6NFK | pdb_00006nfk

Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B with loop 7 from APOBEC3G bound to iodide

• PDB DOI: https://doi.org/10.2210/pdb6NFK/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-12-20 Released: 2019-12-25 
• Deposition Author(s): Shi, K., Orellana, K., Aihara, H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.238 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B

Shi, K., Demir, O., Carpenter, M.A., Banerjee, S., Harki, D.A., Amaro, R.E., Harris, R.S., Aihara, H.

(2020) FASEB Bioadv 2: 49-58

• DOI: https://doi.org/10.1096/fba.2019-00068

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 23.16 kDa 
• Atom Count: 1,607 
• Modeled Residue Count: 182 
• Deposited Residue Count: 193 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA dC->dU-editing enzyme APOBEC-3B	A	193	Homo sapiens	Mutation(s): 12  Gene Names: APOBEC3B EC: 3.5.4.38
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UH17 (Homo sapiens) Explore Q9UH17  Go to UniProtKB:  Q9UH17
PHAROS:  Q9UH17 GTEx:  ENSG00000179750

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	E [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO	B [auth A], C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.238 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.6	α = 90
b = 50.6	β = 90
c = 149.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Shi, K., Orellana, K., Aihara, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118047

Revision History  

• Version 1.0: 2019-12-25
  Type: Initial release
  
• Version 1.1: 2020-01-29
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary