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(-) Description

Title :  MOUSE ZFP57 ZINC FINGERS IN COMPLEX WITH METHYLATED DNA
 
Authors :  Y. Liu, X. Zhang, X. Cheng
Date :  06 Sep 12  (Deposition) - 17 Oct 12  (Release) - 21 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.99
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Zinc Finger, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Liu, H. Toh, H. Sasaki, X. Zhang, X. Cheng
An Atomic Model Of Zfp57 Recognition Of Cpg Methylation Within A Specific Dna Sequence.
Genes Dev. V. 26 2374 2012
PubMed-ID: 23059534  |  Reference-DOI: 10.1101/GAD.202200.112

(-) Compounds

Molecule 1 - DNA (5'-D(*TP*AP*TP*TP*GP*CP*(5CM)P*GP*CP*AP*G)-3')
    Chains: A
    Engineered: YES
    Fragment: ZINC FINGER DOMAIN, UNP RESIDUES 137-195
    Other Details: THE DNA SEQUENCE OCCURS NATURALLY IN MOUSE.
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(*AP*CP*TP*GP*(5CM)P*GP*GP*CP*AP*AP*T)-3')
    Chains: B
    Engineered: YES
    Other Details: THE DNA SEQUENCE OCCURS NATURALLY IN MOUSE.
    Synthetic: YES
 
Molecule 3 - ZINC FINGER PROTEIN 57
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ZFP57
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: ZFP-57

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2ACT1Ligand/IonACETATE ION
3CA1Ligand/IonCALCIUM ION
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:101 , HOH A:103 , HOH B:203 , HOH B:204 , HOH B:206 , HOH B:208 , HOH B:209BINDING SITE FOR RESIDUE CA B 101
2AC2SOFTWAREHOH A:168 , PHE C:141 , ASN C:184 , HOH C:313 , HOH C:328 , HOH C:329 , HOH C:377BINDING SITE FOR RESIDUE MPD C 201
3AC3SOFTWARE5CM B:5 , HOH B:265 , HIS C:158 , ALA C:161 , HIS C:162 , GLY C:164 , HOH C:333BINDING SITE FOR RESIDUE MPD C 202
4AC4SOFTWARECYS C:170 , CYS C:173 , HIS C:186 , HIS C:190BINDING SITE FOR RESIDUE ZN C 203
5AC5SOFTWARECYS C:142 , CYS C:145 , HIS C:158 , HIS C:162BINDING SITE FOR RESIDUE ZN C 204
6AC6SOFTWAREHOH A:111 , LEU C:163 , TYR C:165 , HIS C:190 , HOH C:337 , HOH C:352 , HOH C:392BINDING SITE FOR RESIDUE ACT C 205

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GZN)

(-) 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:DNA  Length:11
                                           
                 4gzn A   1 TATTGCcGCAG  11
                                  | 10 
                                  7-5CM


Chain B from PDB  Type:DNA  Length:11
                                           
                 4gzn B   1 ACTGcGGCAAT  11
                                |   10 
                                5-5CM  


Chain C from PDB  Type:PROTEIN  Length:59
                                                                                           
               SCOP domains ----------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 4gzn C 136 SERPFFCNFCGKTYRDASGLSRHRRAHLGYRPRSCPECGKCFRDQSEVNRHLKVHQNKP 194
                                   145       155       165       175       185
   Legend:   → Mismatch (orange background)
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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 4GZN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4gzn
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  ZFP57_MOUSE | Q8C6P8
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 Related Entries

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

UniProtKB/Swiss-Prot
        ZFP57_MOUSE | Q8C6P8: 4m9v

(-) Related Entries Specified in the PDB File

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