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UniProtKB - P48382 (RFX5_HUMAN)

Protein

DNA-binding protein RFX5

Gene

RFX5

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

View the complete GO annotation on QuickGO ...

GO - Biological processi

View the complete GO annotation on QuickGO ...

Keywordsi

Molecular functionActivator, DNA-binding
Biological processTranscription, Transcription regulation

Enzyme and pathway databases

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 lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

EuPathDBiHostDB:ENSG00000143390.17
HGNCiHGNC:9986 RFX5
MIMi601863 gene
neXtProtiNX_P48382

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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 dbSNP:rs137853099EnsemblClinVar.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
ProteomicsDBi55886

PTM databases

iPTMnetiP48382
PhosphoSitePlusiP48382

Expressioni

Tissue specificityi

Ubiquitous.

Gene expression databases

BgeeiENSG00000143390 Expressed in 226 organ(s), highest expression level in female gonad
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
CORUMiP48382
ELMiP48382
IntActiP48382, 9 interactors
MINTiP48382
STRINGi9606.ENSP00000290524

Structurei

Secondary structure

1616
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

Phylogenomic databases

eggNOGiKOG3712 Eukaryota
ENOG410XSHE LUCA
GeneTreeiENSGT00550000074532
HOGENOMiHOG000037928
HOVERGENiHBG014939
InParanoidiP48382
KOiK08061
OMAiTENREVG
OrthoDBiEOG091G0LV2
PhylomeDBiP48382
TreeFamiTF321340

Family and domain databases

Gene3Di1.10.10.10, 1 hit
InterProiView protein in InterPro
IPR003150 DNA-bd_RFX
IPR039779 RFX-like
IPR033486 RFX5
IPR029298 RFX5_C
IPR036388 WH-like_DNA-bd_sf
IPR036390 WH_DNA-bd_sf
PANTHERiPTHR12619 PTHR12619, 1 hit
PTHR12619:SF18 PTHR12619:SF18, 1 hit
PfamiView protein in Pfam
PF14621 RFX5_DNA_bdg, 1 hit
PF02257 RFX_DNA_binding, 1 hit
SMARTiView protein in SMART
SM01306 RFX5_DNA_bdg, 1 hit
SUPFAMiSSF46785 SSF46785, 1 hit
PROSITEiView protein in PROSITE
PS51526 RFX_DBD, 1 hit

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

This entry has 2 described isoforms and 12 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 12 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H0Y4B4H0Y4B4_HUMAN
DNA-binding protein RFX5
RFX5
235Annotation score:
F8W689F8W689_HUMAN
DNA-binding protein RFX5
RFX5
596Annotation score:
F6UE82F6UE82_HUMAN
DNA-binding protein RFX5
RFX5
184Annotation score:
F6R6G4F6R6G4_HUMAN
DNA-binding protein RFX5
RFX5
165Annotation score:
F6X9D6F6X9D6_HUMAN
DNA-binding protein RFX5
RFX5
123Annotation score:
A0A0A0MSQ2A0A0A0MSQ2_HUMAN
DNA-binding protein RFX5
RFX5
229Annotation score:
F6S3S0F6S3S0_HUMAN
DNA-binding protein RFX5
RFX5
96Annotation score:
F8WDU3F8WDU3_HUMAN
DNA-binding protein RFX5
RFX5
42Annotation score:
F8WFE4F8WFE4_HUMAN
DNA-binding protein RFX5
RFX5
44Annotation score:
A0A0A0MSM9A0A0A0MSM9_HUMAN
DNA-binding protein RFX5
RFX5
117Annotation score:
There are more potential isoformsShow all

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_015550149R → Q in BLS2. 1 PublicationCorresponds to variant dbSNP:rs137853099EnsemblClinVar.1
Natural variantiVAR_034448197R → Q. Corresponds to variant dbSNP:rs2233851EnsemblClinVar.1
Natural variantiVAR_034449409P → R. Corresponds to variant dbSNP:rs2233854EnsemblClinVar.1
Natural variantiVAR_034450499P → S. Corresponds to variant dbSNP:rs2233855EnsemblClinVar.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 No translation available.
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

Similar proteinsi

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 No translation available.
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
CORUMiP48382
ELMiP48382
IntActiP48382, 9 interactors
MINTiP48382
STRINGi9606.ENSP00000290524

PTM databases

iPTMnetiP48382
PhosphoSitePlusiP48382

Polymorphism and mutation databases

BioMutaiRFX5
DMDMi1350587

Proteomic databases

EPDiP48382
MaxQBiP48382
PaxDbiP48382
PeptideAtlasiP48382
PRIDEiP48382
ProteomicsDBi55886

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
EuPathDBiHostDB:ENSG00000143390.17
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
GeneTreeiENSGT00550000074532
HOGENOMiHOG000037928
HOVERGENiHBG014939
InParanoidiP48382
KOiK08061
OMAiTENREVG
OrthoDBiEOG091G0LV2
PhylomeDBiP48382
TreeFamiTF321340

Enzyme and pathway databases

SIGNORiP48382

Miscellaneous databases

ChiTaRSiRFX5 human
EvolutionaryTraceiP48382
GeneWikiiRFX5
GenomeRNAii5993
PROiPR:P48382
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000143390 Expressed in 226 organ(s), highest expression level in female gonad
CleanExiHS_RFX5
ExpressionAtlasiP48382 baseline and differential
GenevisibleiP48382 HS

Family and domain databases

Gene3Di1.10.10.10, 1 hit
InterProiView protein in InterPro
IPR003150 DNA-bd_RFX
IPR039779 RFX-like
IPR033486 RFX5
IPR029298 RFX5_C
IPR036388 WH-like_DNA-bd_sf
IPR036390 WH_DNA-bd_sf
PANTHERiPTHR12619 PTHR12619, 1 hit
PTHR12619:SF18 PTHR12619:SF18, 1 hit
PfamiView protein in Pfam
PF14621 RFX5_DNA_bdg, 1 hit
PF02257 RFX_DNA_binding, 1 hit
SMARTiView protein in SMART
SM01306 RFX5_DNA_bdg, 1 hit
SUPFAMiSSF46785 SSF46785, 1 hit
PROSITEiView protein in PROSITE
PS51526 RFX_DBD, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRFX5_HUMAN
AccessioniPrimary (citable) accession number: P48382
Secondary accession number(s): B7Z848
, D3DV19, E9PFU4, Q5VWC3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: November 7, 2018
This is version 163 of the entry and version 1 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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