8DR5

Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) with NTD


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 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

Multistep loading of a DNA sliding clamp onto DNA by replication factor C.

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

(2022) Elife 11

  • DOI: https://doi.org/10.7554/eLife.78253
  • Primary Citation of Related Structures:  
    8DQW, 8DQX, 8DQZ, 8DR0, 8DR1, 8DR3, 8DR4, 8DR5, 8DR6, 8DR7

  • PubMed Abstract: 

    The DNA sliding clamp proliferating cell nuclear antigen (PCNA) is an essential co-factor for many eukaryotic DNA metabolic enzymes. PCNA is loaded around DNA by the ATP-dependent clamp loader replication factor C (RFC), which acts at single-stranded (ss)/double-stranded DNA (dsDNA) junctions harboring a recessed 3' end (3' ss/dsDNA junctions) and at DNA nicks. To illuminate the loading mechanism we have investigated the structure of RFC:PCNA bound to ATPγS and 3' ss/dsDNA junctions or nicked DNA using cryogenic electron microscopy. Unexpectedly, we observe open and closed PCNA conformations in the RFC:PCNA:DNA complex, revealing that PCNA can adopt an open, planar conformation that allows direct insertion of dsDNA, and raising the question of whether PCNA ring closure is mechanistically coupled to ATP hydrolysis. By resolving multiple DNA-bound states of RFC:PCNA we observe that partial melting facilitates lateral insertion into the central channel formed by RFC:PCNA. We also resolve the Rfc1 N-terminal domain and demonstrate that its single BRCT domain participates in coordinating DNA prior to insertion into the central RFC channel, which promotes PCNA loading on the lagging strand of replication forks in vitro. Combined, our data suggest a comprehensive and fundamentally revised model for the RFC-catalyzed loading of PCNA onto DNA.


  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 1918Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC1CDC44YOR217WYOR50-7
UniProt
Find proteins for P38630 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP38630
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 4323Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC4YOL094CO0923
UniProt
Find proteins for P40339 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40339
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 3340Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC3YNL290WN0533
UniProt
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UniProt GroupP38629
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 2353Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC2YJR068WJ1808
UniProt
Find proteins for P40348 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40348
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Replication factor C subunit 5354Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RFC5YBR087WYBR0810
UniProt
Find proteins for P38251 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP38251
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferating cell nuclear antigen
F, G, H
277Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PCNAPOL30GI527_G0000300
UniProt
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP15873
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*CP*GP*GP*GP*GP*GP*GP*GP*CP*C)-3')13Saccharomyces cerevisiae
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*GP*CP*CP*CP*CP*CP*CP*CP*GP*GP*C)-3')12Saccharomyces cerevisiae
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Entity ID: 9
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')11Saccharomyces cerevisiae
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Entity ID: 10
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*TP*TP*T)-3')13Saccharomyces cerevisiae
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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 
N [auth A],
P [auth B],
R [auth C],
T [auth D]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
U [auth E]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC3.3

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA008748
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM107239
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM127428

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-17
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references
  • Version 1.2: 2024-02-14
    Changes: Data collection