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(-) Description

Title :  CRYSTAL STRUCTURE OF KAISO ZINC FINGER DNA BINDING DOMAIN IN COMPLEX WITH KAISO BINDING 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 :  2.40
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*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: KAISO BINDING SEQUENCE DNA STRAND 1
    Other Details - Source: THIS SEQUENCE OCCURS IN HUMANS
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*AP*C)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: KAISO BINDING SEQUENCE 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  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
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:544 , HOH A:847BINDING SITE FOR RESIDUE ZN A 702
3AC3SOFTWARECYS A:552 , CYS A:555 , HIS A:568 , HIS A:573BINDING SITE FOR RESIDUE ZN A 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F6M)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:581 -Lys A:582
2Gln A:596 -Tyr A:597

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F6M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F6M)

(-) Exons   (0, 0)

(no "Exon" information available for 4F6M)

(-) 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:116
                                                                                                                                                    
               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
                 4f6m A 482 DHYELIVDGRVYYICIVCKRSYVCLTSLRRHFNIHSWEKKYPCRYCEKVFPLAEYRTKHEIHHTGERRYQCLACGKSFINYQFMSSHIKSVHSQDPSGDSKLYRLHPCRSLQIRQY 597
                                   491       501       511       521       531       541       551       561       571       581       591      


Chain D from PDB  Type:DNA  Length:19
                                                   
                 4f6m D   1 GTGCTTCCTGCCAATAACG  19
                                    10         


Chain E from PDB  Type:DNA  Length:19
                                                   
                 4f6m E  20 CGTTATTGGCAGGAAGCAC  38
                                    29
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4F6M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F6M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F6M)

(-) Gene Ontology  (16, 16)

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
        KAISO_HUMAN | Q86T24: 2lt7 3fkc 3m4t 3m8v 4f6n

(-) Related Entries Specified in the PDB File

4f6n