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(-) Description

Title :  WILMS TUMOR PROTEIN (WT1) ZNF2-4 IN COMPLEX WITH DNA
 
Authors :  H. Hashimoto, X. Cheng
Date :  23 Jun 16  (Deposition) - 14 Sep 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Wilms Tumor Protein, Wt1, Zinc Finger, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hashimoto, X. Zhang, Y. Zheng, G. G. Wilson, X. Cheng
Denys-Drash Syndrome Associated Wt1 Glutamine 369 Mutants Have Altered Sequence-Preferences And Altered Responses To Epigenetic Modifications.
Nucleic Acids Res. V. 44 10165 2016
PubMed-ID: 27596598  |  Reference-DOI: 10.1093/NAR/GKW766

(-) Compounds

Molecule 1 - WILMS TUMOR PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PXC1295
    Expression System Strain: BL21 (DE3) RIL CODON PLUS
    Expression System Taxid: 469008
    Expression System Vector Type: PGEX6P-1
    Fragment: UNP RESIDUES 333-420
    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*AP*GP*T)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2NA1Ligand/IonSODIUM ION
3ZN3Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:368 , GLN A:369 , ARG A:372 , DA B:9 , DA C:2 , DC C:3binding site for residue EDO A 501
2AC2SOFTWARELYS A:381 , PHE A:392 , SER A:393 , ARG A:394 , HIS A:397 , DT B:5binding site for residue EDO A 502
3AC3SOFTWAREASP A:426 , GLU A:427 , ARG A:430 , DC B:3 , DA C:8 , DC C:9 , DG C:10binding site for residue EDO A 503
4AC4SOFTWAREPRO A:410 , SER A:412 , ARG A:414binding site for residue EDO A 504
5AC5SOFTWARECYS A:355 , CYS A:360 , HIS A:373 , HIS A:377binding site for residue ZN A 505
6AC6SOFTWARECYS A:385 , CYS A:388 , HIS A:401 , HIS A:405binding site for residue ZN A 506
7AC7SOFTWARECYS A:413 , CYS A:418 , HIS A:431 , HIS A:435binding site for residue ZN A 507
8AC8SOFTWAREHOH C:206binding site for residue EDO C 101
9AC9SOFTWARESER A:395 , HOH A:637 , DC C:3binding site for residue NA C 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KL2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KL2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KL2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KL2)

(-) Exons   (0, 0)

(no "Exon" information available for 5KL2)

(-) 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
                 5kl2 A 350 EKPYQCDFKDCERRFSRSDQLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRTHTGEKPFSCRWPSCQKKFARSDELVRHHNMHQR 437
                                   359       369       379       389       399       409       419       429        


Chain B from PDB  Type:DNA  Length:11
                                           
                 5kl2 B   1 AGCGTGGGAGT  11
                                    10 


Chain C from PDB  Type:DNA  Length:11
                                           
                 5kl2 C   1 TACTCCCACGC  11
                                    10
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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 5KL2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KL2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KL2)

(-) Gene Ontology  (65, 65)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4r2q 4r2r 4r2s 4wuu 5kl3 5kl4 5kl5 5kl6 5kl7

(-) Related Entries Specified in the PDB File

5kl3 5kl4 5kl5 5kl6 5kl7