8UI9

Cryo-EM map of human clamp-clamp loader ATAD5-RFC-cracked PCNA complex in intermediate state 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

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 31: 1680-1691

  • 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase family AAA domain-containing protein 51,032Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96QE3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 2354Homo sapiensMutation(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 
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UniProt GroupP35250
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 5340Homo sapiensMutation(s): 0 
Gene Names: RFC5
UniProt & NIH Common Fund Data Resources
Find proteins for P40937 (Homo sapiens)
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Go to UniProtKB:  P40937
PHAROS:  P40937
GTEx:  ENSG00000111445 
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UniProt GroupP40937
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 4363Homo sapiensMutation(s): 0 
Gene Names: RFC4
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Find proteins for P35249 (Homo sapiens)
Explore P35249 
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PHAROS:  P35249
GTEx:  ENSG00000163918 
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UniProt GroupP35249
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 3356Homo sapiensMutation(s): 0 
Gene Names: RFC3
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Find proteins for P40938 (Homo sapiens)
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PHAROS:  P40938
GTEx:  ENSG00000133119 
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UniProt GroupP40938
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferating cell nuclear antigen
F, G, H
261Homo sapiensMutation(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 
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UniProt GroupP12004
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
J [auth A],
L [auth B],
N [auth C],
P [auth D]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
Q [auth E]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
K [auth B],
M [auth C],
O [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM131754
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115809
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Database references
  • Version 1.2: 2024-06-26
    Changes: Data collection, Database references
  • Version 1.3: 2024-11-27
    Changes: Data collection, Database references, Structure summary