25RY | pdb_000025ry

Cryo-EM structure of the E. coli beta sliding clamp-Hda heterooctamer

PDB DOI: https://doi.org/10.2210/pdb25RY/pdb
EM Map EMD-80334: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2026-04-16 Released: 2026-10-07
Deposition Author(s): Jiang, X., Danev, R., Kikkawa, M.
Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.12 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: other
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wwPDB Validation 3D Report Full Report

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

Literature

Reversible autoinhibition of the bacterial replication-licensing Hda-beta clamp complex.

Jiang, X., Danev, R., Luan, Y., Nakakido, M.,, Tsumoto, K., Kikkawa, M.

(2026) Nucleic Acids Res

Macromolecule Content

Total Structure Weight: 280.19 kDa
Atom Count: 18,587
Modeled Residue Count: 2,384
Deposited Residue Count: 2,480
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta sliding clamp	A, B, C, D	387	Escherichia coli	Mutation(s): 0 Gene Names: dnaN, Z5192, ECs4636
UniProt
Find proteins for P0A990 (Escherichia coli O157:H7) Explore P0A990 Go to UniProtKB: P0A990
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A990
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DnaA regulatory inactivator Hda	E, F, G, H	233	Escherichia coli	Mutation(s): 0 Gene Names: hda, idaB, yfgE, b2496, JW5397, f248c
UniProt
Find proteins for P69931 (Escherichia coli (strain K12)) Explore P69931 Go to UniProtKB: P69931
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69931
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain I [auth E] SDF format, chain K [auth F] SDF format, chain M [auth G] SDF format, chain O [auth H] MOL2 format, chain I [auth E] MOL2 format, chain K [auth F] MOL2 format, chain M [auth G] MOL2 format, chain O [auth H] mmCIF format, chain I [auth E] mmCIF format, chain K [auth F] mmCIF format, chain M [auth G] mmCIF format, chain O [auth H]	I [auth E], K [auth F], M [auth G], O [auth H]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth E] Focus chain K [auth F] Focus chain M [auth G] Focus chain O [auth H] Interactions & Density Focus chain I [auth E] Focus chain K [auth F] Focus chain M [auth G] Focus chain O [auth H]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth E] SDF format, chain L [auth F] SDF format, chain N [auth G] SDF format, chain P [auth H] MOL2 format, chain J [auth E] MOL2 format, chain L [auth F] MOL2 format, chain N [auth G] MOL2 format, chain P [auth H] mmCIF format, chain J [auth E] mmCIF format, chain L [auth F] mmCIF format, chain N [auth G] mmCIF format, chain P [auth H]	J [auth E], L [auth F], N [auth G], P [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth E] Focus chain L [auth F] Focus chain N [auth G] Focus chain P [auth H] Interactions & Density Focus chain J [auth E] Focus chain L [auth F] Focus chain N [auth G] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.12 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	5.0.0
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-07

Deposition Author(s):

Jiang, X.

Danev, R.

Kikkawa, M.

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJER2202
Japan Society for the Promotion of Science (JSPS)	Japan	JP21H05247
Japan Society for the Promotion of Science (JSPS)	Japan	JP24KF0141
Japan Society for the Promotion of Science (JSPS)	Japan	JP24K18106