5YEH

Crystal struture of CTCF ZFs4-8-eCBS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.328 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.0 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:  5YEF, 5YEG, 5YEL

  • 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 ...

    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

    Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional repressor CTCF
A, B
142Homo sapiensGene Names: CTCF
Find proteins for P49711 (Homo sapiens)
Go to Gene View: CTCF
Go to UniProtKB:  P49711
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*GP*GP*TP*TP*TP*CP*CP*GP*CP*TP*AP*GP*AP*GP*GP*GP*CP*G)-3')C,E20synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*GP*CP*CP*CP*TP*CP*TP*AP*GP*CP*GP*GP*AP*AP*AP*CP*CP*G)-3')D,F20synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.328 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.222 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 45.845α = 81.17
b = 54.876β = 80.11
c = 66.938γ = 79.72
Software Package:
Software NamePurpose
HKL-3000data scaling
PHASERphasing
PHENIXrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant 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