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(-) Description

Title :  HOMO SAPIENS CCCTC-BINDING FACTOR (CTCF) ZNF3-7 AND DNA COMPLEX STRUCTURE
 
Authors :  H. Hashimoto, D. Wang, X. Cheng
Date :  22 Jun 16  (Deposition) - 24 May 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  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, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PXC1551
    Expression System Strain: BL21 (DE3) RIL-CODON PLUS
    Expression System Taxid: 469008
    Expression System Vector Type: PGEX-6P-1
    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(*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP*C)-3')
    Chains: B, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*CP*TP*A)-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  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1ZN10Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-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 5KKQ)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KKQ)

(-) 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:147
                                                                                                                                                                                   
               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......eee....eee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kkq A 317 PLGSPHKCPDCDMAFVTSGELVRHRRYKHTHEKPFKCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSYI 463
                                   326       336       346       356       366       376       386       396       406       416       426       436       446       456       


Chain B from PDB  Type:DNA  Length:17
                                                 
                 5kkq B   1 TAGCGCCCCCTGCTGGC  17
                                    10       


Chain C from PDB  Type:DNA  Length:17
                                                 
                 5kkq C   1 GCCAGCAGGGGGCGCTA  17
                                    10       


Chain D from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               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.hhhhhhhhhhhhhh.....ee......ee.hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kkq D 321 PHKCPDCDMAFVTSGELVRHRRYKHTHEKPFKCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSYIEQ 465
                                   330       340       350       360       370       380       390       400       410       420       430       440       450       460     


Chain E from PDB  Type:DNA  Length:17
                                                 
                 5kkq E   1 TAGCGCCCCCTGCTGGC  17
                                    10       


Chain F from PDB  Type:DNA  Length:17
                                                 
                 5kkq F   1 GCCAGCAGGGGGCGCTA  17
                                    10
   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 5KKQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (39, 39)

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  5kkq
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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 5t00 5t0u 5und

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5KKQ)