7Q2Y

Cryo-EM structure of clamped S.cerevisiae condensin-DNA complex (form II)

PDB DOI: https://doi.org/10.2210/pdb7Q2Y/pdb
NAKB: 7Q2Y
EM Map EMD-13784: 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: 2022-03-23
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: 3.00 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

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 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 534.23 kDa
Atom Count: 17,754
Modelled Residue Count: 2,132
Deposited Residue Count: 4,574
Unique protein chains: 4
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural maintenance of chromosomes protein 2	A	1,170	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: SMC2, YFR031C
UniProt
Find proteins for P38989 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38989 Go to UniProtKB: P38989
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38989
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural maintenance of chromosomes protein 4	B	1,418	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: SMC4, YLR086W, L9449.5
UniProt
Find proteins for Q12267 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12267 Go to UniProtKB: Q12267
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12267
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Condensin complex subunit 2	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38170
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Condensin complex subunit 1	D	1,176	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: YCS4, LOC7, YLR272C, L8479.14
UniProt
Find proteins for Q06156 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06156 Go to UniProtKB: Q06156
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q06156
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (28-MER)	E [auth F]	28	synthetic construct
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (28-MER)	F [auth G]	28	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B]	G [auth A], J [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
BEF Query on BEF Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B]	H [auth A], K [auth B]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B]	I [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-03-23

Deposition Author(s):

Lee, B.-G.

Rhodes, J.

Lowe, J.

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

Revision History (Full details and data files)

Version 1.0: 2022-03-23
Type: Initial release
Version 1.1: 2022-04-06
Changes: Database references
Version 1.2: 2022-04-20
Changes: Source and taxonomy
Version 1.3: 2023-09-13
Changes: Data collection, Data processing, Refinement description, Structure summary