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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DNA BINDING DOMAIN OF ARABIDOPSIS THALIANA AUXIN RESPONSE FACTOR 1 (ARF1) IN COMPLEX WITH PROTOMOR-LIKE SEQUENCE ER7
 
Authors :  D. R. Boer, A. Freire-Rios, W. M. A. Van Den Berg, D. Weijers, M. Coll
Date :  25 Jun 13  (Deposition) - 12 Feb 14  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Transcription Factor, Promotor Dna, Nucleus, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. R. Boer, A. Freire-Rios, W. A. Van Den Berg, T. Saaki, I. W. Manfield, S. Kepinski, I. Lopez-Vidrieo, J. M. Franco-Zorrilla S. C. De Vries, R. Solano, D. Weijers, M. Coll
Structural Basis For Dna Binding Specificity By The Auxin-Dependent Arf Transcription Factors.
Cell(Cambridge, Mass. ) V. 156 577 2014
PubMed-ID: 24485461  |  Reference-DOI: 10.1016/J.CELL.2013.12.027

(-) Compounds

Molecule 1 - AUXIN RESPONSE FACTOR 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTWIN1
    Expression System Strain: ROSETTA DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN, UNP RESIDUES 1-355
    Gene: ARF1, AT1G59750, F23H11.7
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
 
Molecule 2 - ER7, FORWARD SEQUENCE
    Chains: C
    Engineered: YES
    Other Details: THE SEQUENCE RESEMBLES NATURALLY OCCURRING PROMOTORS AND IS KNOWN TO BIND ARF PROTEINS
    Synthetic: YES
 
Molecule 3 - ER7, REVERSE SEQUENCE
    Chains: D
    Engineered: YES
    Other Details: THE SEQUENCE RESEMBLES NATURALLY OCCURRING PROMOTORS AND IS KNOWN TO BIND ARF PROTEINS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4LDX)

(-) Sites  (0, 0)

(no "Site" information available for 4LDX)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LDX)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gln A:158 -Pro A:159
2Gln A:183 -Pro A:184
3Gln B:158 -Pro B:159
4Gln B:183 -Pro B:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LDX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LDX)

(-) Exons   (0, 0)

(no "Exon" information available for 4LDX)

(-) 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:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..........eeeehhhhhhhhhhhhhh...............eeeeeeeeeeee......eeeeeeeee.....................eeeeeee.hhhhhh....eeehhhhhhhhh..........eeeeeee.....eeeeeeeee....eeee..hhhhhhhhh......eeeeeee....eeeeee..........hhhhhhhhhhhhhhhhhhh...eeeee.........eeehhhhhhhhhh......eeeee....eeeeeeee................eeeee..........eehhhhhee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ldx A  16 SDALCRELWHACAGPLVTLPREGERVYYFPEGHMEQLEASMHQGLEQQMPSFNLPSKILCKVINIQRRAEPETDEVYAQITLLPELDQSEPTSPDAPVQEPEKCTVHSFCKTLTASDTSTHGGFSVLRRHADDCLPPLDMSQQPPWQELVATDLHNSEWHFRHIFRGQPRRHLLTTGWSVFVSSKKLVAGDAFIFLRGENEELRVGVRRHMRQPSSVISSHSMHIGVLATAAHAITTGTIFSVFYKPRTSRSEFIVSVNRYLEAKTQKLSVGMRFKMRFEGKRFSGTIVGVQENKSSVWHDSEWRSLKVQWDEPSSVFRPERVSPWELEPLN 356
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225  ||   239       249       259       269       279       289       299||     314       324       334       344       354  
                                                                                                                                                                                                                                              228|                                                                300|                                                  
                                                                                                                                                                                                                                               233                                                                 306                                                  


Chain B from PDB  Type:PROTEIN  Length:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..........eeeehhhhhhhhhhhhhh...............eeeeeeeeeeee......eeeeeeeee.....................eeeeeee.hhhhhh....eeehhhhhhhhh..........eeeeeee.....eeeeeeeee....eeee..hhhhhhhhh......eeeeeee....eeeeee..............hhhhhhhhhhhhhhhhhhh...eeeee.........eeehhhhhhhhhh......eeeeee...eeeeeeeee................eeeee..........eehhhhhee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ldx B  15 LSDALCRELWHACAGPLVTLPREGERVYYFPEGHMEQLEASMHQGLEQQMPSFNLPSKILCKVINIQRRAEPETDEVYAQITLLPELDQSEPTSPDAPVQEPEKCTVHSFCKTLTASDTSTHGGFSVLRRHADDCLPPLDMSQQPPWQELVATDLHNSEWHFRHIFRGQPRRHLLTTGWSVFVSSKKLVAGDAFIFLRGENEELRVGVRRHMRQQTNIPSSVISSHSMHIGVLATAAHAITTGTIFSVFYKPRTSRSEFIVSVNRYLEAKTQKLSVGMRFKMRFEPEKRFSGTIVGVQENKSSVWHDSEWRSLKVQWDEPSSVFRPERVSPWELEPL 355
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294    || 308       318       328       338       348       
                                                                                                                                                                                                                                                                                                                      299|                                                   
                                                                                                                                                                                                                                                                                                                       304                                                   


Chain C from PDB  Type:DNA  Length:21
                                                     
                 4ldx C   1 TTGTCTCCCTTTGGGAGACAA  21
                                    10        20 


Chain D from PDB  Type:DNA  Length:21
                                                     
                 4ldx D   1 TTGTCTCCCAAAGGGAGACAA  21
                                    10        20
   Legend:   → Mismatch (orange background)
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  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 4LDX)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gln A:158 - Pro A:159   [ RasMol ]  
    Gln A:183 - Pro A:184   [ RasMol ]  
    Gln B:158 - Pro B:159   [ RasMol ]  
    Gln B:183 - Pro B:184   [ RasMol ]  
 

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        ARFA_ARATH | Q8L7G0: 4ldv 4ldw 4ldy

(-) Related Entries Specified in the PDB File

4ldu 4ldv 4ldw 4ldy