4QF1

Crystal structure of unliganded CH59UA, the inferred unmutated ancestor of the RV144 anti-HIV antibody lineage producing CH59


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Antibody Light-Chain-Restricted Recognition of the Site of Immune Pressure in the RV144 HIV-1 Vaccine Trial Is Phylogenetically Conserved.

Wiehe, K.Easterhoff, D.Luo, K.Nicely, N.I.Bradley, T.Jaeger, F.H.Dennison, S.M.Zhang, R.Lloyd, K.E.Stolarchuk, C.Parks, R.Sutherland, L.L.Scearce, R.M.Morris, L.Kaewkungwal, J.Nitayaphan, S.Pitisuttithum, P.Rerks-Ngarm, S.Sinangil, F.Phogat, S.Michael, N.L.Kim, J.H.Kelsoe, G.Montefiori, D.C.Tomaras, G.D.Bonsignori, M.Santra, S.Kepler, T.B.Alam, S.M.Moody, M.A.Liao, H.X.Haynes, B.F.

(2014) Immunity 41: 909-918

  • DOI: 10.1016/j.immuni.2014.11.014
  • Primary Citation of Related Structures:  
    4QF1

  • PubMed Abstract: 
  • In HIV-1, the ability to mount antibody responses to conserved, neutralizing epitopes is critical for protection. Here we have studied the light chain usage of human and rhesus macaque antibodies targeted to a dominant region of the HIV-1 envelope se ...

    In HIV-1, the ability to mount antibody responses to conserved, neutralizing epitopes is critical for protection. Here we have studied the light chain usage of human and rhesus macaque antibodies targeted to a dominant region of the HIV-1 envelope second variable (V2) region involving lysine (K) 169, the site of immune pressure in the RV144 vaccine efficacy trial. We found that humans and rhesus macaques used orthologous lambda variable gene segments encoding a glutamic acid-aspartic acid (ED) motif for K169 recognition. Structure determination of an unmutated ancestor antibody demonstrated that the V2 binding site was preconfigured for ED motif-mediated recognition prior to maturation. Thus, light chain usage for recognition of the site of immune pressure in the RV144 trial is highly conserved across species. These data indicate that the HIV-1 K169-recognizing ED motif has persisted over the diversification between rhesus macaques and humans, suggesting an evolutionary advantage of this antibody recognition mode.


    Organizational Affiliation

    Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Electronic address: barton.haynes@dm.duke.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CH59UA Fab fragment of heavy chainAH225Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Inferred unmutated ancestor (UA) of anti-HIV antibody CH59BL214Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

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A, H
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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B, L
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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B, L
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.332α = 90
b = 70.803β = 96.84
c = 107.314γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Revision History 

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description