8FII

Wild type APOBEC3A in complex with TT(FdZ)-hairpin inhibitor (crystal form 1)

• PDB DOI: https://doi.org/10.2210/pdb8FII/pdb
• NAKB: 8FII

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-12-16 Released: 2023-09-06 
• Deposition Author(s): Harjes, S., Jameson, G.B., Harjes, E., Filichev, V.V., Kurup, H.M.
• Funding Organization(s): Health Research Council (HRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 0.310 
• R-Value Work: 0.251 
• R-Value Observed: 0.254 

Literature

DNA-based inhibitors restrict mutagenic activity of APOBEC3 in cells

Harjes, S., Kurup, H.M., Filichev, V., Harjes, E., Jameson, G.B.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 53.57 kDa 
• Atom Count: 3,375 
• Modelled Residue Count: 379 
• Deposited Residue Count: 420 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA dC->dU-editing enzyme APOBEC-3A	A, B	199	Homo sapiens	Mutation(s): 0  Gene Names: APOBEC3A EC: 3.5.4.38
UniProt & NIH Common Fund Data Resources
Find proteins for P31941 (Homo sapiens) Explore P31941  Go to UniProtKB:  P31941
PHAROS:  P31941 GTEx:  ENSG00000128383

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*CP*GP*CP*TP*TP*(UFP)P*GP*CP*GP*C)-3')	C [auth E], D [auth F]	11	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	H [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 0.310 
• R-Value Work: 0.251 
• R-Value Observed: 0.254 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.323	α = 90
b = 57.197	β = 99.37
c = 91.422	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
JBluIce-EPICS	data collection
Aimless	data scaling
pointless	data scaling
MOLREP	phasing
REFMAC	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-06 
Deposition Author(s): Harjes, S., Jameson, G.B., Harjes, E., Filichev, V.V., Kurup, H.M.

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Funding Organization	Location	Grant Number
Health Research Council (HRC)	New Zealand	20/1355

Revision History  

• Version 1.0: 2023-09-06
  Type: Initial release