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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DNA BINDING DOMAIN OF ARABIDOPSIS THALIANA AUXIN RESPONSE FACTOR 1, P21 STRUCTURE
 
Authors :  D. R. Boer, M. Coll
Date :  25 Jun 13  (Deposition) - 12 Feb 14  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.67
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription Factor, Dna Binding, Nucleus, Transcription (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, AUXIN RESPONSE FACTOR 1, F23H11.7
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:270 , GLU A:299BINDING SITE FOR RESIDUE CL A 401
2AC2SOFTWAREHIS A:25 , LEU A:34BINDING SITE FOR RESIDUE CL A 402

(-) SS Bonds  (0, 0)

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

(-) 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 4LDW)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LDW)

(-) 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:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..........eeeehhhhhhhhhhh.........eeeeeeeeeeee......eeeeeeeee.................eeeeeee...........eeehhhhhhhh...........eeeeeee.....eeeeeeeee....eeee..hhhhhhhhhh.....eeeeeee....eeeeee....hhhhhhhhhhhhhhhhhh..eeeee.........eeehhhhhhhhhh......eee........eeeeee................eeeee..........eehhhhhee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ldw A  16 SDALCRELWHACAGPLVTLPREGERVYYFPEGHMEQLEAMPSFNLPSKILCKVINIQRRAEPETDEVYAQITLLPELDQSEPTSPDAPVKCTVHSFCKTLTASDTSTHGGFSVLRRHADDCLPPLDMSQQPPWQELVATDLHNSEWHFRHIFRGQPRRHLLTTGWSVFVSSKKLVAGDAFIFLRGENEELRVGVRRHMSHSMHIGVLATAAHAITTGTIFSVFYKPRTSRSEFIVSVNRYLEAKTQKLSVGMRFKMRFEGKRFSGTIVGVQENKSSVWHDSEWRSLKVQWDEPSSVFRPERVSPWELEPLN 356
                                    25        35        45        64        74        84        94       104       118       128       138       148       158       168       178       188       198       208       218       240       250       260       270       280       290       300|      315       325       335       345       355 
                                                                 54|                                              113|                                                                                                         226|                                                          300|                                                  
                                                                  64                                               118                                                                                                          239                                                           306                                                  


Chain B from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..........eeeehhhhhhhhhh.................eeeeeeeeeeee......eeeeeeeee..................eeeeeee.hhhhhh....eeehhhhhhhhh..........eeeeeee.....eeeeeeeee....eeee..hhhhhhhhh......eeeeeee...eeeeeee........hhhhhhhhhhhhhhhhhhhh..eeeee.........eeehhhhhhhhhh......eeeee....eeeeeeee................eeeee..........eehhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ldw B  16 SDALCRELWHACAGPLVTLPREGERVYYFPEGHMEQLEASQGLEQQMPSFNLPSKILCKVINIQRRAEPETDEVYAQITLLPELDQSEPTSPDAPVQKCTVHSFCKTLTASDTSTHGGFSVLRRHADDCLPPLDMSQQPPWQELVATDLHNSEWHFRHIFRGQPRRHLLTTGWSVFVSSKKLVAGDAFIFLRGENEELRVGVRRHMRSSVISSHSMHIGVLATAAHAITTGTIFSVFYKPRTSRSEFIVSVNRYLEAKTQKLSVGMRFKMRFEEKRFSGTIVGVQENKSSVWHDSEWRSLKVQWDEPSSVFRPERVSPWELEPL 355
                                    25        35        45        55|       67        77        87        97       107      |120       130       140       150       160       170       180       190       200       210       220      |236       246       256       266       276       286       296  ||   311       321       331       341       351    
                                                                  55|                                                     114|                                                                                                          227|                                                              299|                                                  
                                                                   58                                                      118                                                                                                           234                                                               305
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  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 4LDW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LDW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LDW)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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        ARFA_ARATH | Q8L7G0: 4ldv 4ldx 4ldy

(-) Related Entries Specified in the PDB File

4ldu 4ldv 4ldx 4ldy