5W3V

Crystal Structure of macaque APOBEC3H in complex with RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.243 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

APOBEC3H structure reveals an unusual mechanism of interaction with duplex RNA.

Bohn, J.A.Thummar, K.York, A.Raymond, A.Brown, W.C.Bieniasz, P.D.Hatziioannou, T.Smith, J.L.

(2017) Nat Commun 8: 1021-1021

  • DOI: 10.1038/s41467-017-01309-6

  • PubMed Abstract: 
  • The APOBEC3 family of cytidine deaminases cause lethal hypermutation of retroviruses via deamination of newly reverse-transcribed viral DNA. Their ability to bind RNA is essential for virion infiltration and antiviral activity, yet the mechanisms of ...

    The APOBEC3 family of cytidine deaminases cause lethal hypermutation of retroviruses via deamination of newly reverse-transcribed viral DNA. Their ability to bind RNA is essential for virion infiltration and antiviral activity, yet the mechanisms of viral RNA recognition are unknown. By screening naturally occurring, polymorphic, non-human primate APOBEC3H variants for biological and crystallization properties, we obtained a 2.24-Å crystal structure of pig-tailed macaque APOBEC3H with bound RNA. Here, we report that APOBEC3H forms a dimer around a short RNA duplex and, despite the bound RNA, has potent cytidine deaminase activity. The structure reveals an unusual RNA-binding mode in which two APOBEC3H molecules at opposite ends of a seven-base-pair duplex interact extensively with both RNA strands, but form no protein-protein contacts. CLIP-seq analysis revealed that APOBEC3H preferentially binds to sequences in the viral genome predicted to contain duplexes, a property that may facilitate both virion incorporation and catalytic activity.


    Organizational Affiliation

    Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apobec3H
A
215N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Apobec3H
B, C, D
215N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*AP*CP*CP*CP*GP*GP*GP*GP*A)-3')E,H10synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-R(P*AP*AP*CP*CP*CP*CP*GP*GP*GP*C)-3')F,G10synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
B, C, D
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.243 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.182 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.960α = 90.00
b = 89.310β = 90.00
c = 134.370γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
XDSdata reduction
PHENIXrefinement
XDSdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Database references