8GJ0

E. coli clamp loader with open clamp on primed template DNA (form 1)

PDB DOI: https://doi.org/10.2210/pdb8GJ0/pdb
NAKB: 8GJ0
EM Map EMD-40081: EMDB EMDataResource

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Escherichia coli K-12, Escherichia coli
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: 2.90 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: 415.59 kDa
Atom Count: 20,899
Modelled Residue Count: 2,579
Deposited Residue Count: 3,566
Unique protein chains: 5
Unique nucleic acid chains: 2

Macromolecules

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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

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III subunit tau	B, C, D	643	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
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Reference Sequence

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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
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Reference Sequence

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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
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Reference Sequence

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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

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Entity ID: 6
Molecule	Chains	Length	Organism	Image
Primer	I [auth X]	23	Escherichia coli
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Length	Organism	Image
Template	J [auth Y]	68	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D]	K [auth B], O [auth C], S [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D]
ALF Query on ALF Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain R [auth D] SDF format, chain U [auth D] MOL2 format, chain M [auth B] MOL2 format, chain R [auth D] MOL2 format, chain U [auth D]	M [auth B], R [auth D], U [auth D]	TETRAFLUOROALUMINATE ION Al F₄ UYOMQIYKOOHAMK-UHFFFAOYSA-J		Interactions Focus chain M [auth B] Focus chain R [auth D] Focus chain U [auth D] Interactions & Density Focus chain M [auth B] Focus chain R [auth D] Focus chain U [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] SDF format, chain W [auth E] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth E]	N [auth B], Q [auth C], V [auth D], W [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth D] Focus chain W [auth E] Interactions & Density Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth D] Focus chain W [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D]	L [auth B], P [auth C], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D]