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P25208

- NFYB_HUMAN

UniProt

P25208 - NFYB_HUMAN

Protein

Nuclear transcription factor Y subunit beta

Gene

NFYB

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 149 (01 Oct 2014)
      Sequence version 2 (01 Jul 1993)
      Previous versions | rss
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    Functioni

    Component of the sequence-specific heterotrimeric transcription factor (NF-Y) which specifically recognizes a 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors.

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi59 – 657By similarity

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB
    2. protein binding Source: UniProtKB
    3. repressing transcription factor binding Source: UniProtKB
    4. sequence-specific DNA binding Source: InterPro
    5. sequence-specific DNA binding transcription factor activity Source: ProtInc

    GO - Biological processi

    1. cellular lipid metabolic process Source: Reactome
    2. positive regulation of transcription, DNA-templated Source: Ensembl
    3. regulation of transcription, DNA-templated Source: UniProtKB
    4. small molecule metabolic process Source: Reactome
    5. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Activator

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding

    Enzyme and pathway databases

    ReactomeiREACT_116145. PPARA activates gene expression.
    REACT_147904. Activation of gene expression by SREBF (SREBP).
    REACT_18355. ATF4 activates genes.
    REACT_18423. ATF6-alpha activates chaperone genes.
    SignaLinkiP25208.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Nuclear transcription factor Y subunit beta
    Alternative name(s):
    CAAT box DNA-binding protein subunit B
    Nuclear transcription factor Y subunit B
    Short name:
    NF-YB
    Gene namesi
    Name:NFYB
    Synonyms:HAP3
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 12

    Organism-specific databases

    HGNCiHGNC:7805. NFYB.

    Subcellular locationi

    GO - Cellular componenti

    1. CCAAT-binding factor complex Source: UniProtKB
    2. nucleoplasm Source: Reactome
    3. nucleus Source: UniProtKB

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA31610.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 207207Nuclear transcription factor Y subunit betaPRO_0000204609Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Cross-linki140 – 140Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

    Post-translational modificationi

    Monoubiquitination at Lys-140 plays an important role in transcriptional activation by allowing the deposition of histone H3 methylations as well as histone H2B monoubiquitination at 'Lys-121'.

    Keywords - PTMi

    Isopeptide bond, Ubl conjugation

    Proteomic databases

    MaxQBiP25208.
    PaxDbiP25208.
    PRIDEiP25208.

    PTM databases

    PhosphoSiteiP25208.

    Expressioni

    Gene expression databases

    ArrayExpressiP25208.
    BgeeiP25208.
    CleanExiHS_NFYB.
    GenevestigatoriP25208.

    Organism-specific databases

    HPAiCAB004211.

    Interactioni

    Subunit structurei

    Heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding. Interacts with C1QBP.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    NFYAP235115EBI-389728,EBI-389739
    NFYCQ139523EBI-389728,EBI-389755
    TP53P046376EBI-389728,EBI-366083

    Protein-protein interaction databases

    BioGridi110867. 25 interactions.
    IntActiP25208. 7 interactions.
    MINTiMINT-146867.
    STRINGi9606.ENSP00000240055.

    Structurei

    Secondary structure

    1
    207
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi54 – 563
    Helixi61 – 7010
    Helixi80 – 10728
    Beta strandi111 – 1133
    Helixi115 – 12410
    Helixi128 – 1303
    Helixi131 – 14212

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1N1JX-ray1.67A51-143[»]
    4AWLX-ray3.08B51-143[»]
    ProteinModelPortaliP25208.
    SMRiP25208. Positions 57-143.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP25208.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 5252A domainAdd
    BLAST
    Regioni53 – 14290B domainAdd
    BLAST
    Regioni86 – 9712Subunit association domain (SAD)By similarityAdd
    BLAST
    Regioni143 – 20765C domainAdd
    BLAST

    Domaini

    Can be divided into 3 domains: the weakly conserved A domain, the highly conserved B domain thought to be involved in subunit interaction and DNA binding, and the Glu-rich C domain.

    Sequence similaritiesi

    Belongs to the NFYB/HAP3 subunit family.Curated

    Phylogenomic databases

    eggNOGiCOG2036.
    HOGENOMiHOG000211832.
    HOVERGENiHBG008864.
    InParanoidiP25208.
    KOiK08065.
    OMAiIAGDYIG.
    OrthoDBiEOG7RNK2W.
    PhylomeDBiP25208.
    TreeFamiTF314521.

    Family and domain databases

    Gene3Di1.10.20.10. 1 hit.
    InterProiIPR003958. CBFA_NFYB_domain.
    IPR009072. Histone-fold.
    IPR003956. Transcrpt_fac_NFYB/HAP3_CS.
    [Graphical view]
    PfamiPF00808. CBFD_NFYB_HMF. 1 hit.
    [Graphical view]
    SUPFAMiSSF47113. SSF47113. 1 hit.
    PROSITEiPS00685. NFYB_HAP3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P25208-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTMDGDSSTT DASQLGISAD YIGGSHYVIQ PHDDTEDSMN DHEDTNGSKE    50
    SFREQDIYLP IANVARIMKN AIPQTGKIAK DAKECVQECV SEFISFITSE 100
    ASERCHQEKR KTINGEDILF AMSTLGFDSY VEPLKLYLQK FREAMKGEKG 150
    IGGAVTATDG LSEELTEEAF TNQLPAGLIT TDGQQQNVMV YTTSYQQISG 200
    VQQIQFS 207
    Length:207
    Mass (Da):22,831
    Last modified:July 1, 1993 - v2
    Checksum:i1ADFA0E45F3CF972
    GO

    Sequence cautioni

    The sequence CAA42230.1 differs from that shown. Reason: Erroneous initiation.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti29 – 291I → M in AAH07035. (PubMed:15489334)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L06145 mRNA. Translation: AAA59930.1.
    X59710 mRNA. Translation: CAA42230.1. Different initiation.
    AK291934 mRNA. Translation: BAF84623.1.
    CH471054 Genomic DNA. Translation: EAW97740.1.
    BC005316 mRNA. Translation: AAH05316.1.
    BC005317 mRNA. Translation: AAH05317.1.
    BC007035 mRNA. Translation: AAH07035.1.
    CCDSiCCDS9098.1.
    PIRiS22817.
    RefSeqiNP_006157.1. NM_006166.3.
    UniGeneiHs.84928.

    Genome annotation databases

    EnsembliENST00000240055; ENSP00000240055; ENSG00000120837.
    ENST00000551727; ENSP00000447486; ENSG00000120837.
    GeneIDi4801.
    KEGGihsa:4801.
    UCSCiuc001tkl.1. human.

    Polymorphism databases

    DMDMi399193.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L06145 mRNA. Translation: AAA59930.1 .
    X59710 mRNA. Translation: CAA42230.1 . Different initiation.
    AK291934 mRNA. Translation: BAF84623.1 .
    CH471054 Genomic DNA. Translation: EAW97740.1 .
    BC005316 mRNA. Translation: AAH05316.1 .
    BC005317 mRNA. Translation: AAH05317.1 .
    BC007035 mRNA. Translation: AAH07035.1 .
    CCDSi CCDS9098.1.
    PIRi S22817.
    RefSeqi NP_006157.1. NM_006166.3.
    UniGenei Hs.84928.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1N1J X-ray 1.67 A 51-143 [» ]
    4AWL X-ray 3.08 B 51-143 [» ]
    ProteinModelPortali P25208.
    SMRi P25208. Positions 57-143.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 110867. 25 interactions.
    IntActi P25208. 7 interactions.
    MINTi MINT-146867.
    STRINGi 9606.ENSP00000240055.

    PTM databases

    PhosphoSitei P25208.

    Polymorphism databases

    DMDMi 399193.

    Proteomic databases

    MaxQBi P25208.
    PaxDbi P25208.
    PRIDEi P25208.

    Protocols and materials databases

    DNASUi 4801.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000240055 ; ENSP00000240055 ; ENSG00000120837 .
    ENST00000551727 ; ENSP00000447486 ; ENSG00000120837 .
    GeneIDi 4801.
    KEGGi hsa:4801.
    UCSCi uc001tkl.1. human.

    Organism-specific databases

    CTDi 4801.
    GeneCardsi GC12M104510.
    HGNCi HGNC:7805. NFYB.
    HPAi CAB004211.
    MIMi 189904. gene.
    neXtProti NX_P25208.
    PharmGKBi PA31610.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG2036.
    HOGENOMi HOG000211832.
    HOVERGENi HBG008864.
    InParanoidi P25208.
    KOi K08065.
    OMAi IAGDYIG.
    OrthoDBi EOG7RNK2W.
    PhylomeDBi P25208.
    TreeFami TF314521.

    Enzyme and pathway databases

    Reactomei REACT_116145. PPARA activates gene expression.
    REACT_147904. Activation of gene expression by SREBF (SREBP).
    REACT_18355. ATF4 activates genes.
    REACT_18423. ATF6-alpha activates chaperone genes.
    SignaLinki P25208.

    Miscellaneous databases

    ChiTaRSi NFYB. human.
    EvolutionaryTracei P25208.
    GeneWikii NFYB.
    GenomeRNAii 4801.
    NextBioi 18506.
    PROi P25208.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi P25208.
    Bgeei P25208.
    CleanExi HS_NFYB.
    Genevestigatori P25208.

    Family and domain databases

    Gene3Di 1.10.20.10. 1 hit.
    InterProi IPR003958. CBFA_NFYB_domain.
    IPR009072. Histone-fold.
    IPR003956. Transcrpt_fac_NFYB/HAP3_CS.
    [Graphical view ]
    Pfami PF00808. CBFD_NFYB_HMF. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47113. SSF47113. 1 hit.
    PROSITEi PS00685. NFYB_HAP3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Intron-exon organization of the NF-Y genes. Tissue-specific splicing modifies an activation domain."
      Li X.-Y., Hooft van Huijsduijnen R., Mantovani R., Benoist C.O., Mathis D.
      J. Biol. Chem. 267:8984-8990(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    2. "Sequence of human NF-YB, a transcriptional regulatory protein of MHC class II genes."
      Badley Clarke J., Ting J.P.Y.
      Submitted (NOV-1992) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    3. "Evolutionary variation of the CCAAT-binding transcription factor NF-Y."
      Li X.-Y., Mantovani R., Hooft van Huijsduijnen R., Andre I., Benoist C., Mathis D.
      Nucleic Acids Res. 20:1087-1091(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    4. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    6. "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: Urinary bladder.
    7. "Human p32, interacts with B subunit of the CCAAT-binding factor, CBF/NF-Y, and inhibits CBF-mediated transcription activation in vitro."
      Chattopadhyay C., Hawke D., Kobayashi R., Maity S.N.
      Nucleic Acids Res. 32:3632-3641(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH C1QBP.
    8. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    9. "The NF-YB/NF-YC structure gives insight into DNA binding and transcription regulation by CCAAT factor NF-Y."
      Romier C., Cocchiarella F., Mantovani R., Moras D.
      J. Biol. Chem. 278:1336-1345(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.67 ANGSTROMS) OF 51-143.
    10. "Sequence-specific transcription factor NF-Y displays histone-like DNA binding and H2B-like ubiquitination."
      Nardini M., Gnesutta N., Donati G., Gatta R., Forni C., Fossati A., Vonrhein C., Moras D., Romier C., Bolognesi M., Mantovani R.
      Cell 152:132-143(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.08 ANGSTROMS) OF 51-143 IN COMPLEX WITH NYFA; NYFC AND PROMOTER DNA, SUBUNIT, UBIQUITINATION AT LYS-140.

    Entry informationi

    Entry nameiNFYB_HUMAN
    AccessioniPrimary (citable) accession number: P25208
    Secondary accession number(s): A8K7B9, Q96IY8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1992
    Last sequence update: July 1, 1993
    Last modified: October 1, 2014
    This is version 149 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 12
      Human chromosome 12: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3