5YEL

Crystal structure of CTCF ZFs6-11-gb7CSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.269 

wwPDB Validation   3D Report Full Report


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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: https://doi.org/10.1038/cr.2017.131

  • 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). 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

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional repressor CTCFB [auth A],
C [auth B]
176Homo sapiensMutation(s): 1 
Gene Names: CTCF
UniProt & NIH Common Fund Data Resources
Find proteins for P49711 (Homo sapiens)
Explore P49711 
Go to UniProtKB:  P49711
PHAROS:  P49711
GTEx:  ENSG00000102974 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49711
Sequence Annotations
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (26-MER)A [auth D],
E [auth F]
26synthetic construct
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (26-MER)D [auth C],
F [auth E]
26synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.269 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.993α = 90
b = 69.631β = 116.25
c = 84.445γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references