6B0B

Crystal structure of human APOBEC3H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.362 
  • R-Value Work: 0.353 
  • R-Value Observed: 0.353 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1016/j.molcel.2017.12.010
  • Primary Citation of Related Structures:  
    6B0B, 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
APOBEC3H
A, E
186Homo sapiensMutation(s): 1 
Gene Names: APOBEC3H
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NTF7 (Homo sapiens)
Explore Q6NTF7 
Go to UniProtKB:  Q6NTF7
PHAROS:  Q6NTF7
GTEx:  ENSG00000100298 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NTF7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MCherry
D, H
255Discosoma sp.Mutation(s): 0 
UniProt
Find proteins for D1MPT3 (Discosoma sp.)
Explore D1MPT3 
Go to UniProtKB:  D1MPT3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1MPT3
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*AP*AP*AP*AP*AP*AP*A)-3')
B, F
8Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*U)-3')
C, G
9Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 0.362 
  • R-Value Work: 0.353 
  • R-Value Observed: 0.353 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.293α = 90
b = 101.293β = 90
c = 211.217γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118000
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118047
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA206309

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Database references
  • Version 1.2: 2018-01-10
    Changes: Database references, Structure summary
  • Version 1.3: 2018-01-17
    Changes: Database references
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence