4R4N

Crystal structure of the anti-hiv-1 antibody 2.2c in complex with hiv-1 93ug037 gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.296 
  • R-Value Observed: 0.297 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/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. 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

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 gp120352Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q0ED04 (Human immunodeficiency virus 1)
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Go to UniProtKB:  Q0ED04
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0ED04
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
M48U1 peptide28synthetic constructMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 2.2c LIGHT CHAIN210Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 2.2c heavy CHAIN220Homo sapiensMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
GA [auth A]
HA [auth A]
IA [auth A]
JA [auth A]
KA [auth B]
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth B],
LA [auth B],
MA [auth I],
NA [auth I],
OA [auth I],
PA [auth I],
QA [auth E],
RA [auth E],
SA [auth M],
TA [auth P],
UA [auth P],
VA [auth S],
WA [auth S],
XA [auth S],
YA [auth V]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
U2X
Query on U2X
C [auth a]
DA [auth v]
G [auth b]
K [auth e]
N [auth i]
C [auth a],
DA [auth v],
G [auth b],
K [auth e],
N [auth i],
R [auth m],
V [auth p],
Z [auth s]
L-PEPTIDE LINKINGC16 H23 N O3TYR
OAS
Query on OAS
BA [auth T]
F [auth H]
FA [auth W]
I [auth C]
M [auth F]
BA [auth T],
F [auth H],
FA [auth W],
I [auth C],
M [auth F],
P [auth J],
T [auth N],
X [auth Q]
L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.296 
  • R-Value Observed: 0.297 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.967α = 110.58
b = 144.178β = 92.3
c = 158.351γ = 99.19
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Experimental preparation
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Structure summary