6P59

Crystal structure of SIVrcm Vif-CBFbeta-ELOB-ELOC complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

wwPDB Validation 3D Report Full Report



Literature

Structural Basis for a Species-Specific Determinant of an SIV Vif Protein toward Hominid APOBEC3G Antagonism.

Binning, J.M.Chesarino, N.M.Emerman, M.Gross, J.D.

(2019) Cell Host Microbe 26: 739-747.e4

  • DOI: 10.1016/j.chom.2019.10.014
  • Primary Citation of Related Structures:  
    6P59

  • PubMed Abstract: 
  • Primate lentiviruses encode a Vif protein that counteracts the host antiviral APOBEC3 (A3) family members. The adaptation of Vif to species-specific A3 determinants is a critical event that allowed the spillover of a lentivirus from monkey reservoirs ...

    Primate lentiviruses encode a Vif protein that counteracts the host antiviral APOBEC3 (A3) family members. The adaptation of Vif to species-specific A3 determinants is a critical event that allowed the spillover of a lentivirus from monkey reservoirs to chimpanzees and subsequently to humans, which gave rise to HIV-1 and the acquired immune deficiency syndrome (AIDS) pandemic. How Vif-A3 protein interactions are remodeled during evolution is unclear. Here, we report a 2.94 Å crystal structure of the Vif substrate receptor complex from simian immunodeficiency virus isolated from red-capped mangabey (SIVrcm). The structure of the SIVrcm Vif complex illuminates the stage of lentiviral Vif evolution that is immediately prior to entering hominid primates. Structure-function studies reveal the adaptations that allowed SIVrcm Vif to antagonize hominid A3G. These studies show a partitioning between an evolutionarily dynamic specificity determinant and a conserved protein interacting surface on Vif that enables adaptation while maintaining protein interactions required for potent A3 antagonism.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address: jdgross@cgl.ucsf.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Core-binding factor subunit betaA, C165Homo sapiensMutation(s): 0 
Gene Names: CBFB
Find proteins for Q13951 (Homo sapiens)
Explore Q13951 
Go to UniProtKB:  Q13951
NIH Common Fund Data Resources
PHAROS  Q13951
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Elongin-BD, W118Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
Find proteins for Q15370 (Homo sapiens)
Explore Q15370 
Go to UniProtKB:  Q15370
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PHAROS  Q15370
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Elongin-CE, Z112Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  Q15369
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PHAROS  Q15369
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Virion infectivity factorB, F220Simian immunodeficiency virusMutation(s): 0 
Gene Names: vif
Find proteins for E1ANT9 (Simian immunodeficiency virus)
Explore E1ANT9 
Go to UniProtKB:  E1ANT9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B, F
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
B, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.22α = 90
b = 112.489β = 90
c = 125.697γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM082250
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI120867

Revision History 

  • Version 1.0: 2019-12-25
    Type: Initial release