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(-) Description

Title :  HOMO SAPIENS CCCTC-BINDING FACTOR (CTCF) ZNF4-7 AND DNA COMPLEX STRUCTURE
 
Authors :  H. Hashimoto, X. Cheng
Date :  23 May 16  (Deposition) - 24 May 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.11
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ccctc-Binding Factor, Ctcf, Zinc Finger, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hashimoto, D. Wang, J. R. Horton, X. Zhang, V. G. Corces, X. Cheng
Structural Basis For The Versatile And Methylation-Dependen Binding Of Ctcf To Dna.
Mol. Cell V. 66 711 2017
PubMed-ID: 28529057  |  Reference-DOI: 10.1016/J.MOLCEL.2017.05.004

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REPRESSOR CTCF
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PXC1202
    Expression System Strain: BL21 (DE3) RIL-CODON PLUS
    Expression System Taxid: 562
    Expression System Vector Type: PGEX-6P-1
    Fragment: UNP RESIDUES 348-464
    Gene: CTCF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 11-ZINC FINGER PROTEIN,CCCTC-BINDING FACTOR,CTCFL PARALOG
 
Molecule 2 - DNA (5'-D(*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*C)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*G)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:353 , MET A:355 , CYS A:356 , HIS A:369 , HIS A:373binding site for residue ZN A 501
2AC2SOFTWARECYS A:381 , CYS A:384 , HIS A:397 , HIS A:401binding site for residue ZN A 502
3AC3SOFTWARECYS A:409 , CYS A:412 , HIS A:425 , HIS A:430binding site for residue ZN A 503
4AC4SOFTWARECYS A:439 , CYS A:442 , HIS A:455 , HIS A:460binding site for residue ZN A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K5H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5K5H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K5H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K5H)

(-) Exons   (0, 0)

(no "Exon" information available for 5K5H)

(-) 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:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhh..............hhhhhhhhhh.......ee......ee.hhhhhhhhhhhhh......ee......ee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5k5h A 350 PFKCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQH 460
                                   359       369       379       389       399       409       419       429       439       449       459 


Chain B from PDB  Type:DNA  Length:13
                                             
                 5k5h B   1 CAGCAGGGGGCGC  13
                                    10   


Chain C from PDB  Type:DNA  Length:13
                                             
                 5k5h C   3 CGCCCCCTGCTGG  15
                                    12
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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 5K5H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K5H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K5H)

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)

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  5k5h
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  CTCF_HUMAN | P49711
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 Related Entries

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

UniProtKB/Swiss-Prot
        CTCF_HUMAN | P49711: 1x6h 2ct1 5k5i 5k5j 5k5l 5kkq 5t00 5t0u 5und

(-) Related Entries Specified in the PDB File

5k5i 5k5j 5k5l