Modomics - A Database of RNA Modifications

ID Card:

Full name: DNA dC->dU-editing enzyme APOBEC-3C
GI: 48474983
UniProt: Q9NRW3
Structures: | 3VM8 | 3VOW |
Alpha Fold Predicted Structure: AF-Q9NRW3-F1
Enzyme type: deaminase


PDB Structures:


3VM8

Structure Description:

Title: Crystal structure of the human APOBEC3C having HIV-1 Vif-binding interface
Classification: HYDROLASE
Technique: X-Ray Diffraction
Resolution: 3.0
R value free: 0.302
R value observed: 0.232
R value work: 0.228

Abstract of the PDB Structure's related Publication:

The human apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3, referred to as A3) proteins are cellular cytidine deaminases that potently restrict retrovirus replication. However, HIV-1 viral infectivity factor (Vif) counteracts the antiviral activity of most A3 proteins by targeting them for proteasomal degradation. To date, the structure of an A3 protein containing a Vif-binding interface has not been solved. Here, we report a high-resolution crystal structure of APOBEC3C and identify the HIV-1 Vif-interaction interface. Extensive structure-guided mutagenesis revealed the role of a shallow cavity composed of hydrophobic or negatively charged residues between the α2 and α3 helices. This region is distant from the DPD motif (residues 128-130) of APOBEC3G that participates in HIV-1 Vif interaction. These findings provide insight into Vif-A3 interactions and could lead to the development of new pharmacologic anti-HIV-1 compounds.

Download RCSB-PDB Structures:

Pdb Files   3VM8.pdb   3VOW.pdb  
Pdbx/mmCIF Files   3VM8.cif   3VOW.cif  


Protein sequence:

MNPQIRNPMKAMYPGTFYFQFKNLWEANDRNETWLCFTVEGIKRRSVVSWKTGVFRNQVDSETHCHAERCFLSWFCDDILSPNTKYQVTWYTSWSPCPDCAGEVAEFLARHSNVNLTIFTARLYYFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPFKPWKGLKTNFRLLKRRLRESLQ

Comments:





Alpha Fold Predicted Structure:




Parsing response... [191747/191747]


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Protein sequence:

M N P Q I R N P M K A M Y P G T F Y F Q F K N L W E A N D R N E T W L C F T V E G I K R R S V V S W K T G V F R N Q V D S E T H C H A E R C F L S W F C D D I L S P N T K Y Q V T W Y T S W S P C P D C A G E V A E F L A R H S N V N L T I F T A R L Y Y F Q Y P C Y Q E G L R S L S Q E G V A V E I M D Y E D F K Y C W E N F V Y N D N E P F K P W K G L K T N F R L L K R R L R E S L Q
20406080100120140160180MNPQIRNPMKAMYPGTFYFQFKNLWEANDRNETWLCFTVEGIKRRSVVSWKTGVFRNQVDSETHCHAERCFLSWFCDDILSPNTKYQVTWYTSWSPCPDCAGEVAEFLARHSNVNLTIFTARLYYFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPFKPWKGLKTNFRLLKRRLRESLQSequenceHITBSN

Enter the variants

Position

Original

Variant

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-Q9NRW3-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q9NRW3-F1.cif  
DSSP Secondary Structures   Q9NRW3.dssp  





Publications: