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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DNA BINDING DOMAIN OF THE G245A MUTANT OF ARABIDOPSIS THALIANA AUXIN REPONSE FACTOR 1
 
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 :  2.30
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, F23H11.7
    Mutation: YES
    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
1AC1SOFTWAREPRO A:159 , ARG A:177BINDING SITE FOR RESIDUE CL A 401
2AC2SOFTWAREARG B:177 , ARG B:181BINDING SITE FOR RESIDUE CL B 401

(-) SS Bonds  (0, 0)

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

(-) 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 4LDY)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LDY)

(-) 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:319
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..........eeeehhhhhhhhhhh.........eeeeeeeeeeee......eeeeeeeee......................eeeeee...........eeehhhhhhhhh..........eeeeeee.....eeeeeeeee....eeee..hhhhhhhhhh.....eeeeee.....eeeeee.....hhhhhhhhhhhhhhhh..eeeee.........eeehhhhhhhhhh......eeeeee.......eeeeeeeee................eeeee..........eehhhhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ldy A  16 SDALCRELWHACAGPLVTLPREGERVYYFPEGHMEQLEAMPSFNLPSKILCKVINIQRRAEPETDEVYAQITLLPELDQSEPTSPDAPVQEPEKCTVHSFCKTLTASDTSTHGGFSVLRRHADDCLPPLDMSQQPPWQELVATDLHNSEWHFRHIFRGQPRRHLLTTGWSVFVSSKKLVAGDAFIFLRGENEELRVGVRRHMRSMHIAVLATAAHAITTGTIFSVFYKPRTSRSEFIVSVNRYLEAKTQKLSVGMRFKMRFEGEEAPEKRFSGTIVGVQENKSSVWHDSEWRSLKVQWDEPSSVFRPERVSPWELEPLN 356
                                    25        35        45        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224  ||   247       257       267       277       287       297       307       317       327       337       347         
                                                                 54|                                                                                                                                                                227|                                                                                                                   
                                                                  64                                                                                                                                                                 241                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..........eeeehhhhhhhhhhhhh.............eeeeeeeeeeee......eeeeeeeee....................eeeeee.hhhhhh....eeehhhhhhhhh..........eeeeeee.....eeeeeeeee....eeee..hhhhhhhhhh.....eeeeee.....eeeeee.........hhhhhhhhhhhhhhhhhhhh..eeeee.........eeehhhhhhhhhh......eeeeeee.....eeeeeeeeeee...............eeeee..........eehhhhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ldy B  16 SDALCRELWHACAGPLVTLPREGERVYYFPEGHMEQLEASMHQQQMPSFNLPSKILCKVINIQRRAEPETDEVYAQITLLPELDQSEPTSPDAPVQEKCTVHSFCKTLTASDTSTHGGFSVLRRHADDCLPPLDMSQQPPWQELVATDLHNSEWHFRHIFRGQPRRHLLTTGWSVFVSSKKLVAGDAFIFLRGENEELRVGVRRHMRPSSVISSHSMHIAVLATAAHAITTGTIFSVFYKPRTSRSEFIVSVNRYLEAKTQKLSVGMRFKMRFEGEEAPEKRFSGTIVGVQENKSSVWHDSEWRSLKVQWDEPSSVFRPERVSPWELEPLN 356
                                    25        35        45        55  ||    68        78        88        98       108     ||120       130       140       150       160       170       180       190       200       210       220      |235       245       255       265       275       285       295       305       315       325       335       345       355 
                                                                     58|                                                 114|                                                                                                           227|                                                                                                                           
                                                                      62                                                  117                                                                                                            233
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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 4LDY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        ARFA_ARATH | Q8L7G0: 4ldv 4ldw 4ldx

(-) Related Entries Specified in the PDB File

4ldu 4ldv 4ldw 4ldx