Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  HADDOCK STRUCTURE OF ARNT PAS-B HOMODIMER
 
Authors :  P. B. Card, K. H. Gardner
Date :  27 Jul 06  (Deposition) - 07 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (8x)
Keywords :  Arnt Transcription Pas Haddock, Transcription, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. B. Card, K. H. Gardner
Practical Aspects Of Using Paramagnetic Relaxation Enhancements For Protein Docking: Application To The Arnt Pas-B Homodimer
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PHIS-PARALLEL
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL PAS DOMAIN (PAS-B), RESIDUES 356-470
    Gene: ARNT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ARNT PROTEIN, DIOXIN RECEPTOR, NUCLEAR TRANSLOCATOR, HYPOXIA-INDUCIBLE FACTOR 1 BETA, HIF-1 BETA

 Structural Features

(-) Chains, Units

  
NMR Structure (8x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2HV1)

(-) Sites  (0, 0)

(no "Site" information available for 2HV1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HV1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HV1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

NMR Structure (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024280R430QARNT_HUMANPolymorphism2229175A/BR79Q
2UniProtVAR_049537E435KARNT_HUMANPolymorphism2229176A/BE84K
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASPS50112 PAS repeat profile.ARNT_HUMAN161-235
368-419
 		  2-
A:17-68
B:17-68

(-) Exons   (4, 8)

NMR Structure (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003585951aENSE00002062254chr1:150849244-150849019226ARNT_HUMAN1-990--
1.3ENST000003585953ENSE00001717520chr1:150830936-150830825112ARNT_HUMAN9-46380--
1.5bENST000003585955bENSE00001071957chr1:150825282-15082523845ARNT_HUMAN46-61160--
1.6ENST000003585956ENSE00000960027chr1:150818783-15081873945ARNT_HUMAN61-76160--
1.7ENST000003585957ENSE00001263986chr1:150814944-15081490045ARNT_HUMAN76-91160--
1.8bENST000003585958bENSE00000960029chr1:150812130-150811917214ARNT_HUMAN91-162720--
1.9cENST000003585959cENSE00000960030chr1:150808969-150808756214ARNT_HUMAN163-234720--
1.10bENST0000035859510bENSE00000960031chr1:150807116-150807014103ARNT_HUMAN234-268350--
1.11ENST0000035859511ENSE00000960032chr1:150804875-15080481066ARNT_HUMAN268-290230--
1.12aENST0000035859512aENSE00000960033chr1:150804379-15080429486ARNT_HUMAN290-319300--
1.13dENST0000035859513dENSE00001417988chr1:150802456-15080238077ARNT_HUMAN319-344260--
1.15bENST0000035859515bENSE00001414390chr1:150801703-150801569135ARNT_HUMAN345-389452A:7-38
B:7-38		32
32
1.16ENST0000035859516ENSE00001186051chr1:150799093-15079901975ARNT_HUMAN390-414252A:39-63
B:39-63		25
25
1.17ENST0000035859517ENSE00001804030chr1:150795821-150795670152ARNT_HUMAN415-465512A:64-114
B:64-114		51
51
1.18bENST0000035859518bENSE00001044530chr1:150790506-150790396111ARNT_HUMAN465-502382A:114-114
B:114-114		1
1
1.19cENST0000035859519cENSE00001044549chr1:150789909-15078983773ARNT_HUMAN502-526250--
1.20ENST0000035859520ENSE00001044525chr1:150789678-150789558121ARNT_HUMAN527-567410--
1.21ENST0000035859521ENSE00001044520chr1:150789366-150789264103ARNT_HUMAN567-601350--
1.22aENST0000035859522aENSE00001044548chr1:150788882-150788735148ARNT_HUMAN601-650500--
1.23aENST0000035859523aENSE00001151505chr1:150786715-150786553163ARNT_HUMAN651-705550--
1.24aENST0000035859524aENSE00001371736chr1:150785814-150785648167ARNT_HUMAN705-760560--
1.25fENST0000035859525fENSE00001855735chr1:150784586-1507821812406ARNT_HUMAN761-789290--

(-) Sequences/Alignments

NMR Structure
   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:108
 aligned with ARNT_HUMAN | P27540 from UniProtKB/Swiss-Prot  Length:789

    Alignment length:108
                                   367       377       387       397       407       417       427       437       447       457        
           ARNT_HUMAN   358 CQPTEFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVK 465
               SCOP domains d2hv1a_ A: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.....eeee..hhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeeeeeeee......eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------Q----K------------------------------ SAPs(SNPs)
                    PROSITE ----------PAS  PDB: A:17-68 UniProt: 368-419                  ---------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.15b  PDB: A:7-38         Exon 1.16  PDB: A:39-63  Exon 1.17  PDB: A:64-114 UniProt: 415-465           Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------1 Transcript 1 (2)
                 2hv1 A   7 CQPTEFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVK 114
                                    16        26        36        46        56        66        76        86        96       106        


Chain B from PDB  Type:PROTEIN  Length:108
 aligned with ARNT_HUMAN | P27540 from UniProtKB/Swiss-Prot  Length:789

    Alignment length:108
                                   367       377       387       397       407       417       427       437       447       457        
           ARNT_HUMAN   358 CQPTEFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVK 465
               SCOP domains d2hv1b_ B: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.....eeee..hhhhhh..hhhhhh........hhhhhhhhhhhhhhhhhhh..eeeeeeeee.....eeeeeeeeeeeee....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------Q----K------------------------------ SAPs(SNPs)
                    PROSITE ----------PAS  PDB: B:17-68 UniProt: 368-419                  ---------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.15b  PDB: B:7-38         Exon 1.16  PDB: B:39-63  Exon 1.17  PDB: B:64-114 UniProt: 415-465           Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------1 Transcript 1 (2)
                 2hv1 B   7 CQPTEFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVK 114
                                    16        26        36        46        56        66        76        86        96       106
   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)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HV1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HV1)

(-) Gene Ontology  (36, 36)

NMR Structure(hide GO term definitions)
Chain A,B   (ARNT_HUMAN | P27540)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004874    aryl hydrocarbon receptor activity    Combining with an aryl hydrocarbon and transmitting the signal to initiate a change in cell activity. The aryl hydrocarbon receptor is a ligand-activated transcription factor which translocates to the nucleus to activate transcription upon ligand-binding.
    GO:0017162    aryl hydrocarbon receptor binding    Interacting selectively and non-covalently with an aryl hydrocarbon receptor.
    GO:0035326    enhancer binding    Interacting selectively and non-covalently with an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
    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:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    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: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: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:0000989    transcription factor activity, transcription factor binding    Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    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:0001892    embryonic placenta development    The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0030522    intracellular receptor signaling pathway    Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
    GO:0042789    mRNA transcription from RNA polymerase II promoter    The cellular synthesis of messenger RNA (mRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter.
    GO:0001938    positive regulation of endothelial cell proliferation    Any process that activates or increases the rate or extent of endothelial cell proliferation.
    GO:0045648    positive regulation of erythrocyte differentiation    Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation.
    GO:0045821    positive regulation of glycolytic process    Any process that activates or increases the frequency, rate or extent of glycolysis.
    GO:0046886    positive regulation of hormone biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones.
    GO:0033235    positive regulation of protein sumoylation    Any process that activates or increases the frequency, rate or extent of the addition of SUMO groups to a protein.
    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:0010575    positive regulation of vascular endothelial growth factor production    Any process that increases or activates the frequency, rate, or extent of production of vascular endothelial growth factor.
    GO:0030949    positive regulation of vascular endothelial growth factor receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
    GO:0061418    regulation of transcription from RNA polymerase II promoter in response to hypoxia    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
    GO:0043619    regulation of transcription from RNA polymerase II promoter in response to oxidative stress    Modulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0001666    response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0090575    RNA polymerase II transcription factor complex    A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase II.
    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.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2hv1)
 
  Sites
(no "Sites" information available for 2hv1)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2hv1)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2hv1
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ARNT_HUMAN | P27540
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ARNT_HUMAN | P27540
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ARNT_HUMAN | P27540: 1d7g 1x0o 2a24 2arn 2b02 2k7s 3f1n 3f1o 3f1p 3h7w 3h82 4eq1 4ghi 4gs9 4h6j 4lpz 4pky 4xt2 5nj8 5tbm 5ufp 5v0l

(-) Related Entries Specified in the PDB File

2hv3 HADDOCK STRUCTURE OF ARNT PAS-B HOMODIMER