9CAY

Ternary structure of Plasmodium falciparum apicoplast DNA polymerase (exo-minus)

• PDB DOI: https://doi.org/10.2210/pdb9CAY/pdb
• EM Map EMD-45407: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, Plasmodium falciparum 3D7
• Mutation(s): Yes 


• Deposited: 2024-06-18 Released: 2024-11-06 
• Deposition Author(s): Lo, C.-Y., Gao, Y.
• 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: 3.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structures of binary and ternary complexes of the Plasmodium falciparum apicoplast DNA polymerase

Lo, C.-Y., Ung, A., Nelson, S.W., Gao, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 89.6 kDa 
• Atom Count: 5,127 
• Modelled Residue Count: 560 
• Deposited Residue Count: 677 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Plastid replication-repair enzyme	B [auth A]	628	Plasmodium falciparum 3D7	Mutation(s): 2  EC: 2.7.7.7
UniProt
Find proteins for Q8ILY1 (Plasmodium falciparum (isolate 3D7)) Explore Q8ILY1  Go to UniProtKB:  Q8ILY1

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*AP*GP*CP*TP*CP*TP*AP*CP*GP*GP*AP*TP*GP*CP*CP*TP*CP*AP*CP*A)-3')	A [auth E]	29	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*GP*TP*GP*AP*GP*GP*CP*AP*TP*CP*CP*GP*TP*AP*GP*(2DA))-3')	C [auth F]	20	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGT (Subject of Investigation/LOI)	E [auth A]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-N
MG (Subject of Investigation/LOI)	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Lo, C.-Y., Gao, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R35GM142722

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release