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Protein

DNA-binding protein RFX5

Gene

RFX5

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

Functioni

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.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi92 – 168RFX-type winged-helixPROSITE-ProRule annotationAdd BLAST77

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000143390-MONOMER.
SIGNORiP48382.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-binding protein RFX5
Alternative name(s):
Regulatory factor X 5
Gene namesi
Name:RFX5
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:9986. RFX5.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Bare lymphocyte syndrome 2 (BLS2)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:209920
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_015550149R → Q in BLS2. 1 PublicationCorresponds to variant rs137853099dbSNPEnsembl.1

Keywords - Diseasei

Disease mutation, SCID

Organism-specific databases

DisGeNETi5993.
MalaCardsiRFX5.
MIMi209920. phenotype.
OpenTargetsiENSG00000143390.
Orphaneti572. Immunodeficiency by defective expression of HLA class 2.
PharmGKBiPA34356.

Polymorphism and mutation databases

BioMutaiRFX5.
DMDMi1350587.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00002152922 – 616DNA-binding protein RFX5Add BLAST615

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1
Modified residuei10PhosphoserineCombined sources1
Modified residuei185PhosphoserineCombined sources1

Post-translational modificationi

Phosphorylated.

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiP48382.
MaxQBiP48382.
PaxDbiP48382.
PeptideAtlasiP48382.
PRIDEiP48382.

PTM databases

iPTMnetiP48382.
PhosphoSitePlusiP48382.

Expressioni

Tissue specificityi

Ubiquitous.

Gene expression databases

BgeeiENSG00000143390.
CleanExiHS_RFX5.
ExpressionAtlasiP48382. baseline and differential.
GenevisibleiP48382. HS.

Organism-specific databases

HPAiHPA018519.

Interactioni

Subunit structurei

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. Interacts (via PxLPxI/L motif) with RFXANK (via ankyrin repeats); the interaction is direct. RFX forms cooperative DNA binding complexes with X2BP and CBF/NF-Y. RFX associates with CIITA to form an active transcriptional complex.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
HDAC2Q927694EBI-923266,EBI-301821

Protein-protein interaction databases

BioGridi111925. 27 interactors.
IntActiP48382. 7 interactors.
MINTiMINT-7944772.
STRINGi9606.ENSP00000290524.

Structurei

Secondary structure

1616
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi30 – 36Combined sources7
Helixi40 – 54Combined sources15
Helixi58 – 66Combined sources9
Helixi74 – 78Combined sources5
Beta strandi82 – 86Combined sources5
Beta strandi178 – 180Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KW3NMR-A/B24-90[»]
3V30X-ray1.57B167-183[»]
ProteinModelPortaliP48382.
SMRiP48382.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP48382.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni25 – 90N-terminal domainAdd BLAST66
Regioni62 – 66Leucine-rich region; critical for dimer formation and for interaction with RFXAP5

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi173 – 178PxLPxI/L motif; mediates interaction with RFXANK1 Publication6

Domaini

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.1 Publication
The PxLPxI/L motif mediates interaction with ankyrin repeats of RFXANK.1 Publication

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG3712. Eukaryota.
ENOG410XSHE. LUCA.
GeneTreeiENSGT00860000133802.
HOGENOMiHOG000037928.
HOVERGENiHBG014939.
InParanoidiP48382.
KOiK08061.
OMAiSESPEMG.
OrthoDBiEOG091G0LV2.
PhylomeDBiP48382.
TreeFamiTF321340.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR003150. DNA-bd_RFX.
IPR033486. RFX5.
IPR029298. RFX5_C.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PANTHERiPTHR12619:SF18. PTHR12619:SF18. 1 hit.
PfamiPF14621. RFX5_DNA_bdg. 1 hit.
PF02257. RFX_DNA_binding. 1 hit.
[Graphical view]
SMARTiSM01306. RFX5_DNA_bdg. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.
PROSITEiPS51526. RFX_DBD. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P48382-1) [UniParc]FASTAAdd to basket

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

        10         20         30         40         50
MAEDEPDAKS PKTGGRAPPG GAEAGEPTTL LQRLRGTISK AVQNKVEGIL
60 70 80 90 100
QDVQKFSDND KLYLYLQLPS GPTTGDKSSE PSTLSNEEYM YAYRWIRNHL
110 120 130 140 150
EEHTDTCLPK QSVYDAYRKY CESLACCRPL STANFGKIIR EIFPDIKARR
160 170 180 190 200
LGGRGQSKYC YSGIRRKTLV SMPPLPGLDL KGSESPEMGP EVTPAPRDEL
210 220 230 240 250
VEAACALTCD WAERILKRSF SSIVEVARFL LQQHLISARS AHAHVLKAMG
260 270 280 290 300
LAEEDEHAPR ERSSKPKNGL ENPEGGAHKK PERLAQPPKD LEARTGAGPL
310 320 330 340 350
ARGERKKSVV ESSAPGANNL QVNALVARLP LLLPRAPRSL IPPIPVSPPI
360 370 380 390 400
LAPRLSSGAL KVATLPLSSR AGAPPAAVPI INMILPTVPA LPGPGPGPGR
410 420 430 440 450
APPGGLTQPR GTENREVGIG GDQGPHDKGV KRTAEVPVSE ASGQAPPAKA
460 470 480 490 500
AKQDIEDTAS DAKRKRGRPR KKSGGSGERN STPLKSAAAM ESAQSSRLPW
510 520 530 540 550
ETWGSGGEGN SAGGAERPGP MGEAEKGAVL AQGQGDGTVS KGGRGPGSQH
560 570 580 590 600
TKEAEDKIPL VPSKVSVIKG SRSQKEAFPL AKGEVDTAPQ GNKDLKEHVL
610
QSSLSQEHKD PKATPP
Length:616
Mass (Da):65,323
Last modified:February 1, 1996 - v1
Checksum:i5EBB33C677BB717F
GO
Isoform 2 (identifier: P48382-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     78-117: Missing.

Note: No experimental confirmation available.
Show »
Length:576
Mass (Da):60,513
Checksum:iF8DEC5FCB5675383
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_015550149R → Q in BLS2. 1 PublicationCorresponds to variant rs137853099dbSNPEnsembl.1
Natural variantiVAR_034448197R → Q.Corresponds to variant rs2233851dbSNPEnsembl.1
Natural variantiVAR_034449409P → R.Corresponds to variant rs2233854dbSNPEnsembl.1
Natural variantiVAR_034450499P → S.Corresponds to variant rs2233855dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_05586478 – 117Missing in isoform 2. 1 PublicationAdd BLAST40

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X85786 mRNA. Translation: CAA59771.1.
AK302891 mRNA. Translation: BAH13834.1.
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.
CCDSiCCDS994.1. [P48382-1]
PIRiI38155.
RefSeqiNP_000440.1. NM_000449.3. [P48382-1]
NP_001020774.1. NM_001025603.1. [P48382-1]
XP_005245462.1. XM_005245405.1. [P48382-1]
XP_005245463.1. XM_005245406.3. [P48382-1]
XP_011508149.1. XM_011509847.1. [P48382-1]
XP_011508150.1. XM_011509848.1. [P48382-1]
XP_011508151.1. XM_011509849.1. [P48382-1]
XP_011508152.1. XM_011509850.1. [P48382-1]
UniGeneiHs.632472.

Genome annotation databases

EnsembliENST00000290524; ENSP00000290524; ENSG00000143390. [P48382-1]
ENST00000368870; ENSP00000357864; ENSG00000143390. [P48382-1]
ENST00000452671; ENSP00000389130; ENSG00000143390. [P48382-1]
GeneIDi5993.
KEGGihsa:5993.
UCSCiuc001exv.2. human. [P48382-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Web resourcesi

RFX5base

RFX5 mutation db

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X85786 mRNA. Translation: CAA59771.1.
AK302891 mRNA. Translation: BAH13834.1.
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.
CCDSiCCDS994.1. [P48382-1]
PIRiI38155.
RefSeqiNP_000440.1. NM_000449.3. [P48382-1]
NP_001020774.1. NM_001025603.1. [P48382-1]
XP_005245462.1. XM_005245405.1. [P48382-1]
XP_005245463.1. XM_005245406.3. [P48382-1]
XP_011508149.1. XM_011509847.1. [P48382-1]
XP_011508150.1. XM_011509848.1. [P48382-1]
XP_011508151.1. XM_011509849.1. [P48382-1]
XP_011508152.1. XM_011509850.1. [P48382-1]
UniGeneiHs.632472.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KW3NMR-A/B24-90[»]
3V30X-ray1.57B167-183[»]
ProteinModelPortaliP48382.
SMRiP48382.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111925. 27 interactors.
IntActiP48382. 7 interactors.
MINTiMINT-7944772.
STRINGi9606.ENSP00000290524.

PTM databases

iPTMnetiP48382.
PhosphoSitePlusiP48382.

Polymorphism and mutation databases

BioMutaiRFX5.
DMDMi1350587.

Proteomic databases

EPDiP48382.
MaxQBiP48382.
PaxDbiP48382.
PeptideAtlasiP48382.
PRIDEiP48382.

Protocols and materials databases

DNASUi5993.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000290524; ENSP00000290524; ENSG00000143390. [P48382-1]
ENST00000368870; ENSP00000357864; ENSG00000143390. [P48382-1]
ENST00000452671; ENSP00000389130; ENSG00000143390. [P48382-1]
GeneIDi5993.
KEGGihsa:5993.
UCSCiuc001exv.2. human. [P48382-1]

Organism-specific databases

CTDi5993.
DisGeNETi5993.
GeneCardsiRFX5.
HGNCiHGNC:9986. RFX5.
HPAiHPA018519.
MalaCardsiRFX5.
MIMi209920. phenotype.
601863. gene.
neXtProtiNX_P48382.
OpenTargetsiENSG00000143390.
Orphaneti572. Immunodeficiency by defective expression of HLA class 2.
PharmGKBiPA34356.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3712. Eukaryota.
ENOG410XSHE. LUCA.
GeneTreeiENSGT00860000133802.
HOGENOMiHOG000037928.
HOVERGENiHBG014939.
InParanoidiP48382.
KOiK08061.
OMAiSESPEMG.
OrthoDBiEOG091G0LV2.
PhylomeDBiP48382.
TreeFamiTF321340.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000143390-MONOMER.
SIGNORiP48382.

Miscellaneous databases

EvolutionaryTraceiP48382.
GeneWikiiRFX5.
GenomeRNAii5993.
PROiP48382.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000143390.
CleanExiHS_RFX5.
ExpressionAtlasiP48382. baseline and differential.
GenevisibleiP48382. HS.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR003150. DNA-bd_RFX.
IPR033486. RFX5.
IPR029298. RFX5_C.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PANTHERiPTHR12619:SF18. PTHR12619:SF18. 1 hit.
PfamiPF14621. RFX5_DNA_bdg. 1 hit.
PF02257. RFX_DNA_binding. 1 hit.
[Graphical view]
SMARTiSM01306. RFX5_DNA_bdg. 1 hit.
[Graphical view]
SUPFAMiSSF46785. SSF46785. 1 hit.
PROSITEiPS51526. RFX_DBD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRFX5_HUMAN
AccessioniPrimary (citable) accession number: P48382
Secondary accession number(s): B7Z848
, D3DV19, E9PFU4, Q5VWC3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: November 30, 2016
This is version 151 of the entry and version 1 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 1
    Human chromosome 1: 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

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 one 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.