1K5M

Crystal Structure of a Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 V3 Loop Chimeric Virus MN-III-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of a Human Rhinovirus that Displays Part of the HIV-1 V3 Loop and Induces Neutralizing Antibodies against HIV-1

Ding, J.Smith, A.D.Geisler, S.C.Ma, X.Arnold, G.F.Arnold, E.

(2002) Structure 10: 999-1011


  • PubMed Abstract: 
  • We report the 2.7 A resolution structure of a chimeric rhinovirus, MN-III-2, that displays part of the HIV-1 gp120 V3 loop and elicits HIV-neutralizing antibodies. The V3 loop insert is dominated by two type I beta turns. The structures of two adjace ...

    We report the 2.7 A resolution structure of a chimeric rhinovirus, MN-III-2, that displays part of the HIV-1 gp120 V3 loop and elicits HIV-neutralizing antibodies. The V3 loop insert is dominated by two type I beta turns. The structures of two adjacent tripeptides resemble those of analogous segments in three Fab/V3 loop peptide complexes. Although two of the three corresponding antibodies bind and neutralize MN-III-2 well, only one of the three can bind without significant rearrangement. These results suggest that the V3 loop insert: (1) can share some local conformational similarity to V3 loop sequences presented on different structural frameworks; (2) must be able to adopt multiple conformations, even in a relatively constrained environment; and (3) may mimic the conformational variability of the epitope on HIV-1, increasing the likelihood of eliciting appropriate neutralizing immune responses.


    Related Citations: 
    • Human rhinovirus type 14:human immunodeficiency virus type 1 (HIV-1) V3 loop chimeras from a combinational library induce potent neutralizing antibody responses against HIV-1
      Smith, A.D.,Geisler, S.C.,Chen, A.A.,Resnick, D.A.,Roy, B.M.,Lewi, P.J.,Arnold, E.,Arnold, G.F.
      (1998) J.Virol. 72: 651


    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine (CABM) and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 679 Hoes Lane, Piscataway 08854, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COAT PROTEIN VP1 (P1D)
A
289Human rhinovirus 14EC: 3.6.1.15, 3.4.22.28, 3.4.22.29, 2.7.7.48
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CHIMERA OF HRV14 COAT PROTEIN VP2 (P1B) AND the V3 loop of HIV-1 gp120
B
277Human immunodeficiency virus type 1 group M subtype BHuman rhinovirus 14
This entity is chimeric
Gene Names: env,
EC: 3.6.1.15, 3.4.22.28, 3.4.22.29, 2.7.7.48
Find proteins for P05877 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P05877
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
COAT PROTEIN VP3 (P1C)
C
236Human rhinovirus 14EC: 3.6.1.15, 3.4.22.28, 3.4.22.29, 2.7.7.48
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
COAT PROTEIN VP4 (P1A)
D
68Human rhinovirus 14EC: 3.6.1.15, 3.4.22.28, 3.4.22.29, 2.7.7.48
Find proteins for P03303 (Human rhinovirus 14)
Go to UniProtKB:  P03303
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPH
Query on SPH

Download SDF File 
Download CCD File 
A
SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.216 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 318.900α = 90.00
b = 349.300β = 90.00
c = 368.400γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-07-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-08-02
    Type: Data collection, Refinement description, Source and taxonomy