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(-) Description

Title :  WILMS TUMOR PROTEIN (WT1) ZINC FINGERS IN COMPLEX WITH FORMYLATED DNA
 
Authors :  H. Hashimoto, Y. O. Olanrewaju, Y. Zheng, G. G. Wilson, X. Zhang, X. Chen
Date :  12 Aug 14  (Deposition) - 08 Oct 14  (Release) - 19 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Zinc Finger, Transcription, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hashimoto, Y. O. Olanrewaju, Y. Zheng, G. G. Wilson, X. Zhang, X. Cheng
Wilms Tumor Protein Recognizes 5-Carboxylcytosine Within A Specific Dna Sequence.
Genes Dev. V. 28 2304 2014
PubMed-ID: 25258363  |  Reference-DOI: 10.1101/GAD.250746.114

(-) Compounds

Molecule 1 - WILMS TUMOR PROTEIN, ISOFORM 4/CRA_A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P-1, PXC1295
    Expression System Strain: BL21(DE3) CODON PLUS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ZINC FINGER 2-4
    Gene: WT1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: WT33
 
Molecule 2 - DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5FC)P*GP*T)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*AP*(5FC)P*GP*CP*CP*CP*AP*CP*GP*C)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
15FC2Mod. Nucleotide5-FORMYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3ZN3Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:355 , CYS A:360 , HIS A:373 , HIS A:377BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWARECYS A:385 , CYS A:388 , HIS A:401 , HIS A:405BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWARECYS A:413 , CYS A:418 , HIS A:431 , HIS A:435BINDING SITE FOR RESIDUE ZN A 503
4AC4SOFTWAREARG A:390 , HOH A:629BINDING SITE FOR RESIDUE EDO A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R2Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4R2Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R2Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R2Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4R2Q)

(-) 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:88
                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee........ee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 4r2q A 349 SEKPYQCDFKDCERRFSRSDQLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRTHTGEKPFSCRWPSCQKKFARSDELVRHHNMHQ 436
                                   358       368       378       388       398       408       418       428        


Chain B from PDB  Type:DNA  Length:11
                                           
                 4r2q B   1 AGCGTGGGcGT  11
                                    10 
                                    9-5FC


Chain C from PDB  Type:DNA  Length:11
                                           
                 4r2q C   1 TAcGCCCACGC  11
                              |     10 
                              |        
                              3-5FC
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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 4R2Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R2Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R2Q)

(-) Gene Ontology  (65, 65)

Asymmetric/Biological Unit(hide GO term definitions)

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  4r2q
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  WT1_HUMAN | P19544
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 Related Entries

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

UniProtKB/Swiss-Prot
        WT1_HUMAN | P19544: 1lu6 1xf7 2g7t 2g7v 2g7w 2g7x 2jp9 2jpa 2prt 3hpj 3myj 4r2e 4r2p 4r2r 4r2s 4wuu 5kl2 5kl3 5kl4 5kl5 5kl6 5kl7

(-) Related Entries Specified in the PDB File

4r2a 4r2c 4r2d 4r2e 4r2p 4r2r 4r2s