3A07 | pdb_00003a07

Crystal Structure of Actinohivin; Potent anti-HIV Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 
    0.163 (Depositor), 0.172 (DCC) 
  • R-Value Work: 
    0.149 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 
    0.150 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3A07

This is version 1.3 of the entry. See complete history

Literature

Mechanism by which the lectin actinohivin blocks HIV infection of target cells

Tanaka, H.Chiba, H.Inokoshi, J.Kuno, A.Sugai, T.Takahashi, A.Ito, Y.Tsunoda, M.Suzuki, K.Takenaka, A.Sekiguchi, T.Umeyama, H.Hirabayashi, J.Omura, S.

(2009) Proc Natl Acad Sci U S A 106: 15633-15638

  • DOI: https://doi.org/10.1073/pnas.0907572106
  • Primary Citation Related Structures: 
    3A07

  • PubMed Abstract: 

    Various lectins have attracted attention as potential microbicides to prevent HIV transmission. Their capacity to bind glycoproteins has been suggested as a means to block HIV binding and entry into susceptible cells. The previously undescribed lectin actinohivin (AH), isolated by us from an actinomycete, exhibits potent in vitro anti-HIV activity by binding to high-mannose (Man) type glycans (HMTGs) of gp120, an envelope glycoprotein of HIV. AH contains 114 aa and consists of three segments, all of which need to show high affinity to gp120 for the anti-HIV characteristic. To generate the needed mechanistic understanding of AH binding to HIV in anticipation of seeking approval for human testing as a microbicide, we have used multiple molecular tools to characterize it. AH showed a weak affinity to Man alpha(1-2)Man, Man alpha(1-2)Man alpha(1-2)Man, of HMTG (Man8 or Man9) or RNase B (which has a single HMTG), but exhibited a strong and highly specific affinity (K(d) = 3.4 x 10(-8) M) to gp120 of HIV, which contains multiple Man8 and/or Man9 units. We have compared AH to an alternative lectin, cyanovirin-N, which did not display similar levels of discrimination between high- and low-density HMTGs. X-ray crystal analysis of AH revealed a 3D structure containing three sugar-binding pockets. Thus, the strong specific affinity of AH to gp120 is considered to be due to multivalent interaction of the three sugar-binding pockets with three HMTGs of gp120 via the "cluster effect" of lectin. Thus, AH is a good candidate for investigation as a safe microbicide to help prevent HIV transmission.


  • Organizational Affiliation
    • Faculty of Pharmacy and College of Science and Engineering, Iwaki Meisei University, Iwaki, Fukushima 970-8551, Japan. tanakaha@msn.com

Macromolecule Content 

  • Total Structure Weight: 26.07 kDa 
  • Atom Count: 2,146 
  • Modeled Residue Count: 234 
  • Deposited Residue Count: 236 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Actinohivin
A, B
118actinomycete K97-0003Mutation(s): 0 
UniProt
Find proteins for Q9KWN0 (Actinomycete sp. (strain K97-0003))
Explore Q9KWN0 
Go to UniProtKB:  Q9KWN0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KWN0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free:  0.163 (Depositor), 0.172 (DCC) 
  • R-Value Work:  0.149 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 0.150 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.346α = 90
b = 51.633β = 90
c = 175.296γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary