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(-) Description

Title :  ZFP57 MUTANT (E182Q) IN COMPLEX WITH 5-CARBOXYLCYTOSINE DNA
 
Authors :  Y. Liu, Y. O. Olanrewaju, X. Zhang, X. Cheng
Date :  15 Aug 13  (Deposition) - 27 Nov 13  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.97
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  A,B,C,D,E,F  (1x)
Keywords :  Epigenetics, Transcription Factor, 5-Carboxylcytosine, C2H2 Zinc Finger, Dna Binding, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Liu, Y. O. Olanrewaju, X. Zhang, X. Cheng
Dna Recognition Of 5-Carboxylcytosine By A Zfp57 Mutant At An Atomic Resolution Of 0. 97 Angstrom.
Biochemistry V. 52 9310 2013
PubMed-ID: 24236546  |  Reference-DOI: 10.1021/BI401360N

(-) Compounds

Molecule 1 - DNA (5'-D(*TP*AP*TP*TP*GP*CP*(5CM)P*GP*CP*AP*G)-3')
    Chains: A, D
    Engineered: YES
    Other Details: DNA SYNTHESIS
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(*AP*CP*TP*GP*(1CC)P*GP*GP*CP*AP*AP*T)-3')
    Chains: B, E
    Engineered: YES
    Other Details: DNA SYNTHESIS
    Synthetic: YES
 
Molecule 3 - ZINC FINGER PROTEIN 57
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PXC1158
    Expression System Taxid: 562
    Gene: ZFP57
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: ZFP-57

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF
Biological Unit 3 (1x): ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric Unit (6, 18)
No.NameCountTypeFull Name
11CC2Mod. Nucleotide5-CARBOXY-2'-DEOXYCYTIDINE MONOPHOSPHATE
25CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3ACT4Ligand/IonACETATE ION
4CA2Ligand/IonCALCIUM ION
5MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6ZN4Ligand/IonZINC ION
Biological Unit 1 (4, 7)
No.NameCountTypeFull Name
11CC1Mod. Nucleotide5-CARBOXY-2'-DEOXYCYTIDINE MONOPHOSPHATE
25CM1Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3ACT3Ligand/IonACETATE ION
4CA-1Ligand/IonCALCIUM ION
5MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 5)
No.NameCountTypeFull Name
11CC1Mod. Nucleotide5-CARBOXY-2'-DEOXYCYTIDINE MONOPHOSPHATE
25CM1Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3ACT1Ligand/IonACETATE ION
4CA-1Ligand/IonCALCIUM ION
5MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6ZN-1Ligand/IonZINC ION
Biological Unit 3 (4, 12)
No.NameCountTypeFull Name
11CC2Mod. Nucleotide5-CARBOXY-2'-DEOXYCYTIDINE MONOPHOSPHATE
25CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3ACT4Ligand/IonACETATE ION
4CA-1Ligand/IonCALCIUM ION
5MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARE1CC B:5 , HOH B:276 , HIS C:158 , ALA C:161 , HOH C:350 , MPD E:101 , ALA F:161 , HIS F:162 , GLY F:164BINDING SITE FOR RESIDUE MPD B 101
02AC2SOFTWAREHOH A:139 , HOH A:158 , DA B:10 , DT B:11 , HOH B:241 , HOH B:243 , HOH B:264 , HOH B:265 , HOH B:272BINDING SITE FOR RESIDUE ACT B 102
03AC3SOFTWAREHOH A:159 , HOH A:160 , HOH A:161 , HOH B:268 , HOH B:269 , HOH B:270 , HOH B:271BINDING SITE FOR RESIDUE CA B 103
04AC4SOFTWARECYS C:170 , CYS C:173 , HIS C:186 , HIS C:190BINDING SITE FOR RESIDUE ZN C 201
05AC5SOFTWARECYS C:142 , PHE C:144 , CYS C:145 , HIS C:158 , HIS C:162BINDING SITE FOR RESIDUE ZN C 202
06AC6SOFTWAREPHE C:141 , ASN C:184 , HOH C:344 , HOH C:347 , HOH C:358BINDING SITE FOR RESIDUE MPD C 203
07AC7SOFTWAREHOH A:109 , LEU C:163 , TYR C:165 , HOH C:390 , HIS F:190 , HOH F:372BINDING SITE FOR RESIDUE ACT C 204
08AC8SOFTWAREHIS C:190 , HOH C:388 , HOH D:143 , TYR F:165 , HOH F:393BINDING SITE FOR RESIDUE ACT C 205
09AC9SOFTWAREMPD B:101 , ALA C:161 , HIS C:162 , GLY C:164 , HOH C:385 , HOH C:393 , 1CC E:5 , HIS F:158 , ALA F:161BINDING SITE FOR RESIDUE MPD E 101
10BC1SOFTWAREHOH D:132 , DA E:10 , DT E:11 , HOH E:256 , HOH E:277BINDING SITE FOR RESIDUE ACT E 102
11BC2SOFTWAREHOH D:145 , HOH D:146 , HOH D:147 , HOH E:206 , HOH E:279 , HOH E:280 , HOH E:281BINDING SITE FOR RESIDUE CA E 103
12BC3SOFTWARECYS F:170 , CYS F:173 , HIS F:186 , HIS F:190BINDING SITE FOR RESIDUE ZN F 201
13BC4SOFTWARECYS F:142 , PHE F:144 , CYS F:145 , HIS F:158 , HIS F:162BINDING SITE FOR RESIDUE ZN F 202
14BC5SOFTWAREHOH D:133 , PHE F:141 , ASN F:184 , HOH F:345 , HOH F:360 , HOH F:374BINDING SITE FOR RESIDUE MPD F 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M9V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4M9V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M9V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M9V)

(-) Exons   (0, 0)

(no "Exon" information available for 4M9V)

(-) Sequences/Alignments

Asymmetric 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
                                           
                 4m9v A   1 TATTGCcGCAG  11
                                  | 10 
                                  7-5CM


Chain B from PDB  Type:DNA  Length:11
                                           
                 4m9v B   1 ACTGcGGCAAT  11
                                |   10 
                                5-1CC  


Chain C from PDB  Type:PROTEIN  Length:61
                                                                                             
               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
                 4m9v C 132 GPSERPFFCNFCGKTYRDASGLSRHRRAHLGYRPRSCPECGKCFRDQSQVNRHLKVHQNKP 194
                             ||    143       153       163       173       183       193 
                           133|                                                          
                            136                                                          


Chain D from PDB  Type:DNA  Length:11
                                           
                 4m9v D   1 TATTGCcGCAG  11
                                  | 10 
                                  7-5CM


Chain E from PDB  Type:DNA  Length:11
                                           
                 4m9v E   1 ACTGcGGCAAT  11
                                |   10 
                                5-1CC  


Chain F from PDB  Type:PROTEIN  Length:61
                                                                                             
               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
                 4m9v F 132 GPSERPFFCNFCGKTYRDASGLSRHRRAHLGYRPRSCPECGKCFRDQSQVNRHLKVHQNKP 194
                             ||    143       153       163       173       183       193 
                           133|                                                          
                            136
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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 4M9V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M9V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M9V)

(-) Gene Ontology  (13, 13)

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 Related Entries

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

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        ZFP57_MOUSE | Q8C6P8: 4gzn

(-) Related Entries Specified in the PDB File

4gzn MOUSE ZFP57 ZINC FINGERS IN COMPLEX WITH METHYLATED DNA