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: 2.70 Å
  • R-Value Work: 0.216 

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This is version 1.4 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

  • DOI: 10.1016/s0969-2126(02)00793-1
  • Primary Citation of Related Structures:  
    1K5M

  • 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 adjacent tripeptides resemble those of analogous segments in three Fab/V3 loop peptide complexes ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COAT PROTEIN VP1 (P1D) A289Rhinovirus B14Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CHIMERA OF HRV14 COAT PROTEIN VP2 (P1B) AND the V3 loop of HIV-1 gp120 B277Rhinovirus B14HIV-1 M:B_MNMutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P05877 (Human immunodeficiency virus type 1 group M subtype B (isolate MN))
Explore P05877 
Go to UniProtKB:  P05877
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
COAT PROTEIN VP3 (P1C) C236Rhinovirus B14Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
COAT PROTEIN VP4 (P1A) D68Rhinovirus B14Mutation(s): 0 
EC: 3.4.22.29 (UniProt), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P03303 (Human rhinovirus 14)
Explore P03303 
Go to UniProtKB:  P03303
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPH
Query on SPH

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 0.216 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 318.9α = 90
b = 349.3β = 90
c = 368.4γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-02
    Changes: Data collection, Refinement description, Source and taxonomy
  • Version 1.4: 2018-04-18
    Changes: Data collection