8J8G

Monkeypox virus DNA replication holoenzyme F8, A22 and E4 in complex with a DNA duplex and cidofovir diphosphate

• PDB DOI: https://doi.org/10.2210/pdb8J8G/pdb
• NAKB: 8J8G
• EM Map EMD-36069: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Monkeypox virus, DNA molecule
• Expression System: Insect expression vector pBlueBachsGCA1
• Mutation(s): Yes 


• Deposited: 2023-05-01 Released: 2024-05-08 
• Deposition Author(s): Xu, Y., Wu, Y., Wu, X., Zhang, Y., Yang, Y., Li, D., Yang, B., Gao, K., Zhang, Z., Dong, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.79 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of human monkeypox viral DNA replication inhibition by brincidofovir and cidofovir

Xu, Y.X., Wu, Y.Q., Wu, X.Y., Zhang, Y.Y., Yang, Y.X., Li, D.Y., Yang, B., Gao, K., Zhang, Z.Y., Dong, C.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 216.73 kDa 
• Atom Count: 14,157 
• Modelled Residue Count: 1,678 
• Deposited Residue Count: 1,758 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	1,029	Monkeypox virus	Mutation(s): 2  Gene Names: F8L
UniProt
Find proteins for Q5IXW8 (Monkeypox virus) Explore Q5IXW8  Go to UniProtKB:  Q5IXW8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E4R	B	241	Monkeypox virus	Mutation(s): 0  Gene Names: E4R EC: 3.2.2.27
UniProt
Find proteins for Q5IXS4 (Monkeypox virus) Explore Q5IXS4  Go to UniProtKB:  Q5IXS4

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase processivity factor component A20	C	426	Monkeypox virus	Mutation(s): 0  Gene Names: A22R
UniProt
Find proteins for Q5IXP2 (Monkeypox virus) Explore Q5IXP2  Go to UniProtKB:  Q5IXP2

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*CP*TP*GP*CP*TP*AP*TP*GP*AP*GP*AP*TP*TP*AP*AP*GP*TP*TP*AP*T)-3')	D [auth P]	24	DNA molecule

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*GP*AP*TP*AP*AP*CP*TP*TP*AP*AP*TP*CP*TP*CP*AP*CP*AP*TP*AP*GP*CP*AP*GP*CP*T)-3')	E [auth T]	38	DNA molecule

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TXJ (Subject of Investigation/LOI)	F [auth A]	[(2S)-1-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-propan-2-yl]oxymethyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphinic acid C8 H16 N3 O12 P3 FBSIEHDOPYOBJD-LURJTMIESA-N
CA (Subject of Investigation/LOI)	G [auth A], H [auth A], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.79 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Xu, Y., Wu, Y., Wu, X., Zhang, Y., Yang, Y., Li, D., Yang, B., Gao, K., Zhang, Z., Dong, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32250710142

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release