5ZVB

APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dT9)

• PDB DOI: https://doi.org/10.2210/pdb5ZVB/pdb
• NAKB: 5ZVB

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): Homo sapiens, DNA-binding vector pODB80
• Expression System: prokaryotic environmental samples
• Mutation(s): No 


• Deposited: 2018-05-09 Released: 2018-11-21 
• Deposition Author(s): Cheng, C., Zhang, T.L., Wang, C.X., Lan, W.X., Ding, J.P., Cao, C.Y.
• Funding Organization(s): National Science Foundation (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.220 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Literature

Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with DNA

Cheng, C., Zhang, T., Wang, C., Lan, W., Ding, J., Cao, C.

(2018) Chin J Chem 36: 1241-1248

• DOI: https://doi.org/10.1002/cjoc.201800508

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: 53.42 kDa 
• Atom Count: 3,478 
• Modelled Residue Count: 374 
• Deposited Residue Count: 427 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APEBEC3F/ssDNA-T9	A, B	209	Homo sapiens	Mutation(s): 0  Gene Names: APOBEC3G, MDS019, APOBEC3F EC: 3.5.4 (PDB Primary Data), 3.5.4.38 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC16 (Homo sapiens) Explore Q9HC16  Go to UniProtKB:  Q9HC16
PHAROS:  Q9HC16 GTEx:  ENSG00000239713
Find proteins for Q8IUX4 (Homo sapiens) Explore Q8IUX4  Go to UniProtKB:  Q8IUX4
PHAROS:  Q8IUX4 GTEx:  ENSG00000128394
UniProt Groups	Q9HC16Q8IUX4

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*TP*TP*CP*AP*AP*T)-3')	C	9	DNA-binding vector pODB80

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	E [auth A], G [auth B]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
ZN	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.220 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.99	α = 90
b = 92.702	β = 90
c = 93.674	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
ADDREF	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Cheng, C., Zhang, T.L., Wang, C.X., Lan, W.X., Ding, J.P., Cao, C.Y.

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Funding Organization	Location	Grant Number
National Science Foundation (China)	China	91753119, 21778065 and 21472229

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2018-11-28
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary