7Q2Z

Cryo-EM structure of S.cerevisiae condensin Ycg1-Brn1-DNA complex

• PDB DOI: https://doi.org/10.2210/pdb7Q2Z/pdb
• NAKB: 7Q2Z
• EM Map EMD-13786: EMDB EMDataResource

• Classification: CELL CYCLE
• Organism(s): Saccharomyces cerevisiae S288C, synthetic construct
• Expression System: Saccharomyces cerevisiae W303
• Mutation(s): No 


• Deposited: 2021-10-26 Released: 2022-04-06 
• Deposition Author(s): Lee, B.-G., Rhodes, J., Lowe, J.
• Funding Organization(s): Wellcome Trust, Medical Research Council (MRC, United Kingdom)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Clamping of DNA shuts the condensin neck gate.

Lee, B.G., Rhodes, J., Lowe, J.

(2022) Proc Natl Acad Sci U S A 119: e2120006119-e2120006119

• PubMed: 35349345 
• DOI: https://doi.org/10.1073/pnas.2120006119
• Primary Citation of Related Structures:  
  7Q2X, 7Q2Y, 7Q2Z


• PubMed Abstract: 
  

  SignificanceDNA needs to be compacted to fit into nuclei and during cell division, when dense chromatids are formed for their mechanical segregation, a process that depends on the protein complex condensin. It forms and enlarges loops in DNA through loop extrusion. Our work resolves the atomic structure of a DNA-bound state of condensin in which ATP has not been hydrolyzed. The DNA is clamped within a compartment that has been reported previously in other structural maintenance of chromosomes (SMC) complexes, including Rad50, cohesin, and MukBEF. With the caveat of important differences, it means that all SMC complexes cycle through at least some similar states and undergo similar conformational changes in their head modules, while hydrolyzing ATP and translocating DNA.

---

Organizational Affiliation: 

Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 218.41 kDa 
• Atom Count: 8,258 
• Modelled Residue Count: 948 
• Deposited Residue Count: 1,835 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Condensin complex subunit 3	A [auth E]	1,035	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: YCG1, YCS5, YDR325W
UniProt
Find proteins for Q06680 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06680  Go to UniProtKB:  Q06680

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Condensin complex subunit 2	B [auth C]	754	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: BRN1, YBL097W, YBL0830
UniProt
Find proteins for P38170 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38170  Go to UniProtKB:  P38170

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA	C [auth F]	23	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA	D [auth G]	23	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Lee, B.-G., Rhodes, J., Lowe, J.

---

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	202754/Z/16/Z
Medical Research Council (MRC, United Kingdom)	United Kingdom	U105184326
Wellcome Trust	United Kingdom	218621/Z/19/Z

Revision History  

• Version 1.0: 2022-04-06
  Type: Initial release
  
• Version 1.1: 2022-04-13
  Changes: Source and taxonomy