6B0B

Crystal structure of human APOBEC3H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28006 Å
  • R-Value Free: 0.362 
  • R-Value Work: 0.353 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism.

Shaban, N.M.Shi, K.Lauer, K.V.Carpenter, M.A.Richards, C.M.Salamango, D.Wang, J.Lopresti, M.W.Banerjee, S.Levin-Klein, R.Brown, W.L.Aihara, H.Harris, R.S.

(2018) Mol. Cell 69: 75-86.e9

  • DOI: 10.1016/j.molcel.2017.12.010
  • Primary Citation of Related Structures:  6BBO

  • PubMed Abstract: 
  • Human APOBEC3H and homologous single-stranded DNA cytosine deaminases are unique to mammals. These DNA-editing enzymes function in innate immunity by restricting the replication of viruses and transposons. APOBEC3H also contributes to cancer mutagene ...

    Human APOBEC3H and homologous single-stranded DNA cytosine deaminases are unique to mammals. These DNA-editing enzymes function in innate immunity by restricting the replication of viruses and transposons. APOBEC3H also contributes to cancer mutagenesis. Here, we address the fundamental nature of RNA in regulating human APOBEC3H activities. APOBEC3H co-purifies with RNA as an inactive protein, and RNase A treatment enables strong DNA deaminase activity. RNA-binding-defective mutants demonstrate clear separation of function by becoming DNA hypermutators. Biochemical and crystallographic data demonstrate a mechanism in which double-stranded RNA mediates enzyme dimerization. Additionally, APOBEC3H separation-of-function mutants show that RNA binding is required for cytoplasmic localization, packaging into HIV-1 particles, and antiviral activity. Overall, these results support a model in which structured RNA negatively regulates the potentially harmful DNA deamination activity of APOBEC3H while, at the same time, positively regulating its antiviral activity.


    Organizational Affiliation

    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
APOBEC3H
A, E
186Homo sapiensGene Names: APOBEC3H
EC: 3.5.4.-
Find proteins for Q6NTF7 (Homo sapiens)
Go to Gene View: APOBEC3H
Go to UniProtKB:  Q6NTF7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MCherry
D, H
255Discosoma sp.N/A
Find proteins for D1MPT3 (Discosoma sp.)
Go to UniProtKB:  D1MPT3
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*AP*AP*AP*AP*AP*AP*A)-3')B,F8Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*U)-3')C,G9Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28006 Å
  • R-Value Free: 0.362 
  • R-Value Work: 0.353 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 101.293α = 90.00
b = 101.293β = 90.00
c = 211.217γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SHELXDphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM118000
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM118047
National Institutes of Health/National Cancer InstituteUnited StatesCA206309

Revision History 

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Database references
  • Version 1.2: 2018-01-10
    Type: Database references, Structure summary
  • Version 1.3: 2018-01-17
    Type: Database references