6BBO | pdb_00006bbo

Crystal structure of human APOBEC3H/RNA complex

• PDB DOI: https://doi.org/10.2210/pdb6BBO/pdb
• NAKB: 6BBO

• Classification: HYDROLASE/RNA
• Organism(s): Homo sapiens, Escherichia coli, Discosoma sp.
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-10-19 Released: 2018-01-10 
• Deposition Author(s): Shaban, N.M., Shi, K., Banerjee, S., Harris, R.S., Aihara, H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.43 Å
• R-Value Free: 
  0.392 (Depositor), 0.392 (DCC) 
• R-Value Work: 
  0.364 (Depositor), 0.364 (DCC) 
• R-Value Observed: 
  0.365 (Depositor) 

Starting Model: experimental

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

• PubMed: 29290613 
• DOI: https://doi.org/10.1016/j.molcel.2017.12.010
• Primary Citation 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.

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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.
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.
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; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA.
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
Northeastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, IL 60439, USA.
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; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 102.86 kDa 
• Atom Count: 6,934 
• Modeled Residue Count: 802 
• Deposited Residue Count: 830 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APOBEC3H	A, E	180	Homo sapiens	Mutation(s): 2  Gene Names: APOBEC3H EC: 3.5.4.38
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NTF7 (Homo sapiens) Explore Q6NTF7  Go to UniProtKB:  Q6NTF7
PHAROS:  Q6NTF7 GTEx:  ENSG00000100298

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
MCherry fluorescent protein	D, H	219	Discosoma sp.	Mutation(s): 0
UniProt
Find proteins for D1MPT3 (Discosoma sp.) Explore D1MPT3  Go to UniProtKB:  D1MPT3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*AP*AP*AP*AP*AP*AP*A)-3')	B, F	8	Escherichia coli

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*U)-3')	C, G	8	Escherichia coli

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	J [auth A], L [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	I [auth A], K [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.43 Å
• R-Value Free:  0.392 (Depositor), 0.392 (DCC) 
• R-Value Work:  0.364 (Depositor), 0.364 (DCC) 
• R-Value Observed: 0.365 (Depositor) 

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.293	α = 90
b = 101.293	β = 90
c = 211.217	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-10 
Deposition Author(s): Shaban, N.M., Shi, K., Banerjee, S., Harris, R.S., 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	GM118000
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118047
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA206309

Revision History  

• Version 1.0: 2018-01-10
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary