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(-) Description

Title :  EGR1/ZIF268 ZINC FINGERS IN COMPLEX WITH HYDROXYMETHYLATED DNA
 
Authors :  H. Hashimoto, Y. O. Olanrewaju, Y. Zheng, G. G. Wilson, X. Zhang, X. Chen
Date :  11 Aug 14  (Deposition) - 08 Oct 14  (Release) - 19 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Zinc Finger, Transcription, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hashimoto, Y. O. Olanrewaju, Y. Zheng, G. G. Wilson, X. Zhang, X. Cheng
Wilms Tumor Protein Recognizes 5-Carboxylcytosine Within A Specific Dna Sequence.
Genes Dev. V. 28 2304 2014
PubMed-ID: 25258363  |  Reference-DOI: 10.1101/GAD.250746.114

(-) Compounds

Molecule 1 - EARLY GROWTH RESPONSE PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P-1, PXC1272
    Expression System Strain: BL21(DE3) CODON PLUS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ZINC FINGER 1-3
    Gene: EGR1, KROX24, ZNF225
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EGR-1, AT225, NERVE GROWTH FACTOR-INDUCED PROTEIN A, NGFI-A, TRANSCRIPTION FACTOR ETR103, TRANSCRIPTION FACTOR ZIF268, ZINC FINGER PROTEIN 225, ZINC FINGER PROTEIN KROX-24
 
Molecule 2 - DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5HC)P*GP*T)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*AP*(5HC)P*GP*CP*CP*CP*AP*CP*GP*C)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: CHEMICAL SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
15HC2Mod. Nucleotide2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGENPHOSPHATE)
2K1Ligand/IonPOTASSIUM ION
3ZN3Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:340 , CYS A:345 , HIS A:358 , HIS A:362BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWARECYS A:370 , CYS A:373 , HIS A:386 , HIS A:390BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWARECYS A:398 , CYS A:401 , HIS A:414 , HIS A:418BINDING SITE FOR RESIDUE ZN A 503
4AC4SOFTWARECYS A:340 , VAL A:342 , CYS A:345BINDING SITE FOR RESIDUE K A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R2C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4R2C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R2C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R2C)

(-) Exons   (0, 0)

(no "Exon" information available for 4R2C)

(-) 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    
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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:86
                                                                                                                      
               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
                 4r2c A 335 ERPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRHTKIHLR 420
                                   344       354       364       374       384       394       404       414      


Chain B from PDB  Type:DNA  Length:11
                                           
                 4r2c B   1 AGCGTGGGcGT  11
                                    10 
                                    9-5HC


Chain C from PDB  Type:DNA  Length:11
                                           
                 4r2c C   1 TAcGCCCACGC  11
                              |     10 
                              |        
                              3-5HC
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4R2C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R2C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R2C)

(-) Gene Ontology  (38, 38)

Asymmetric/Biological Unit(hide GO term definitions)

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  4r2c
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  EGR1_HUMAN | P18146
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 Related Entries

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

UniProtKB/Swiss-Prot
        EGR1_HUMAN | P18146: 4r2a 4r2d 4x9j

(-) Related Entries Specified in the PDB File

4r2a 4r2d 4r2e 4r2p 4r2q 4r2r 4r2s