8TWA

Cryo-EM structure of S. cerevisiae Ctf18-RFC-PCNA-PolE-DNA complex

PDB DOI: https://doi.org/10.2210/pdb8TWA/pdb
EM Map EMD-41664: EMDB EMDataResource
NAKB: 8TWA

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Saccharomyces cerevisiae, synthetic construct
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2023-08-20 Released: 2024-09-04
Deposition Author(s): Yuan, Z., Georgescu, R., O'Donnell, M., Li, H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM reveals that Ctf18-RFC collaborates with PolE to load the PCNA clamp onto a leading strand DNA

Yuan, Z., Georgescu, R., O'Donnell, M., Li, H.

To be published.

Macromolecule Content

Total Structure Weight: 650.25 kDa
Atom Count: 31,914
Modelled Residue Count: 4,024
Deposited Residue Count: 5,639
Unique protein chains: 10
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
Chromosome transmission fidelity protein 18	A [auth C]	26	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: CTF18
UniProt
Find proteins for P49956 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49956 Go to UniProtKB: P49956
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49956
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase epsilon catalytic subunit A	D [auth E]	2,222	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: POL2, DUN2, YNL262W, N0825 EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data)
UniProt
Find proteins for P21951 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21951 Go to UniProtKB: P21951
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21951
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromosome transmission fidelity protein 8	E [auth D]	132	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: CTF8
UniProt
Find proteins for P38877 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38877 Go to UniProtKB: P38877
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38877
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Sister chromatid cohesion protein DCC1	F [auth B]	380	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: DCC1, YCL016C, YCL16C
UniProt
Find proteins for P25559 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25559 Go to UniProtKB: P25559
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25559
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 4	G [auth 4]	319	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RFC4
UniProt
Find proteins for P40339 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40339 Go to UniProtKB: P40339
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40339
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 3	H [auth 3]	327	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RFC3
UniProt
Find proteins for P38629 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38629 Go to UniProtKB: P38629
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38629
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 2	I [auth 2]	340	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RFC2
UniProt
Find proteins for P40348 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40348 Go to UniProtKB: P40348
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40348
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 5	J [auth 5]	354	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RFC5
UniProt
Find proteins for P38251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38251 Go to UniProtKB: P38251
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38251
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromosome transmission fidelity protein 18	K [auth 1]	741	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: CTF18, CHL12, YMR078C, YM9582.03C
UniProt
Find proteins for P49956 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49956 Go to UniProtKB: P49956
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49956
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferating cell nuclear antigen	L [auth X], M [auth Y], N [auth Z]	258	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: POL30, YBR088C, YBR0811
UniProt
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P15873 Go to UniProtKB: P15873
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15873
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
Primer DNA	B [auth P]	9	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
Template DNA	C [auth T]	15	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS Download Ideal Coordinates CCD File SDF format, chain P [auth 4] SDF format, chain R [auth 3] SDF format, chain T [auth 2] MOL2 format, chain P [auth 4] MOL2 format, chain R [auth 3] MOL2 format, chain T [auth 2]	P [auth 4], R [auth 3], T [auth 2]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain P [auth 4] Focus chain R [auth 3] Focus chain T [auth 2] Interactions & Density Focus chain P [auth 4] Focus chain R [auth 3] Focus chain T [auth 2]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain V [auth 5] MOL2 format, chain V [auth 5]	V [auth 5]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain V [auth 5] Interactions & Density Focus chain V [auth 5]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain O [auth E] MOL2 format, chain O [auth E]	O [auth E]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain O [auth E] Interactions & Density Focus chain O [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Q [auth 4] SDF format, chain S [auth 3] SDF format, chain U [auth 2] MOL2 format, chain Q [auth 4] MOL2 format, chain S [auth 3] MOL2 format, chain U [auth 2]	Q [auth 4], S [auth 3], U [auth 2]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Q [auth 4] Focus chain S [auth 3] Focus chain U [auth 2] Interactions & Density Focus chain Q [auth 4] Focus chain S [auth 3] Focus chain U [auth 2]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM131754
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115809
Howard Hughes Medical Institute (HHMI)	United States	M.E.O.

Revision History (Full details and data files)

Version 1.0: 2024-09-04
Type: Initial release

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 R01GM133198.

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Help and Resources

8TWA

Cryo-EM structure of S. cerevisiae Ctf18-RFC-PCNA-PolE-DNA complex

Cryo-EM reveals that Ctf18-RFC collaborates with PolE to load the PCNA clamp onto a leading strand DNA

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

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Sequence Annotations

Entity ID: 6

UniProt

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Sequence Annotations

Entity ID: 7

UniProt

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Entity ID: 8

UniProt

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Sequence Annotations

Entity ID: 9

UniProt

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Entity ID: 10

UniProt

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Sequence Annotations

Entity ID: 11

UniProt

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Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

Sequence Annotations

Entity ID: 3

Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)