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(-) Description

Title :  HUMAN CTCF ZNF3-7 AND METHYLATED DNA COMPLEX
 
Authors :  H. Hashimoto, D. Wang, X. Cheng
Date :  15 Aug 16  (Deposition) - 24 May 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Ccctc-Binding Factor, Zinc Finger, Ctcf, Transcription Regulator-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, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PXC1551
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: CODON PLUS
    Expression System Vector Type: PGEX6P-1
    Fragment: UNP RESIDUES 321-465
    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'-TAG(5CM)GCCCCCTGCTGGC-3')
    Chains: B, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-GCCAGCAGGGGG(5CM)GCTA-3')
    Chains: C, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
15CM4Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2ZN10Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:324 , CYS A:327 , HIS A:340 , HIS A:345binding site for residue ZN A 501
02AC2SOFTWARECYS A:353 , CYS A:356 , HIS A:369 , HIS A:373binding site for residue ZN A 502
03AC3SOFTWARECYS A:381 , CYS A:384 , HIS A:397 , HIS A:401binding site for residue ZN A 503
04AC4SOFTWARECYS A:409 , CYS A:412 , HIS A:425 , HIS A:430binding site for residue ZN A 504
05AC5SOFTWARECYS A:439 , CYS A:442 , HIS A:455 , HIS A:460binding site for residue ZN A 505
06AC6SOFTWARECYS D:324 , CYS D:327 , HIS D:340 , HIS D:345binding site for residue ZN D 501
07AC7SOFTWARECYS D:353 , CYS D:356 , HIS D:369 , HIS D:373binding site for residue ZN D 502
08AC8SOFTWARECYS D:381 , CYS D:384 , HIS D:397 , HIS D:401binding site for residue ZN D 503
09AC9SOFTWARECYS D:409 , CYS D:412 , HIS D:425 , HIS D:430binding site for residue ZN D 504
10AD1SOFTWARECYS D:439 , CYS D:442 , HIS D:455 , HIS D:460binding site for residue ZN D 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5T00)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5T00)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T00)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T00)

(-) Exons   (0, 0)

(no "Exon" information available for 5T00)

(-) 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:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee.hhhhhhhhhhhhh.....ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhh......ee......ee.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t00 A 320 SPHKCPDCDMAFVTSGELVRHRRYKHTHEKPFKCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSY 462
                                   329       339       349       359       369       379       389       399       409       419       429       439       449       459   


Chain B from PDB  Type:DNA  Length:17
                                                 
                 5t00 B   1 TAGxGCCCCCTGCTGGC  17
                               |    10       
                               4-5CM         


Chain C from PDB  Type:DNA  Length:17
                                                 
                 5t00 C   1 GCCAGCAGGGGGxGCTA  17
                                    10  |    
                                       13-5CM


Chain D from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhh.....ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhh......ee......ee.hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t00 D 322 HKCPDCDMAFVTSGELVRHRRYKHTHEKPFKCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSYIE 464
                                   331       341       351       361       371       381       391       401       411       421       431       441       451       461   


Chain E from PDB  Type:DNA  Length:17
                                                 
                 5t00 E   1 TAGxGCCCCCTGCTGGC  17
                               |    10       
                               4-5CM         


Chain F from PDB  Type:DNA  Length:17
                                                 
                 5t00 F   1 GCCAGCAGGGGGxGCTA  17
                                    10  |    
                                       13-5CM
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5T00)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T00)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T00)

(-) Gene Ontology  (39, 39)

Asymmetric Unit(hide GO term definitions)

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  5t00
    Family and Domain Information: ProDom | SYSTERS
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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 5k5h 5k5i 5k5j 5k5l 5kkq 5t0u 5und

(-) Related Entries Specified in the PDB File

5t0u