8OJD

HSV-1 DNA polymerase beta-hairpin loop

• PDB DOI: https://doi.org/10.2210/pdb8OJD/pdb
• EM Map EMD-16912: EMDB EMDataResource
• NAKB: 8OJD

• Classification: TRANSFERASE
• Organism(s): Human alphaherpesvirus 1 strain KOS, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2023-03-24 Released: 2024-04-03 
• Deposition Author(s): Gustavsson, E., Grunewald, K., Elias, P., Hallberg, B.M.
• Funding Organization(s): Swedish Research Council, German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.46 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM

Gustavsson, E., Grunewald, K., Elias, P., Hallberg, B.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 172.22 kDa 
• Atom Count: 8,674 
• Modelled Residue Count: 1,022 
• Deposited Residue Count: 1,350 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase catalytic subunit	A	1,235	Human alphaherpesvirus 1 strain KOS	Mutation(s): 1  Gene Names: UL30 EC: 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data)
UniProt
Find proteins for P04293 (Human herpesvirus 1 (strain 17)) Explore P04293  Go to UniProtKB:  P04293

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (47-MER)	B [auth C]	47	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (68-MER)	C [auth D]	68	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.46 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot
RECONSTRUCTION	cryoSPARC	4

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Gustavsson, E., Grunewald, K., Elias, P., Hallberg, B.M.

---

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2017-06702
German Research Foundation (DFG)	Germany	152/772-1|152/774-1|152/775-1|152/776-1|152/777-1 FUGG

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release