5YEG

Crystal structure of CTCF ZFs4-8-Hs5-1a complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular mechanism of directional CTCF recognition of a diverse range of genomic sites

Yin, M.Wang, J.Wang, M.Li, X.Zhang, M.Wu, Q.Wang, Y.

(2017) Cell Res 27: 1365-1377

  • DOI: 10.1038/cr.2017.131
  • Primary Citation of Related Structures:  
    5YEL, 5YEF, 5YEH, 5YEG

  • PubMed Abstract: 
  • CTCF, a conserved 3D genome architecture protein, determines proper genome-wide chromatin looping interactions through directional binding to specific sequence elements of four modules within numerous CTCF-binding sites (CBSs) by its 11 zinc fingers (ZFs ...

    CTCF, a conserved 3D genome architecture protein, determines proper genome-wide chromatin looping interactions through directional binding to specific sequence elements of four modules within numerous CTCF-binding sites (CBSs) by its 11 zinc fingers (ZFs). Here, we report four crystal structures of human CTCF in complex with CBSs of the protocadherin (Pcdh) clusters. We show that directional CTCF binding to cognate CBSs of the Pcdh enhancers and promoters is achieved through inserting its ZF3, ZFs 4-7, and ZFs 9-11 into the major groove along CBSs, resulting in a sequence-specific recognition of module 4, modules 3 and 2, and module 1, respectively; and ZF8 serves as a spacer element for variable distances between modules 1 and 2. In addition, the base contact with the asymmetric "A" in the central position of modules 2-3, is essential for directional recognition of the CBSs with symmetric core sequences but lacking module 1. Furthermore, CTCF tolerates base changes at specific positions within the degenerated CBS sequences, permitting genome-wide CTCF binding to a diverse range of CBSs. Together, these complex structures provide important insights into the molecular mechanisms for the directionality, diversity, flexibility, dynamics, and conservation of multivalent CTCF binding to its cognate sites across the entire human genome.


    Organizational Affiliation

    Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional repressor CTCF A142Homo sapiensMutation(s): 0 
Gene Names: CTCF
Find proteins for P49711 (Homo sapiens)
Explore P49711 
Go to UniProtKB:  P49711
NIH Common Fund Data Resources
PHAROS:  P49711
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional repressor CTCF B141Homo sapiensMutation(s): 0 
Gene Names: CTCF
Find proteins for P49711 (Homo sapiens)
Explore P49711 
Go to UniProtKB:  P49711
NIH Common Fund Data Resources
PHAROS:  P49711
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*GP*CP*TP*GP*GP*TP*TP*AP*AP*AP*G)-3')D, E21synthetic construct
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*CP*TP*TP*TP*AP*AP*CP*CP*AP*GP*CP*AP*GP*AP*GP*GP*GP*CP*G)-3')C, F20synthetic construct
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Free: 0.204 
    • R-Value Work: 0.186 
    • R-Value Observed: 0.187 
    • Space Group: P 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 46.167α = 78.41
    b = 56.502β = 79.31
    c = 67.486γ = 78.6
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-3000data reduction
    HKL-3000data scaling
    PHENIXphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Natural Science Foundation of ChinaChina31630015
    National Natural Science Foundation of ChinaChina91440201
    National Natural Science Foundation of ChinaChina31571335
    National Natural Science Foundation of ChinaChina31400640
    National Natural Science Foundation of ChinaChina31630039
    National Natural Science Foundation of ChinaChina91640118
    National Natural Science Foundation of ChinaChina31470820

    Revision History 

    • Version 1.0: 2017-11-29
      Type: Initial release
    • Version 1.1: 2019-10-16
      Changes: Data collection, Structure summary