5K79 | pdb_00005k79

Structure and anti-HIV activity of CYT-CVNH, a new cyanovirin-n homolog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.233 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.7 of the entry. See complete history

Literature

Structure and Glycan Binding of a New Cyanovirin-N Homolog.

Matei, E.Basu, R.Furey, W.Shi, J.Calnan, C.Aiken, C.Gronenborn, A.M.

(2016) J Biological Chem 291: 18967-18976

  • DOI: https://doi.org/10.1074/jbc.M116.740415
  • Primary Citation Related Structures: 
    5K79

  • PubMed Abstract: 

    The HIV-1 envelope glycoprotein gp120 is heavily glycosylated and bears numerous high mannose sugars. These sugars can serve as targets for HIV-inactivating compounds, such as antibodies and lectins, which bind to the glycans and interfere with viral entry into the target cell. We determined the 1.6 Å x-ray structure of Cyt-CVNH, a recently identified lectin from the cyanobacterium Cyanothece(7424), and elucidated its glycan specificity by NMR. The Cyt-CVNH structure and glycan recognition profile are similar to those of other CVNH proteins, with each domain specifically binding to Manα(1-2)Manα units on the D1 and D3 arms of high mannose glycans. However, in contrast to CV-N, no cross-linking and precipitation of the cross-linked species in solution was observed upon Man-9 binding, allowing, for the first time, investigation of the interaction of Man-9 with a member of the CVNH family by NMR. HIV assays showed that Cyt-CVNH is able to inhibit HIV-1 with ∼4-fold higher potency than CV-N(P51G), a stabilized version of wild type CV-N. Therefore, Cyt-CVNH may qualify as a valuable lectin for potential microbicidal use.


  • Organizational Affiliation
    • From the Department of Structural Biology, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania 15260.

Macromolecule Content 

  • Total Structure Weight: 24.15 kDa 
  • Atom Count: 1,912 
  • Modeled Residue Count: 216 
  • Deposited Residue Count: 216 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyanovirin-N domain protein
A, B
108Gloeothece citriformis PCC 7424Mutation(s): 0 
Gene Names: PCC7424_1905
UniProt
Find proteins for B7KDN5 (Gloeothece citriformis (strain PCC 7424))
Explore B7KDN5 
Go to UniProtKB:  B7KDN5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7KDN5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.233 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.84α = 90
b = 74.396β = 90
c = 36.499γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXmodel building
HKL-2000data reduction

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 StatesRO1GM080642

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-07-27
    Changes: Database references
  • Version 1.2: 2016-09-14
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2017-09-27
    Changes: Data collection, Refinement description
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.7: 2024-11-13
    Changes: Structure summary