7STB | pdb_00007stb

Closed state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction

PDB DOI: https://doi.org/10.2210/pdb7STB/pdb
EM Map EMD-25423: EMDB EMDataResource
NAKB: 7STB

Classification: REPLICATION/DNA
Organism(s): Saccharomyces cerevisiae S288C, Saccharomyces cerevisiae
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2021-11-12 Released: 2022-03-23
Deposition Author(s): Castaneda, J.C., Schrecker, M., Remus, D., Hite, R.K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.72 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Mechanisms of loading and release of the 9-1-1 checkpoint clamp.

Castaneda, J.C., Schrecker, M., Remus, D., Hite, R.K.

(2022) Nat Struct Mol Biol 29: 369-375

PubMed: 35314831 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-022-00741-7
Primary Citation Related Structures:
7ST9, 7STB, 7STE

PubMed Abstract:
Single-stranded or double-stranded DNA junctions with recessed 5' ends serve as loading sites for the checkpoint clamp, 9-1-1, which mediates activation of the apical checkpoint kinase, ATR ^Mec1. However, the basis for 9-1-1's recruitment to 5' junctions is unclear. Here, we present structures of the yeast checkpoint clamp loader, Rad24-replication factor C (RFC), in complex with 9-1-1 and a 5' junction and in a post-ATP-hydrolysis state. Unexpectedly, 9-1-1 adopts both closed and planar open states in the presence of Rad24-RFC and DNA. Moreover, Rad24-RFC associates with the DNA junction in the opposite orientation of processivity clamp loaders with Rad24 exclusively coordinating the double-stranded region. ATP hydrolysis stimulates conformational changes in Rad24-RFC, leading to disengagement of DNA-loaded 9-1-1. Together, these structures explain 9-1-1's recruitment to 5' junctions and reveal new principles of sliding clamp loading.

Organizational Affiliation

Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Macromolecule Content

Total Structure Weight: 431.36 kDa
Atom Count: 22,814
Modeled Residue Count: 2,789
Deposited Residue Count: 3,658
Unique protein chains: 8
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Checkpoint protein RAD24	A	696	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RAD24, YER173W, SYGP-ORF60
UniProt
Find proteins for P32641 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32641 Go to UniProtKB: P32641
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32641
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 4	B	323	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RFC4, YOL094C, O0923
UniProt
Find proteins for P40339 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40339 Go to UniProtKB: P40339
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40339
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 3	C	340	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RFC3, YNL290W, N0533
UniProt
Find proteins for P38629 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38629 Go to UniProtKB: P38629
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38629
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 2	D	353	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RFC2, YJR068W, J1808
UniProt
Find proteins for P40348 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40348 Go to UniProtKB: P40348
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40348
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 5	E	354	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RFC5, YBR087W, YBR0810
UniProt
Find proteins for P38251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38251 Go to UniProtKB: P38251
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38251
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage checkpoint control protein RAD17	F	401	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: RAD17, YOR368W
UniProt
Find proteins for P48581 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P48581 Go to UniProtKB: P48581
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48581
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage checkpoint protein 1	G	646	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: DDC1, YPL194W
UniProt
Find proteins for Q08949 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08949 Go to UniProtKB: Q08949
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08949
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage checkpoint control protein MEC3	H	474	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: MEC3, PIP3, PSO9, YLR288C, L8003.15
UniProt
Find proteins for Q02574 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02574 Go to UniProtKB: Q02574
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02574
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 9
DNA (50-MER)	I [auth J]	50	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 10
DNA (5'-D(PCPGPCPTPCPCPTPTPCPCPTPGPAPCPTPCPGPTPCPC)-3')	J [auth I]	21	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D]	K [auth A], N [auth B], P [auth C], R [auth D]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Interactions & Density Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain S [auth E] MOL2 format, chain S [auth E] mmCIF format, chain S [auth E]	S [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain S [auth E] Interactions & Density Focus chain S [auth E]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain L [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D]	L [auth A], M [auth B], O [auth C], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Interactions & Density Focus chain L [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.72 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-23

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)		GM107239
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)		GM127428
National Institutes of Health/National Cancer Institute (NIH/NCI)		CA008748

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: 2022-04-27
Changes: Database references
Version 1.3: 2024-06-05
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

7STB | pdb_00007stb

Closed state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction

Literature

Mechanisms of loading and release of the 9-1-1 checkpoint clamp.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

Sequence Annotations

Entity ID: 10

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)