5W4L

Crystal structure of the non-neutralizing and ADCC-potent C11-like antibody N12-i3 in complex with HIV-1 clade A/E gp120, the CD4 mimetic M48U1, and the antibody N5-i5.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

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Literature

Targeting the Late Stage of HIV-1 Entry for Antibody-Dependent Cellular Cytotoxicity: Structural Basis for Env Epitopes in the C11 Region.

Tolbert, W.D., Gohain, N., Alsahafi, N., Van, V., Orlandi, C., Ding, S., Martin, L., Finzi, A., Lewis, G.K., Ray, K., Pazgier, M.

(2017) Structure 25: 1719-1731.e4

  • DOI: https://doi.org/10.1016/j.str.2017.09.009
  • Primary Citation of Related Structures:  
    5W4L

  • PubMed Abstract: 

    • Antibodies can have an impact on HIV-1 infection in multiple ways, including antibody-dependent cellular cytotoxicity (ADCC), a correlate of protection observed in the RV144 vaccine trial. One of the most potent ADCC-inducing epitopes on HIV-1 Env is recognized by the C11 antibody ...

    Antibodies can have an impact on HIV-1 infection in multiple ways, including antibody-dependent cellular cytotoxicity (ADCC), a correlate of protection observed in the RV144 vaccine trial. One of the most potent ADCC-inducing epitopes on HIV-1 Env is recognized by the C11 antibody. Here, we present the crystal structure, at 2.9 Å resolution, of the C11-like antibody N12-i3, in a quaternary complex with the HIV-1 gp120, a CD4-mimicking peptide M48U1, and an A32-like antibody, N5-i5. Antibody N12-i3 recognizes an epitope centered on the N-terminal "eighth strand" of a critical β sandwich, which our analysis indicates to be emblematic of a late-entry state, after the gp120 detachment. In prior entry states, this sandwich comprises only seven strands, with the eighth strand instead pairing with a portion of the gp120 C terminus. The conformational gymnastics of HIV-1 gp120 thus includes altered β-strand pairing, possibly to reduce immunogenicity, although nevertheless still recognized by the human immune system.

    Organizational Affiliation: 

    Division of Vaccine Research, Institute of Human Virology, Baltimore, MD, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA. Electronic address: mpazgier@ihv.umaryland.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
clade A/E 93TH057 HIV-1 gp120 coreA [auth G],
G [auth A]		385Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: HIV-1 Env
UniProt
Find proteins for A0A0M3KKW9 (Human immunodeficiency virus 1)
Explore A0A0M3KKW9 
Go to UniProtKB:  A0A0M3KKW9
Entity Groups  
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UniProt GroupA0A0M3KKW9
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CD4 mimetic peptide M48U1B [auth N],
H [auth M]		28synthetic constructMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody N5-i5 Fab heavy chainC [auth H],
I [auth F]		226Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody N5-i5 light chainD [auth L],
J [auth I]		217Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody N12-i3 Fab heavy chainE [auth D],
K [auth B]		225Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody N12-i3 light chainF [auth E],
L [auth C]		215Homo sapiensMutation(s): 0 
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
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AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
M [auth G],
N [auth G],
O [auth G],
P [auth G],
Q [auth G],
R [auth G],
S [auth G],
T [auth G],
U [auth G],
V [auth G],
W [auth G],
Y [auth A],
Z [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
CL
Query on CL
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IA [auth A],
X [auth N]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
U2X
Query on U2X		B [auth N],
H [auth M]		L-PEPTIDE LINKINGC16 H23 N O3TYR
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001094
Query on PRD_001094		 B [auth M],
H [auth N]		CD4-MIMETIC MINIPROTEIN M48U1Peptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 311.018α = 90
b = 53.291β = 128.89
c = 223.577γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI116274

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2018-04-18
    Changes: Data collection
  • Version 1.3: 2018-05-30
    Changes: Data collection, Structure summary
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary