8UI8

Cryo-EM map of human clamp-clamp loader ATAD5-RFC-two PCNAs complex in intermediate state 3

PDB DOI: https://doi.org/10.2210/pdb8UI8/pdb
EM Map EMD-42288: EMDB EMDataResource

Classification: MOTOR PROTEIN
Organism(s): Homo sapiens
Expression System: Insect cell expression vector pTIE1
Mutation(s): No

Deposited: 2023-10-10 Released: 2024-05-29
Deposition Author(s): Wang, F., He, Q., 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: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The human ATAD5 has evolved unique structural elements to function exclusively as a PCNA unloader.

Wang, F., He, Q., Yao, N.Y., O'Donnell, M.E., Li, H.

(2024) Nat Struct Mol Biol

PubMed: 38871854 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41594-024-01332-4
Primary Citation of Related Structures:
8UI7, 8UI8, 8UI9, 8UII

PubMed Abstract:
Humans have three different proliferating cell nuclear antigen (PCNA) clamp-loading complexes: RFC and CTF18-RFC load PCNA onto DNA, but ATAD5-RFC can only unload PCNA from DNA. The underlying structural basis of ATAD5-RFC unloading is unknown. We show here that ATAD5 has two unique locking loops that appear to tie the complex into a rigid structure, and together with a domain that plugs the DNA-binding chamber, prevent conformation changes required for DNA binding, likely explaining why ATAD5-RFC is exclusively a PCNA unloader. These features are conserved in the yeast PCNA unloader Elg1-RFC. We observe intermediates in which PCNA bound to ATAD5-RFC exists as a closed planar ring, a cracked spiral or a gapped spiral. Surprisingly, ATAD5-RFC can open a PCNA gap between PCNA protomers 2 and 3, different from the PCNA protomers 1 and 3 gap observed in all previously characterized clamp loaders.

Organizational Affiliation

Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.

Macromolecule Content

Total Structure Weight: 334.61 kDa
Atom Count: 19,822
Modelled Residue Count: 2,499
Deposited Residue Count: 2,967
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase family AAA domain-containing protein 5	A	1,032	Homo sapiens	Mutation(s): 0 Gene Names: ATAD5
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QE3 (Homo sapiens) Explore Q96QE3 Go to UniProtKB: Q96QE3
PHAROS: Q96QE3 GTEx: ENSG00000176208
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96QE3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 2	B	354	Homo sapiens	Mutation(s): 0 Gene Names: RFC2
UniProt & NIH Common Fund Data Resources
Find proteins for P35250 (Homo sapiens) Explore P35250 Go to UniProtKB: P35250
PHAROS: P35250 GTEx: ENSG00000049541
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35250
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 5	C	340	Homo sapiens	Mutation(s): 0 Gene Names: RFC5
UniProt & NIH Common Fund Data Resources
Find proteins for P40937 (Homo sapiens) Explore P40937 Go to UniProtKB: P40937
PHAROS: P40937 GTEx: ENSG00000111445
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40937
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 4	D	363	Homo sapiens	Mutation(s): 0 Gene Names: RFC4
UniProt & NIH Common Fund Data Resources
Find proteins for P35249 (Homo sapiens) Explore P35249 Go to UniProtKB: P35249
PHAROS: P35249 GTEx: ENSG00000163918
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35249
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 3	E	356	Homo sapiens	Mutation(s): 0 Gene Names: RFC3
UniProt & NIH Common Fund Data Resources
Find proteins for P40938 (Homo sapiens) Explore P40938 Go to UniProtKB: P40938
PHAROS: P40938 GTEx: ENSG00000133119
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40938
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferating cell nuclear antigen	F, G	261	Homo sapiens	Mutation(s): 0 Gene Names: PCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P12004 (Homo sapiens) Explore P12004 Go to UniProtKB: P12004
PHAROS: P12004 GTEx: ENSG00000132646
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12004
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 I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C]	I [auth A], K [auth B], M [auth C]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain O [auth E] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E]	N [auth D], O [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain N [auth D] Focus chain O [auth E] Interactions & Density Focus chain N [auth D] Focus chain O [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C]	H [auth A], J [auth B], L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-29

Deposition Author(s):

Wang, F.

He, Q.

Li, H.

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	--