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 1.1 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 

  • DOI: 10.1126/science.abb0981
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • As a ring-shaped 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 c ...

    As a ring-shaped 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, we determine 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Structural maintenance of chromosomes protein 1A
A
1233Homo sapiensMutation(s): 1 
Gene Names: SMC1ADXS423EKIAA0178SB1.8SMC1SMC1L1
Find proteins for Q14683 (Homo sapiens)
Go to UniProtKB:  Q14683
NIH Common Fund Data Resources
PHAROS  Q14683

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Structural maintenance of chromosomes protein 3
B
1217Homo sapiensMutation(s): 1 
Gene Names: SMC3BAMBMHCSPG6SMC3L1
Find proteins for Q9UQE7 (Homo sapiens)
Go to UniProtKB:  Q9UQE7
NIH Common Fund Data Resources
PHAROS  Q9UQE7

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Double-strand-break repair protein rad21 homolog
C
631Homo sapiensMutation(s): 3 
Gene Names: RAD21HR21KIAA0078NXP1SCC1
Find proteins for O60216 (Homo sapiens)
Go to UniProtKB:  O60216
NIH Common Fund Data Resources
PHAROS  O60216

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Nipped-B-like protein
E
1652Homo sapiensMutation(s): 0 
Gene Names: NIPBLIDN3SCC2
Find proteins for Q6KC79 (Homo sapiens)
Go to UniProtKB:  Q6KC79
NIH Common Fund Data Resources
PHAROS  Q6KC79

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Cohesin subunit SA-1
D
1272Homo sapiensMutation(s): 0 
Gene Names: STAG1SA1SCC3
Find proteins for Q8WVM7 (Homo sapiens)
Go to UniProtKB:  Q8WVM7
NIH Common Fund Data Resources
PHAROS  Q8WVM7

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsLengthOrganism
DNA (51-MER)G51Homo sapiens

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsLengthOrganism
DNA (51-MER)F51Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references