6VVO

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

• PDB DOI: https://doi.org/10.2210/pdb6VVO/pdb
• EM Map EMD-21405: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN, REPLICATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-02-18 Released: 2020-02-26 
• Deposition Author(s): Gaubitz, C., Liu, X., Stone, N.P., Kelch, B.A.
• Funding Organization(s): American Cancer Society, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Swiss National Science Foundation

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Experimental Data Snapshot

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

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 

• DOI: https://doi.org/10.1101/2020.02.18.953257

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A3B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A3B3C2 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication factor C subunit 1	A	595	Homo sapiens	Mutation(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 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 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 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 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 ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferating cell nuclear antigen	F, G, H	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS (Subject of Investigation/LOI)	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)	Q [auth E]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	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:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.0.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Gaubitz, C., Liu, X., Stone, N.P., Kelch, B.A.

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Funding Organization	Location	Grant Number
American Cancer Society	United States	440685
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM127776
Swiss National Science Foundation	Switzerland	177859

Revision History  

• 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