
PF02257. RFX_DNA_binding. 1 hit.
[Graphical view]
PROSITEiPS51526. RFX_DBD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P22670-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATQAYTELQ AAPPPSQPPQ APPQAQPQPP PPPPPAAPQP PQPPTAAATP
60 70 80 90 100
QPQYVTELQS PQPQAQPPGG QKQYVTELPA VPAPSQPTGA PTPSPAPQQY
110 120 130 140 150
IVVTVSEGAM RASETVSEAS PGSTASQTGV PTQVVQQVQG TQQRLLVQTS
160 170 180 190 200
VQAKPGHVSP LQLTNIQVPQ QALPTQRLVV QSAAPGSKGG QVSLTVHGTQ
210 220 230 240 250
QVHSPPEQSP VQANSSSSKT AGAPTGTVPQ QLQVHGVQQS VPVTQERSVV
260 270 280 290 300
QATPQAPKPG PVQPLTVQGL QPVHVAQEVQ QLQQVPVPHV YSSQVQYVEG
310 320 330 340 350
GDASYTASAI RSSTYSYPET PLYTQTASTS YYEAAGTATQ VSTPATSQAV
360 370 380 390 400
ASSGSMPMYV SGSQVVASST STGAGASNSS GGGGSGGGGG GGGGGGGGGS
410 420 430 440 450
GSTGGGGSGA GTYVIQGGYM LGSASQSYSH TTRASPATVQ WLLDNYETAE
460 470 480 490 500
GVSLPRSTLY CHYLLHCQEQ KLEPVNAASF GKLIRSVFMG LRTRRLGTRG
510 520 530 540 550
NSKYHYYGLR IKASSPLLRL MEDQQHMAMR GQPFSQKQRL KPIQKMEGMT
560 570 580 590 600
NGVAVGQQPS TGLSDISAQV QQYQQFLDAS RSLPDFTELD LQGKVLPEGV
610 620 630 640 650
GPGDIKAFQV LYREHCEAIV DVMVNLQFTL VETLWKTFWR YNLSQPSEAP
660 670 680 690 700
PLAVHDEAEK RLPKAILVLL SKFEPVLQWT KHCDNVLYQG LVEILIPDVL
710 720 730 740 750
RPIPSALTQA IRNFAKSLES WLTHAMVNIP EEMLRVKVAA AGAFAQTLRR
760 770 780 790 800
YTSLNHLAQA ARAVLQNTAQ INQMLSDLNR VDFANVQEQA SWVCRCEDRV
810 820 830 840 850
VQRLEQDFKV TLQQQNSLEQ WAAWLDGVVS QVLKPYQGSA GFPKAAKLFL
860 870 880 890 900
LKWSFYSSMV IRDLTLRSAA SFGSFHLIRL LYDEYMYYLI EHRVAQAKGE
910 920 930 940 950
TPIAVMGEFA NLATSLNPLD PDKDEEEEEE EESEDELPQD ISLAAGGESP
960 970
ALGPETLEPP AKLARTDARG LFVQALPSS
Length:979
Mass (Da):104,758
Last modified:February 9, 2010 - v2
Checksum:i4FD8EA9C4AB1A411
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti370 – 3701T → A.2 Publications
Corresponds to variant rs2305780 [ dbSNP | Ensembl ].
VAR_059781

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X58964 mRNA. Translation: CAA41730.1.
AC020916 Genomic DNA. No translation available.
AC022098 Genomic DNA. No translation available.
BC049826 mRNA. Translation: AAH49826.1.
CCDSiCCDS12301.1.
PIRiA35913.
RefSeqiNP_002909.4. NM_002918.4.
UniGeneiHs.655215.

Genome annotation databases

EnsembliENST00000254325; ENSP00000254325; ENSG00000132005.
GeneIDi5989.
KEGGihsa:5989.
UCSCiuc002mxv.3. human.

Polymorphism and mutation databases

BioMutaiRFX1.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X58964 mRNA. Translation: CAA41730.1.
AC020916 Genomic DNA. No translation available.
AC022098 Genomic DNA. No translation available.
BC049826 mRNA. Translation: AAH49826.1.
CCDSiCCDS12301.1.
PIRiA35913.
RefSeqiNP_002909.4. NM_002918.4.
UniGeneiHs.655215.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DP7X-ray1.50P438-513[»]
ProteinModelPortaliP22670.
SMRiP22670. Positions 438-513.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111921. 17 interactions.
IntActiP22670. 8 interactions.
MINTiMINT-1186898.
STRINGi9606.ENSP00000254325.

PTM databases

PhosphoSiteiP22670.

Polymorphism and mutation databases

BioMutaiRFX1.
DMDMi288558824.

Proteomic databases

MaxQBiP22670.
PaxDbiP22670.
PRIDEiP22670.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000254325; ENSP00000254325; ENSG00000132005.
GeneIDi5989.
KEGGihsa:5989.
UCSCiuc002mxv.3. human.

Organism-specific databases

CTDi5989.
GeneCardsiGC19M014072.
H-InvDBHIX0027643.
HGNCiHGNC:9982. RFX1.
HPAiHPA048722.
MIMi600006. gene.
neXtProtiNX_P22670.
PharmGKBiPA34352.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG264634.
GeneTreeiENSGT00550000074532.
HOGENOMiHOG000294091.
HOVERGENiHBG002753.
InParanoidiP22670.
KOiK09173.
OMAiGGQKQYV.
OrthoDBiEOG7TF793.
PhylomeDBiP22670.
TreeFamiTF321340.

Enzyme and pathway databases

SignaLinkiP22670.

Miscellaneous databases

ChiTaRSiRFX1. human.
EvolutionaryTraceiP22670.
GeneWikiiRFX1.
GenomeRNAii5989.
NextBioi23325.
PROiP22670.
SOURCEiSearch...

Gene expression databases

BgeeiP22670.
CleanExiHS_RFX1.
ExpressionAtlasiP22670. baseline and differential.
GenevestigatoriP22670.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR003150. DNA-bd_RFX.
IPR007668. RFX1_trans_act.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF04589. RFX1_trans_act. 1 hit.
PF02257. RFX_DNA_binding. 1 hit.
[Graphical view]
PROSITEiPS51526. RFX_DBD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "MHC class II regulatory factor RFX has a novel DNA-binding domain and a functionally independent dimerization domain."
    Reith W., Sanchez-Herrero C., Kobr M., Silacci P., Berte C., Barras E., Mach B.
    Genes Dev. 4:1528-1540(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT ALA-370.
  2. "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].
  3. "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], VARIANT ALA-370.
    Tissue: Testis.
  4. "RFX1 is identical to enhancer factor C and functions as a transactivator of the hepatitis B virus enhancer."
    Siegrist C.A., Durand B., Emery P., David E., Hearing P., Mach B., Reith W.
    Mol. Cell. Biol. 13:6375-6384(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTITY OF RFX1 AND EF-C.
  5. "Transcription factor RFX1 helps control the promoter of the mouse ribosomal protein-encoding gene rpL30 by binding to its alpha element."
    Safrany G., Perry R.P.
    Gene 132:279-283(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: BINDING TO RPL30 PROMOTER.
  6. "The DNA-binding defect observed in major histocompatibility complex class II regulatory mutants concerns only one member of a family of complexes binding to the X boxes of class II promoters."
    Sanchez-Herrero C., Reith W., Silacci P., Mach B.
    Mol. Cell. Biol. 12:4076-4083(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: SHOWS THAT BLS II IS NOT DUE TO RFX1.
  7. "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle."
    Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M.
    Mol. Cell 31:438-448(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  8. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  9. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
    Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
    Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Leukemic T-cell.
  10. "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-978 AND SER-979, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  11. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding."
    Gajiwala K.S., Chen H., Cornille F., Roques B.P., Reith W., Mach B., Burley S.K.
    Nature 403:916-921(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 438-513 IN COMPLEX WITH DNA.

Entry informationi

Entry nameiRFX1_HUMAN
AccessioniPrimary (citable) accession number: P22670
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: February 9, 2010
Last modified: April 29, 2015
This is version 148 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, 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.