6WG3

Cryo-EM structure of human Cohesin-NIPBL-DNA complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-EM structure of the human cohesin-NIPBL-DNA complex.

Shi, Z.Gao, H.Bai, X.C.Yu, H.

(2020) Science 368: 1454-1459

  • DOI: https://doi.org/10.1126/science.abb0981
  • Primary Citation of Related Structures:  
    6WG3, 6WG4, 6WG6, 6WGE

  • PubMed Abstract: 

    As a ring-shaped adenosine triphosphatase (ATPase) machine, cohesin organizes the eukaryotic genome by extruding DNA loops and mediates sister chromatid cohesion by topologically entrapping DNA. How cohesin executes these fundamental DNA transactions is not understood. Using cryo-electron microscopy (cryo-EM), we determined the structure of human cohesin bound to its loader NIPBL and DNA at medium resolution. Cohesin and NIPBL interact extensively and together form a central tunnel to entrap a 72-base pair DNA. NIPBL and DNA promote the engagement of cohesin's ATPase head domains and ATP binding. The hinge domains of cohesin adopt an "open washer" conformation and dock onto the STAG1 subunit. Our structure explains the synergistic activation of cohesin by NIPBL and DNA and provides insight into DNA entrapment by cohesin.


  • Organizational Affiliation

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 1A1,233Homo sapiensMutation(s): 1 
Gene Names: SMC1ADXS423EKIAA0178SB1.8SMC1SMC1L1
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Find proteins for Q14683 (Homo sapiens)
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Go to UniProtKB:  Q14683
PHAROS:  Q14683
GTEx:  ENSG00000072501 
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UniProt GroupQ14683
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 31,217Homo sapiensMutation(s): 1 
Gene Names: SMC3BAMBMHCSPG6SMC3L1
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Find proteins for Q9UQE7 (Homo sapiens)
Explore Q9UQE7 
Go to UniProtKB:  Q9UQE7
PHAROS:  Q9UQE7
GTEx:  ENSG00000108055 
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UniProt GroupQ9UQE7
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Double-strand-break repair protein rad21 homolog631Homo sapiensMutation(s): 3 
Gene Names: RAD21HR21KIAA0078NXP1SCC1
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Find proteins for O60216 (Homo sapiens)
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Go to UniProtKB:  O60216
PHAROS:  O60216
GTEx:  ENSG00000164754 
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UniProt GroupO60216
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cohesin subunit SA-11,272Homo sapiensMutation(s): 0 
Gene Names: STAG1SA1SCC3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WVM7 (Homo sapiens)
Explore Q8WVM7 
Go to UniProtKB:  Q8WVM7
PHAROS:  Q8WVM7
GTEx:  ENSG00000118007 
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UniProt GroupQ8WVM7
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Nipped-B-like protein1,652Homo sapiensMutation(s): 0 
Gene Names: NIPBLIDN3SCC2
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Find proteins for Q6KC79 (Homo sapiens)
Explore Q6KC79 
Go to UniProtKB:  Q6KC79
PHAROS:  Q6KC79
GTEx:  ENSG00000164190 
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UniProt GroupQ6KC79
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  • Reference Sequence
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (51-MER)51Homo sapiens
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (51-MER)51Homo sapiens
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17.1-3660
RECONSTRUCTIONRELION3

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Prevention and Research Institute of Texas (CPRIT)United States--
Welch FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 1.2: 2020-07-08
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references