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(-) Description

Title :  CRYSTAL STRUCTURE OF KAISO ZINC FINGER DNA BINDING PROTEIN IN COMPLEX WITH METHYLATED CPG SITE DNA
 
Authors :  B. A. Buck-Koehntop, R. L. Stanfield, D. C. Ekiert, M. A. Martinez-Yamo H. J. Dyson, I. A. Wilson, P. E. Wright
Date :  15 May 12  (Deposition) - 05 Sep 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,D,E
Keywords :  Zinc Finger, Protein-Dna Complex, Double Helix, Dna Binding, Dna, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. A. Buck-Koehntop, R. L. Stanfield, D. C. Ekiert, M. A. Martinez-Yamout, H. J. Dyson, I. A. Wilson, P. E. Wright
Molecular Basis For Recognition Of Methylated And Specific Dna Sequences By The Zinc Finger Protein Kaiso.
Proc. Natl. Acad. Sci. Usa V. 109 15229 2012
PubMed-ID: 22949637  |  Reference-DOI: 10.1073/PNAS.1213726109

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR KAISO
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21D
    Expression System Strain: BL21(DE3)[DNAY]
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ZINC FINGER DNA BINDING DOMAIN
    Gene: ZBTB33, KAISO, ZNF348
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ZINC FINGER AND BTB DOMAIN-CONTAINING PROTEIN 33
 
Molecule 2 - DNA (5'-D(*GP*TP*GP*TP*CP*AP*CP*(5CM)P*GP*(5CM) P*GP*TP*CP*TP*AP*TP*AP*CP*G)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: MEECAD DNA STRAND 1
    Other Details - Source: THIS SEQUENCE OCCURS IN HUMANS
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*GP*TP*AP*TP*AP*GP*AP*(5CM)P*GP*(5CM) P*GP*GP*TP*GP*AP*CP*AP*C)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: MEECAD DNA STRAND 2
    Other Details - Source: THIS SEQUENCE OCCURS IN HUMANS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ADE

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
15CM4Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3ZN3Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:496 , CYS A:499 , HIS A:512 , HIS A:516BINDING SITE FOR RESIDUE ZN A 701
2AC2SOFTWARECYS A:524 , CYS A:527 , HIS A:540 , HIS A:544BINDING SITE FOR RESIDUE ZN A 702
3AC3SOFTWARECYS A:552 , CYS A:555 , HIS A:568 , HIS A:573BINDING SITE FOR RESIDUE ZN A 703
4AC4SOFTWARETYR A:536 , LYS A:539 , DA D:6BINDING SITE FOR RESIDUE GOL A 704
5AC5SOFTWAREDG D:3 , DT D:4 , DC D:5 , HOH D:201 , DC E:36 , DA E:37BINDING SITE FOR RESIDUE GOL D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F6N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F6N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F6N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F6N)

(-) Exons   (0, 0)

(no "Exon" information available for 4F6N)

(-) 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:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..eeeeee.....ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...eee.....ee.hhhhhhhhhhhhhh.........eee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f6n A 481 DDHYELIVDGRVYYICIVCKRSYVCLTSLRRHFNIHSWEKKYPCRYCEKVFPLAEYRTKHEIHHTGERRYQCLACGKSFINYQFMSSHIKSVHSQDPSGDSKLYRLHPCRSLQIRQYAYL 600
                                   490       500       510       520       530       540       550       560       570       580       590       600


Chain D from PDB  Type:DNA  Length:19
                                                   
                 4f6n D   1 GTGTCACcGcGTCTATACG  19
                                   |10         
                                   8-5CM       
                                    10-5CM     


Chain E from PDB  Type:DNA  Length:18
                                                  
                 4f6n E  21 GTATAGAcGcGGTGACAC  38
                                   |30        
                                  28-5CM      
                                    30-5CM
   Legend:   → Mismatch (orange background)
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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 4F6N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F6N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F6N)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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  4f6n
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  KAISO_HUMAN | Q86T24
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 Related Entries

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

UniProtKB/Swiss-Prot
        KAISO_HUMAN | Q86T24: 2lt7 3fkc 3m4t 3m8v 4f6m

(-) Related Entries Specified in the PDB File

4f6m