6WGE

Cryo-EM structure of human Cohesin-NIPBL-DNA complex without STAG1

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 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 ...

    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

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 1A1,233Homo sapiensMutation(s): 1 
Gene Names: SMC1A, DXS423E, KIAA0178, SB1.8, SMC1, SMC1L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q14683 (Homo sapiens)
Explore Q14683 
Go to UniProtKB:  Q14683
PHAROS:  Q14683
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14683
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 31,217Homo sapiensMutation(s): 1 
Gene Names: SMC3, BAM, BMH, CSPG6, SMC3L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQE7 (Homo sapiens)
Explore Q9UQE7 
Go to UniProtKB:  Q9UQE7
PHAROS:  Q9UQE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQE7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Double-strand-break repair protein rad21 homolog631Homo sapiensMutation(s): 3 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60216
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nipped-B-like proteinD [auth E]1,642Homo sapiensMutation(s): 0 
Gene Names: NIPBL, IDN3, SCC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q6KC79 (Homo sapiens)
Explore Q6KC79 
Go to UniProtKB:  Q6KC79
PHAROS:  Q6KC79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6KC79
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (43-MER)E [auth F]43Homo sapiens
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (43-MER)F [auth G]43Homo sapiens
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP
Download Ideal Coordinates CCD File 
G [auth A],
I [auth B]		PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N		 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG
Download Ideal Coordinates CCD File 
H [auth A],
J [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX1.17.1-3660

Structure Validation

View Full Validation Report



View more in-depth experimental data
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