8GIY

E. coli clamp loader with closed clamp

PDB DOI: https://doi.org/10.2210/pdb8GIY/pdb
EM Map EMD-40079: EMDB EMDataResource

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2023-03-14 Released: 2024-03-27
Deposition Author(s): Oakley, A.J., Xu, Z.-Q., Dixon, N.E.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural characterisation of the complete cycle of sliding clamp loading in E. coli

Xu, Z.-Q., Oakley, A.J., Dixon, N.E.

To be published.

Macromolecule Content

Total Structure Weight: 316.88 kDa
Atom Count: 19,865
Modelled Residue Count: 2,532
Deposited Residue Count: 2,839
Unique protein chains: 5

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III subunit delta	A	343	Escherichia coli K-12	Mutation(s): 0 Gene Names: holA, b0640, JW0635 EC: 2.7.7.7
UniProt
Find proteins for P28630 (Escherichia coli (strain K12)) Explore P28630 Go to UniProtKB: P28630
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28630
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III subunit tau	B, C, D	431	Escherichia coli K-12	Mutation(s): 0 Gene Names: dnaX, dnaZ, dnaZX, b0470, JW0459 EC: 2.7.7.7
UniProt
Find proteins for P06710 (Escherichia coli (strain K12)) Explore P06710 Go to UniProtKB: P06710
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06710
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III subunit delta'	E	334	Escherichia coli K-12	Mutation(s): 0 Gene Names: holB, b1099, JW1085 EC: 2.7.7.7
UniProt
Find proteins for P28631 (Escherichia coli (strain K12)) Explore P28631 Go to UniProtKB: P28631
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28631
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III subunit psi	F	137	Escherichia coli K-12	Mutation(s): 0 Gene Names: holD, b4372, JW4334 EC: 2.7.7.7
UniProt
Find proteins for P28632 (Escherichia coli (strain K12)) Explore P28632 Go to UniProtKB: P28632
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28632
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta sliding clamp	G [auth H], H [auth I]	366	Escherichia coli K-12	Mutation(s): 0 Gene Names: dnaN, b3701, JW3678
UniProt
Find proteins for P0A988 (Escherichia coli (strain K12)) Explore P0A988 Go to UniProtKB: P0A988
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A988
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D]	I [auth B], L [auth C], O [auth D]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth E] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E]	K [auth B], N [auth C], Q [auth D], R [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth E] Interactions & Density Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D]	J [auth B], M [auth C], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]