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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.1 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

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

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

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35251
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35250
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40937
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35249
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40938
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12004
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D]	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		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain Q [auth E] MOL2 format, chain Q [auth E]	Q [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain Q [auth E] Interactions & Density Focus chain Q [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D]	I [auth A], K [auth B], M [auth C], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D]

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-02-26

Deposition Author(s):

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