4R4B

Crystal structure of the anti-hiv-1 antibody 2.2c

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

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This is version 1.2 of the entry. See complete history. 


Literature

Structural Definition of an Antibody-Dependent Cellular Cytotoxicity Response Implicated in Reduced Risk for HIV-1 Infection.

Acharya, P., Tolbert, W.D., Gohain, N., Wu, X., Yu, L., Liu, T., Huang, W., Huang, C.C., Kwon, Y.D., Louder, R.K., Luongo, T.S., McLellan, J.S., Pancera, M., Yang, Y., Zhang, B., Flinko, R., Foulke, J.S., Sajadi, M.M., Kamin-Lewis, R., Robinson, J.E., Martin, L., Kwong, P.D., Guan, Y., DeVico, A.L., Lewis, G.K., Pazgier, M.

(2014) J Virol 88: 12895-12906

  • DOI: 10.1128/JVI.02194-14
  • Primary Citation of Related Structures:  
    4H8W, 4R4B, 4R4F, 4R4H, 4R4N

  • PubMed Abstract: 

    • The RV144 vaccine trial implicated epitopes in the C1 region of gp120 (A32-like epitopes) as targets of potentially protective antibody-dependent cellular cytotoxicity (ADCC) responses. A32-like epitopes are highly immunogenic, as infected or vaccinated individuals frequently produce antibodies specific for these determinants ...

    The RV144 vaccine trial implicated epitopes in the C1 region of gp120 (A32-like epitopes) as targets of potentially protective antibody-dependent cellular cytotoxicity (ADCC) responses. A32-like epitopes are highly immunogenic, as infected or vaccinated individuals frequently produce antibodies specific for these determinants. Antibody titers, as measured by enzyme-linked immunosorbent assay (ELISA) against these epitopes, however, do not consistently correlate with protection. Here, we report crystal structures of CD4-stabilized gp120 cores complexed with the Fab fragments of two nonneutralizing, A32-like monoclonal antibodies (MAbs), N5-i5 and 2.2c, that compete for antigen binding and have similar antigen-binding affinities yet exhibit a 75-fold difference in ADCC potency. We find that these MAbs recognize overlapping epitopes formed by mobile layers 1 and 2 of the gp120 inner domain, including the C1 and C2 regions, but bind gp120 at different angles via juxtaposed VH and VL contact surfaces. A comparison of structural and immunological data further showed that antibody orientation on bound antigen and the capacity to form multivalent antigen-antibody complexes on target cells were key determinants of ADCC potency, with the latter process having the greater impact. These studies provide atomic-level definition of A32-like epitopes implicated as targets of protective antibodies in RV144. Moreover, these studies establish that epitope structure and mode of antibody binding can dramatically affect the potency of Fc-mediated effector function against HIV-1. These results provide key insights for understanding, refining, and improving the outcome of HIV vaccine trials, in which relevant immune responses are facilitated by A32-like elicited responses.

    Organizational Affiliation: 

    Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA mpazgier@ihv.umaryland.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FAB 2.2C LIGHT CHAINC [auth A],
E [auth C],
G [auth E],
A [auth L]		210Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FAB 2.2C HEAVY CHAIND [auth B],
F [auth D],
H [auth F],
B [auth H]		220Homo sapiensMutation(s): 0 
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Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
LA [auth D],
O [auth H],
PA [auth F],
Z [auth B]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
I [auth L],
IA [auth C],
J [auth L],
JA [auth C],
K [auth L],
KA [auth C],
L,
M [auth L],
MA [auth D],
N [auth L],
NA [auth E],
OA [auth E],
P [auth H],
Q [auth H],
QA [auth F],
R [auth H],
RA [auth F],
S [auth H],
SA [auth F],
T [auth H],
TA [auth F],
U [auth A],
UA [auth F],
V [auth A],
VA [auth F],
W [auth A],
X [auth A],
Y [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 195.011α = 90
b = 133.559β = 91.36
c = 90.774γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary