9E5Y | pdb_00009e5y

T4 Bacteriophage Replicative Polymerase Captured in Polymerase Exchange State 1

• PDB DOI: https://doi.org/10.2210/pdb9E5Y/pdb
• NAKB: 9E5Y
• EM Map EMD-47531: EMDB EMDataResource

• Classification: replication/DNA
• Organism(s): Escherichia phage T4, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-10-28 Released: 2025-11-19 
• Deposition Author(s): Li, H., Feng, X.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.57 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico

Literature

Structural insights into the exchange mechanism of a replicative DNA polymerase

Feng, X., Spiering, M.M., Santos, R., Benkovic, S.J., Li, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 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 and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 300.17 kDa 
• Atom Count: 20,896 
• Modeled Residue Count: 2,533 
• Deposited Residue Count: 2,539 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed DNA polymerase	A, C	898	Escherichia phage T4	Mutation(s): 1  Gene Names: 43 EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data)
UniProt
Find proteins for P04415 (Enterobacteria phage T4) Explore P04415  Go to UniProtKB:  P04415

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sliding clamp	B, D, E	228	Escherichia phage T4	Mutation(s): 0  Gene Names: 45
UniProt
Find proteins for P04525 (Enterobacteria phage T4) Explore P04525  Go to UniProtKB:  P04525

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-AGC TAT GAC CAT GAT TAC GAA TTG ddC-3')	F [auth P]	21	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (38-MER)	G [auth T]	38	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.57 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.2.1
MODEL REFINEMENT	PHENIX	1.20
MODEL REFINEMENT	Coot	0.9.8

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Li, H., Feng, X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM013306
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM131754

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release