Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL BASIS FOR ARYL HYDROCARBON RECEPTOR MEDIATED GENE ACTIVATION
 
Authors :  O. Daumke, K. W. Schulte
Date :  28 Mar 17  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
Keywords :  Basic Helix Loop Helix Pas Domain Transcription Factor, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. W. Schulte, E. Green, A. Wilz, M. Platten, O. Daumke
Structural Basis For Aryl Hydrocarbon Receptor-Mediated Gen Activation.
Structure 2017
PubMed-ID: 28602820  |  Reference-DOI: 10.1016/J.STR.2017.05.008

(-) Compounds

Molecule 1 - ARYL HYDROCARBON RECEPTOR
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTE
    GeneAHR, BHLHE76
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAHR,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 76,BHLHE76
 
Molecule 2 - ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneARNT, BHLHE2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsINTERNAL DELETION OF 274-301
    SynonymARNT PROTEIN,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 2, BHLHE2,DIOXIN RECEPTOR,NUCLEAR TRANSLOCATOR,HYPOXIA-INDUCIBLE FACTOR 1-BETA,HIF1-BETA
 
Molecule 3 - DNA (5'-D(*GP*GP*TP*CP*AP*CP*GP*CP*AP*AP*CP*C)-3')
    ChainsE, G
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsDIOXIN RESPONSE ELEMENT
    SyntheticYES
 
Molecule 4 - DNA (5'-D(*GP*GP*TP*TP*GP*CP*GP*TP*GP*AP*CP*C)-3')
    ChainsF, H
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsDIOXIN RESPONSE ELEMENT
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)AB  EF  
Biological Unit 2 (1x)  CD  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ER312Ligand/IonERBIUM (III) ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ER36Ligand/IonERBIUM (III) ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2ER36Ligand/IonERBIUM (III) ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:165binding site for residue ER3 A 301
02AC2SOFTWARELEU A:112 , GLU A:116 , ASP B:161 , ACT B:405binding site for residue ER3 B 401
03AC3SOFTWAREGLU B:203binding site for residue ER3 B 402
04AC4SOFTWAREASP B:173binding site for residue ER3 B 403
05AC5SOFTWAREGLU B:87binding site for residue ER3 B 404
06AC6SOFTWAREGLU A:116 , LYS B:155 , ER3 B:401binding site for residue ACT B 405
07AC7SOFTWAREGLU C:165 , GLU C:169binding site for residue ER3 C 301
08AC8SOFTWAREASP B:326 , LEU C:112 , GLU C:116 , ASP D:161binding site for residue ER3 C 302
09AC9SOFTWAREASP D:173binding site for residue ER3 D 401
10AD1SOFTWAREASN D:93binding site for residue ER3 D 402
11AD2SOFTWAREASP A:65 , DT E:3binding site for residue ER3 E 101
12AD3SOFTWAREASP C:65 , DT G:3binding site for residue ER3 G 101
13AD4SOFTWAREDT H:8binding site for residue ER3 H 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5NJ8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5NJ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5NJ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5NJ8)

(-) Exons   (0, 0)

(no "Exon" information available for 5NJ8)

(-) Sequences/Alignments

Asymmetric 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:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...eeeee....eeee..hhhhhhh.hhhhh...hhhhhhhhhhhhhhhhhhh.........eeeeeeee.........eeeeeeeeeeee.....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5nj8 A  34 NPSKRHRDRLNTELDRLASLLPFPQDVINKLDKLSVLRLSVSYLRAKSFFDVALKGLNLQEGEFLLQALNGFVLVVTTDALVFYASSTIQDYLGFQQSDVIHQSVYELIHTEDRAEFQRQLHWPPENSPLMERCFICRLRCLLDSSGFLAMNFQGKLKYLHGQKPQLALFAIATPL 272
                                    43        53        63        73        83    || 113       123       133       143       153       163       173  ||   215       225   ||  236       246   ||  266      
                                                                                 88|                                                                176|                 229|                250|           
                                                                                 109                                                                 209                  231                 261           

Chain B from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.eeeeeee.....eeee.hhhh.............hhhhhhhhhhhhhhhh......eeeeeeee....eeeeeeeeeee.........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5nj8 B  85 DKERLARENHSEIERRRRNKMTAYITELSDMVPTCPDKLTILRMAVSHMKSLRGSYKPSFLTDQELKHLILEAADGFLFIVSCETGRVVYVSDSVTPVLNQPQSEWFGSTLYDQVHPDDVDKLREQLSTSSRRSFICRMRCHFVVVHCTGYIKAWPDDDPEAKFCLVAIGRLQV 345
                                    94       104       114    || 130       140  ||   158       168       178       188       198       208       218       228|      268||     310     ||327 ||    341    
                                                            119|              143|                                                                         228|       269|           316|  329|           
                                                             126               152                                                                          259        302            324   334           

Chain C from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...eeeee....eeee..hhhhhh..hhhhhh..hhhhhhhhhhhhhhhhh..........ee........ee.ee..ee..............eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5nj8 C  32 KSNPSKRHRDRLNTELDRLASLLPFPQDVINKLDKLSVLRLSVSYLRAKSFFDVALKREGLNLQEGEFLLQALNGFVLVVTTDALVFYASSTIQDYLGFQQSDVIHQSVYELIHTEDRAEFQRQENSPLMERCFICRLRCLFLAMNFQGKLKYLHGQKKDGSILPPQLALFAIATP 271
                                    41        51        61        71        81      |109       119       129       139       149       159       169   ||  216       226||     242       255       265      
                                                                                   88|                                                               173|             227|              251|                
                                                                                   107                                                                211              234               255                

Chain D from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhh.....hhhhh........................eeee....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5nj8 D  84 ADKERLARENHSEIERRRRNKMTAYITELSDMVPTCSALARKPDKLTILRMAVSHMKSLRGTSTDGSYKPSFLTDQELKHLILEAADFLFYVSDSVTPVQPQSESTLYDSRRSFICRMRCHCTGYIKALVAIGR 342
                                    93       103       113       123       133       143||     156       166      |177|      199   ||  259       269|      338    
                                                                                      144|                      173| ||     196| 203| 211|       269|    314|     
                                                                                       148                       175 ||      199  207  259        307     337     
                                                                                                                   177|                                           
                                                                                                                    188                                           

Chain E from PDB  Type:DNA  Length:12
                                            
                 5nj8 E   1 GGTCACGCAACC  12
                                    10  

Chain F from PDB  Type:DNA  Length:12
                                            
                 5nj8 F   1 GGTTGCGTGACC  12
                                    10  

Chain G from PDB  Type:DNA  Length:12
                                            
                 5nj8 G   1 GGTCACGCAACC  12
                                    10  

Chain H from PDB  Type:DNA  Length:12
                                            
                 5nj8 H   1 GGTTGCGTGACC  12
                                    10  

   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  (0, 0)

(no "SCOP Domain" information available for 5NJ8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5NJ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5NJ8)

(-) Gene Ontology  (61, 78)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ER3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5nj8)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5nj8
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AHR_HUMAN | P35869
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  ARNT_HUMAN | P27540
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  AHR_HUMAN | P35869
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  ARNT_HUMAN | P27540
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ARNT_HUMAN | P275401d7g 1x0o 2a24 2arn 2b02 2hv1 2k7s 3f1n 3f1o 3f1p 3h7w 3h82 4eq1 4ghi 4gs9 4h6j 4lpz 4pky 4xt2 5tbm 5ufp 5v0l

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5NJ8)