[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleMultistep loading of a DNA sliding clamp onto DNA by replication factor C.
Journal, issue, pagesElife, Vol. 11, Year 2022
Publish dateAug 8, 2022
AuthorsMarina Schrecker / Juan C Castaneda / Sujan Devbhandari / Charanya Kumar / Dirk Remus / Richard K Hite /
PubMed AbstractThe 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 ...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.
External linksElife / PubMed:35939393 / PubMed Central
MethodsEM (single particle)
Resolution2.1 - 2.92 Å
Structure data

27662

8dqw

EMDB-27662, PDB-8dqw:
Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction
Method: EM (single particle) / Resolution: 2.1 Å

27663

8dqx

EMDB-27663, PDB-8dqx:
Open state of RFC:PCNA bound to a 3' ss/dsDNA junction
Method: EM (single particle) / Resolution: 2.1 Å

27666

8dqz

EMDB-27666, PDB-8dqz:
Intermediate state of RFC:PCNA bound to a 3' ss/dsDNA junction
Method: EM (single particle) / Resolution: 2.92 Å

27667

8dr0

EMDB-27667, PDB-8dr0:
Closed state of RFC:PCNA bound to a 3' ss/dsDNA junction
Method: EM (single particle) / Resolution: 2.42 Å

27668

8dr1

EMDB-27668, PDB-8dr1:
Consensus closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2)
Method: EM (single particle) / Resolution: 2.14 Å

27669

8dr3

EMDB-27669, PDB-8dr3:
Closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) with NTD
Method: EM (single particle) / Resolution: 2.2 Å

27670

8dr4

EMDB-27670, PDB-8dr4:
Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) without NTD
Method: EM (single particle) / Resolution: 2.45 Å

27671

8dr5

EMDB-27671, PDB-8dr5:
Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) with NTD
Method: EM (single particle) / Resolution: 2.76 Å

27672

8dr6

EMDB-27672, PDB-8dr6:
Closed state of RFC:PCNA bound to a nicked dsDNA
Method: EM (single particle) / Resolution: 2.39 Å

27673

8dr7

EMDB-27673, PDB-8dr7:
Open state of RFC:PCNA bound to a nicked dsDNA
Method: EM (single particle) / Resolution: 2.7 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

ChemComp-HOH:
WATER / Water

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

Source
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsREPLICATION/DNA / DNA damage checkpoint / REPLICATION-DNA complex

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more