6VVO | pdb_00006vvo

Structure of the human clamp loader (Replication Factor C, RFC) bound to the sliding clamp (Proliferating Cell Nuclear Antigen, PCNA)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6VVO

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

Literature

Structure of the human clamp loader bound to the sliding clamp: a further twist on AAA+ mechanism

Gaubitz, C., Liu, X., Magrino, J., Stone, N.P., Landeck, J., Hedglin, M., Kelch, B.A.

(2020) bioRxiv 

Macromolecule Content 

  • Total Structure Weight: 313.34 kDa 
  • Atom Count: 19,668 
  • Modeled Residue Count: 2,493 
  • Deposited Residue Count: 2,791 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Replication factor C subunit 1595Homo sapiensMutation(s): 0 
Gene Names: RFC1, RFC140
UniProt & NIH Common Fund Data Resources
Find proteins for P35251 (Homo sapiens)
Explore P35251 
Go to UniProtKB:  P35251
PHAROS:  P35251
GTEx:  ENSG00000035928 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35251
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35250
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
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)
Explore P40937 
Go to UniProtKB:  P40937
PHAROS:  P40937
GTEx:  ENSG00000111445 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40937
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Replication factor C subunit 4363Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35249
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Replication factor C subunit 3356Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40938
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12004
Sequence Annotations
Expand
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: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.0.2

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
American Cancer SocietyUnited States440685
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM127776
Swiss National Science FoundationSwitzerland177859

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary