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(-) Description

Title :  CRYSTAL STRUCTURE OF HEPATOCYTE NUCLEAR FACTOR 4ALPHA IN COMPLEX WITH DNA: DIABETES GENE PRODUCT
 
Authors :  P. Lu, G. B. Rha, M. Melikishvili, B. C. Adkins, M. G. Fried, Y. I. Chi
Date :  21 Feb 08  (Deposition) - 07 Oct 08  (Release) - 22 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Zinc Finger, Protein-Dna Complex, Diabetes, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Lu, G. B. Rha, M. Melikishvili, G. Wu, B. C. Adkins, M. G. Fried, Y. I. Chi
Structural Basis Of Natural Promoter Recognition By A Unique Nuclear Receptor, Hnf4Alpha. Diabetes Gene Product.
J. Biol. Chem. V. 283 33685 2008
PubMed-ID: 18829458  |  Reference-DOI: 10.1074/JBC.M806213200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEPATOCYTE NUCLEAR FACTOR 4-ALPHA, DNA BINDING DOMAIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET41A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN
    Gene: HNF4A, HNF4, NR2A1, TCF14
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HNF-4-ALPHA
 
Molecule 2 - HEPATOCYTE NUCLEAR FACTOR 4-ALPHA PROMOTER ELEMENT DNA
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - HEPATOCYTE NUCLEAR FACTOR 4-ALPHA PROMOTER ELEMENT DNA
    Chains: D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:51 , CYS A:54 , CYS A:68 , CYS A:71BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWARECYS A:87 , CYS A:93 , CYS A:103 , CYS A:106BINDING SITE FOR RESIDUE ZN A 1002
3AC3SOFTWARECYS B:51 , CYS B:54 , CYS B:68 , CYS B:71BINDING SITE FOR RESIDUE ZN B 2001
4AC4SOFTWARECYS B:87 , CYS B:93 , CYS B:103 , CYS B:106BINDING SITE FOR RESIDUE ZN B 2002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CBB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CBB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071951R85WHNF4A_HUMANDisease (FRTS4)587777732A/BR76W
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUCLEAR_REC_DBD_1PS00031 Nuclear hormones receptors DNA-binding region signature.HNF4A_HUMAN60-86
 		  2A:51-77
B:51-77

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003160992bENSE00001216307chr20:43029924-43030127204HNF4A_HUMAN1-39390--
1.4ENST000003160994ENSE00000662238chr20:43034698-43034872175HNF4A_HUMAN39-97592A:49-88
B:49-88		40
40
1.5ENST000003160995ENSE00000662239chr20:43036021-4303611595HNF4A_HUMAN97-129332A:88-120
B:88-120		33
33
1.6ENST000003160996ENSE00000662240chr20:43042334-43042440107HNF4A_HUMAN129-164362A:120-124
B:120-126		5
7
1.7ENST000003160997ENSE00000662241chr20:43043147-43043302156HNF4A_HUMAN165-216520--
1.8ENST000003160998ENSE00000662242chr20:43047065-4304715288HNF4A_HUMAN217-246300--
1.9ENST000003160999ENSE00000662243chr20:43048361-43048516156HNF4A_HUMAN246-298530--
1.10aENST0000031609910aENSE00000662244chr20:43052658-43052894237HNF4A_HUMAN298-377800--
1.11bENST0000031609911bENSE00000662245chr20:43056975-43057127153HNF4A_HUMAN377-428520--
1.12bENST0000031609912bENSE00001216325chr20:43058163-430600261864HNF4A_HUMAN428-474470--

(-) 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:76
 aligned with HNF4A_HUMAN | P41235 from UniProtKB/Swiss-Prot  Length:474

    Alignment length:76
                                    67        77        87        97       107       117       127      
          HNF4A_HUMAN    58 ALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNE 133
               SCOP domains d3cbba_ A: automated matches                                                 SCOP domains
               CATH domains 3cbbA00 A:49-124 Erythroid Transcription Factor GATA-1, subunit A            CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee..ee.hhhhhhhhhhhhhh.....................hhhhhhhhhhhhh.hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------W------------------------------------------------ SAPs(SNPs)
                    PROSITE --NUCLEAR_REC_DBD_1          ----------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:49-88 UniProt: 39-97   -------------------------------1.6   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.5  PDB: A:88-120          ---- Transcript 1 (2)
                 3cbb A  49 ALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNE 124
                                    58        68        78        88        98       108       118      


Chain B from PDB  Type:PROTEIN  Length:78
 aligned with HNF4A_HUMAN | P41235 from UniProtKB/Swiss-Prot  Length:474

    Alignment length:78
                                    67        77        87        97       107       117       127        
          HNF4A_HUMAN    58 ALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERD 135
               SCOP domains d3cbbb_ B: automated matches                                                   SCOP domains
               CATH domains 3cbbB00 B:49-126 Erythroid Transcription Factor GATA-1, subunit A              CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............ee..ee.hhhhhhhhhhhhhh.....................hhhhhhhhhhhh..hhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------W-------------------------------------------------- SAPs(SNPs)
                    PROSITE --NUCLEAR_REC_DBD_1          ------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: B:49-88 UniProt: 39-97   -------------------------------1.6     Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.5  PDB: B:88-120          ------ Transcript 1 (2)
                 3cbb B  49 ALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERD 126
                                    58        68        78        88        98       108       118        


Chain C from PDB  Type:DNA  Length:21
                                                     
                 3cbb C   1 TGAAGTCCAAAGTTCAGTCCC  21
                                    10        20 


Chain D from PDB  Type:DNA  Length:21
                                                     
                 3cbb D   1 AGGGACTGAACTTTGGACTTC  21
                                    10        20
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CBB)

(-) Gene Ontology  (65, 65)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HNF4A_HUMAN | P41235)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001102    RNA polymerase II activating transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
    GO:0000979    RNA polymerase II core promoter sequence-specific DNA binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery.
    GO:0004879    RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding    Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
    GO:0005504    fatty acid binding    Interacting selectively and non-covalently with fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0000062    fatty-acyl-CoA binding    Interacting selectively and non-covalently with acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016290    palmitoyl-CoA hydrolase activity    Catalysis of the reaction: palmitoyl-CoA + H2O = CoA + palmitate.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    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:0003707    steroid hormone receptor activity    Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function.
    GO:0003705    transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
    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.
    GO:0001228    transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0060395    SMAD protein signal transduction    The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell.
    GO:0006637    acyl-CoA metabolic process    The chemical reactions and pathways involving acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with an acyl group.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0045216    cell-cell junction organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell-cell junction. A cell-cell junction is a specialized region of connection between two cells.
    GO:0007164    establishment of tissue polarity    Coordinated organization of groups of cells in a tissue, such that they all orient to similar coordinates.
    GO:0042593    glucose homeostasis    Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
    GO:0030522    intracellular receptor signaling pathway    Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
    GO:0055088    lipid homeostasis    Any process involved in the maintenance of an internal steady state of lipid within an organism or cell.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:1902569    negative regulation of activation of Janus kinase activity    Any process that stops, prevents or reduces the frequency, rate or extent of activation of JAK (Janus Activated Kinase) kinase activity.
    GO:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0045930    negative regulation of mitotic cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle.
    GO:0033159    negative regulation of protein import into nucleus, translocation    Any process that stops, prevents or reduces the vectorial transfer of a protein from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0006591    ornithine metabolic process    The chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis.
    GO:0055091    phospholipid homeostasis    Any process involved in the maintenance of an internal steady state of phospholipid within an organism or cell.
    GO:2000189    positive regulation of cholesterol homeostasis    Any process that activates or increases the frequency, rate or extent of cholesterol homeostasis.
    GO:0045723    positive regulation of fatty acid biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids.
    GO:0045722    positive regulation of gluconeogenesis    Any process that activates or increases the frequency, rate or extent of gluconeogenesis.
    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:0010470    regulation of gastrulation    Any process that modulates the rate or extent of gastrulation. Gastrulation is the complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals.
    GO:0060398    regulation of growth hormone receptor signaling pathway    Any process that modulates the rate, frequency or extent of the growth hormone receptor signaling pathway. The growth hormone receptor signaling pathway is the series of molecular signals generated as a consequence of growth hormone receptor binding to its physiological ligand.
    GO:0050796    regulation of insulin secretion    Any process that modulates the frequency, rate or extent of the regulated release of insulin.
    GO:0019216    regulation of lipid metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids.
    GO:0032534    regulation of microvillus assembly    A process that modulates the formation of a microvillus.
    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:0051591    response to cAMP    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0009749    response to glucose    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
    GO:0007548    sex differentiation    The establishment of the sex of an organism by physical differentiation.
    GO:0023019    signal transduction involved in regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another.
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    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:0006367    transcription initiation from RNA polymerase II promoter    Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0070328    triglyceride homeostasis    Any process involved in the maintenance of an internal steady state of triglyceride within an organism or cell.
    GO:0006805    xenobiotic metabolic process    The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HNF4A_HUMAN | P41235: 1pzl 3fs1 4b7w 4iqr

(-) Related Entries Specified in the PDB File

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