6WG6

Crystal structure of human SMC1-SMC3 hinge domain heterodimer in north-open conformation

  • Classification: CELL CYCLE/DNA
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2020-04-04 Released: 2020-05-20 
  • Deposition Author(s): Shi, Z.B., Yu, H.
  • Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT), Welch Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.54 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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

    School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein
A, C, E, G, I, K
A, C, E, G, I, K
233Homo sapiensMutation(s): 0 
Gene Names: SMC1ADXS423EKIAA0178SB1.8SMC1SMC1L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q14683 (Homo sapiens)
Explore Q14683 
Go to UniProtKB:  Q14683
PHAROS:  Q14683
GTEx:  ENSG00000072501 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14683
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 3
B, D, F, H, J, L
B, D, F, H, J, L
256Homo sapiensMutation(s): 0 
Gene Names: SMC3BAMBMHCSPG6SMC3L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQE7 (Homo sapiens)
Explore Q9UQE7 
Go to UniProtKB:  Q9UQE7
PHAROS:  Q9UQE7
GTEx:  ENSG00000108055 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQE7
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
poly(dT)M, N 10Homo sapiens
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.54 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.985α = 90
b = 145.021β = 90
c = 315.949γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
Cootmodel building

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-04-04 
  • Released Date: 2020-05-20 
  • Deposition Author(s): Shi, Z.B., Yu, H.

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