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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NF-YB/NF-YC HISTONE PAIR
 
Authors :  C. Romier, F. Cocchiarella, R. Mantovani, D. Moras
Date :  18 Oct 02  (Deposition) - 18 Feb 03  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Histone-Like Pair, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Romier, F. Cocchiarella, R. Mantovani, D. Moras
The Nf-Yb/Nf-Yc Structure Gives Insight Into Dna Binding An Transcription Regulation By Ccaat Factor Nf-Y
J. Biol. Chem. V. 278 1336 2003
PubMed-ID: 12401788  |  Reference-DOI: 10.1074/JBC.M209635200

(-) Compounds

Molecule 1 - NF-YB
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPACYC11B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentNF-YB3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA
 
Molecule 2 - NF-YC
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentNF-YC2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1N1J)

(-) Sites  (0, 0)

(no "Site" information available for 1N1J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N1J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N1J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N1J)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NFYB_HAP3PS00685 NF-YB/HAP3 subunit signature.NFYB_HUMAN89-105  1A:87-103

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002400551ENSE00001193640chr12:104532040-104531919122NFYB_HUMAN-00--
1.2ENST000002400552ENSE00001193633chr12:104529310-10452922685NFYB_HUMAN1-220--
1.3ENST000002400553ENSE00000922958chr12:104522295-10452220294NFYB_HUMAN3-34320--
1.4ENST000002400554ENSE00000922957chr12:104520022-104519892131NFYB_HUMAN34-77441A:55-7521
1.5ENST000002400555ENSE00000937932chr12:104517201-104517004198NFYB_HUMAN78-143661A:76-14166
1.6ENST000002400556ENSE00000937933chr12:104515099-10451501882NFYB_HUMAN144-171280--
1.7ENST000002400557ENSE00001104711chr12:104514257-10451417880NFYB_HUMAN171-197270--
1.8ENST000002400558ENSE00001104713chr12:104513547-1045108582690NFYB_HUMAN198-207100--

2.13cENST0000030873313cENSE00001428593chr1:41204510-41204620111NFYC_HUMAN1-35350--
2.14bENST0000030873314bENSE00001643321chr1:41213206-4121327772NFYC_HUMAN36-59241B:43-5917
2.15bENST0000030873315bENSE00001609714chr1:41215245-41215358114NFYC_HUMAN60-97381B:60-9738
2.16bENST0000030873316bENSE00002187131chr1:41218823-4121891896NFYC_HUMAN98-129321B:98-12023
2.17bENST0000030873317bENSE00001145012chr1:41223793-41223966174NFYC_HUMAN130-187580--
2.18bENST0000030873318bENSE00000870110chr1:41228560-41228718159NFYC_HUMAN188-240530--
2.21dENST0000030873321dENSE00001662239chr1:41232268-41232375108NFYC_HUMAN241-276360--
2.21hENST0000030873321hENSE00001080407chr1:41232590-4123264657NFYC_HUMAN277-295190--
2.22cENST0000030873322cENSE00001683645chr1:41235028-4123508760NFYC_HUMAN296-315200--
2.23dENST0000030873323dENSE00001433396chr1:41236069-412372751207NFYC_HUMAN316-4581430--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:87
 aligned with NFYB_HUMAN | P25208 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:87
                                    66        76        86        96       106       116       126       136       
           NFYB_HUMAN    57 IYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLYLQKFRE 143
               SCOP domains d1n1ja_ A: Nuclear transcription factor Y subunit beta (Nf-Yb3)                         SCOP domains
               CATH domains 1n1jA00 A:55-141 Histone, subunit A                                                     CATH domains
               Pfam domains CBFD_NFYB_HMF-1n1jA01 A:55-120                                    --------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------NFYB_HAP3        -------------------------------------- PROSITE
               Transcript 1 Exon 1.4  PDB: A:55-7Exon 1.5  PDB: A:76-141 UniProt: 78-143                            Transcript 1
                 1n1j A  55 IYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLYLQKFRE 141
                                    64        74        84        94       104       114       124       134       

Chain B from PDB  Type:PROTEIN  Length:78
 aligned with NFYC_HUMAN | Q13952 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:78
                                    52        62        72        82        92       102       112        
           NFYC_HUMAN    43 LPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPR 120
               SCOP domains d1n1jb_ B: Nuclear transcription factor Y subunit gamma (Nf-Yc2)               SCOP domains
               CATH domains 1n1jB00 B:43-120 Histone, subunit A                                            CATH domains
               Pfam domains CBFD_NFYB_HMF-1n1jB01 B:43-105                                 --------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
               Transcript 2 Exon 2.14b       Exon 2.15b  PDB: B:60-97              Exon 2.16b [INCOMPLETE] Transcript 2
                 1n1j B  43 LPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPR 120
                                    52        62        72        82        92       102       112        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Histone (49)

(-) Gene Ontology  (23, 35)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NFYB_HUMAN | P25208)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0070491    repressing transcription factor binding    Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0016602    CCAAT-binding factor complex    A heteromeric transcription factor complex that binds to the CCAAT-box upstream of promoters; functions as both an activator and a repressor, depending on its interacting cofactors. Typically trimeric consisting of NFYA, NFYB and NFYC subunits. In Saccharomyces, it activates the transcription of genes in response to growth in a nonfermentable carbon source and consists of four known subunits: HAP2, HAP3, HAP4 and HAP5.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0032993    protein-DNA complex    A macromolecular complex containing both protein and DNA molecules.

Chain B   (NFYC_HUMAN | Q13952)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0016602    CCAAT-binding factor complex    A heteromeric transcription factor complex that binds to the CCAAT-box upstream of promoters; functions as both an activator and a repressor, depending on its interacting cofactors. Typically trimeric consisting of NFYA, NFYB and NFYC subunits. In Saccharomyces, it activates the transcription of genes in response to growth in a nonfermentable carbon source and consists of four known subunits: HAP2, HAP3, HAP4 and HAP5.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0032993    protein-DNA complex    A macromolecular complex containing both protein and DNA molecules.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NFYB_HUMAN | P252084awl 4csr
        NFYC_HUMAN | Q139524awl 4csr

(-) Related Entries Specified in the PDB File

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