6QNX

Structure of the SA2/SCC1/CTCF complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The structural basis for cohesin-CTCF-anchored loops.

Li, Y., Haarhuis, J.H.I., Sedeno Cacciatore, A., Oldenkamp, R., van Ruiten, M.S., Willems, L., Teunissen, H., Muir, K.W., de Wit, E., Rowland, B.D., Panne, D.

(2020) Nature 578: 472-476

  • DOI: 10.1038/s41586-019-1910-z
  • Primary Citation of Related Structures:  
    6QNX

  • PubMed Abstract: 

    • Cohesin catalyses the folding of the genome into loops that are anchored by CTCF 1 . The molecular mechanism of how cohesin and CTCF structure the 3D genome has remained unclear. Here we show that a segment within the CTCF N terminus interacts with the SA2-SCC1 subunits of human cohesin ...

    Cohesin catalyses the folding of the genome into loops that are anchored by CTCF 1 . The molecular mechanism of how cohesin and CTCF structure the 3D genome has remained unclear. Here we show that a segment within the CTCF N terminus interacts with the SA2-SCC1 subunits of human cohesin. We report a crystal structure of SA2-SCC1 in complex with CTCF at a resolution of 2.7 Å, which reveals the molecular basis of the interaction. We demonstrate that this interaction is specifically required for CTCF-anchored loops and contributes to the positioning of cohesin at CTCF binding sites. A similar motif is present in a number of established and newly identified cohesin ligands, including the cohesin release factor WAPL 2,3 . Our data suggest that CTCF enables the formation of chromatin loops by protecting cohesin against loop release. These results provide fundamental insights into the molecular mechanism that enables the dynamic regulation of chromatin folding by cohesin and CTCF.

    Organizational Affiliation: 

    Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK. daniel.panne@le.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cohesin subunit SA-2A1231Homo sapiensMutation(s): 0 
Gene Names: STAG2, SA2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N3U4 (Homo sapiens)
Explore Q8N3U4 
Go to UniProtKB:  Q8N3U4
PHAROS:  Q8N3U4
GTEx:  ENSG00000101972 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N3U4
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Double-strand-break repair protein rad21 homologB631Homo sapiensMutation(s): 0 
Gene Names: RAD21, HR21, KIAA0078, NXP1, SCC1
UniProt & NIH Common Fund Data Resources
Find proteins for O60216 (Homo sapiens)
Explore O60216 
Go to UniProtKB:  O60216
PHAROS:  O60216
GTEx:  ENSG00000164754 
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UniProt GroupO60216
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional repressor CTCFC727Homo sapiensMutation(s): 0 
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  
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UniProt GroupP49711
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.029α = 90
b = 107.255β = 90
c = 176.49γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 1.2: 2020-04-29
    Changes: Advisory