4LAJ

Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex with CD4-mimetic miniprotein, M48U1, and llama single-domain, broadly neutralizing, co-receptor binding site antibody, JM4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Heavy Chain-Only IgG2b Llama Antibody Effects Near-Pan HIV-1 Neutralization by Recognizing a CD4-Induced Epitope That Includes Elements of Coreceptor- and CD4-Binding Sites.

Acharya, P.Luongo, T.S.Georgiev, I.S.Matz, J.Schmidt, S.D.Louder, M.K.Kessler, P.Yang, Y.McKee, K.O'Dell, S.Chen, L.Baty, D.Chames, P.Martin, L.Mascola, J.R.Kwong, P.D.

(2013) J Virol 87: 10173-10181

  • DOI: https://doi.org/10.1128/JVI.01332-13
  • Primary Citation of Related Structures:  
    4LAJ

  • PubMed Abstract: 

    The conserved HIV-1 site of coreceptor binding is protected from antibody-directed neutralization by conformational and steric restrictions. While inaccessible to most human antibodies, the coreceptor site has been shown to be accessed by antibody fragments. In this study, we used X-ray crystallography, surface plasmon resonance, and pseudovirus neutralization to characterize the gp120-envelope glycoprotein recognition and HIV-1 neutralization of a heavy chain-only llama antibody, named JM4. We describe full-length IgG2b and IgG3 versions of JM4 that target the coreceptor-binding site and potently neutralize over 95% of circulating HIV-1 isolates. Contrary to established trends that show improved access to the coreceptor-binding region by smaller antibody fragments, the single-domain (VHH) version of JM4 neutralized less well than the full-length IgG2b version of JM4. The crystal structure at 2.1-Å resolution of VHH JM4 bound to HIV-1 YU2 gp120 stabilized in the CD4-bound state by the CD4-mimetic miniprotein, M48U1, revealed a JM4 epitope that combined regions of coreceptor recognition (including the gp120 bridging sheet, V3 loop, and β19 strand) with gp120 structural elements involved in recognition of CD4 such as the CD4-binding loop. The structure of JM4 with gp120 thus defines a novel CD4-induced site of vulnerability involving elements of both coreceptor- and CD4-binding sites. The potently neutralizing JM4 IgG2b antibody that targets this newly defined site of vulnerability adds to the expanding repertoire of broadly neutralizing antibodies that effectively neutralize HIV-1 and thereby potentially provides a new template for vaccine development and target for HIV-1 therapy.


  • Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA. acharyap@mail.nih.gov


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 YU2 gp120 envelope glycoproteinA [auth J],
B [auth F],
C [auth A],
D [auth B]
376Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: Env
UniProt
Find proteins for P35961 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2))
Explore P35961 
Go to UniProtKB:  P35961
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35961
Glycosylation
Glycosylation Sites: 8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CD4-mimetic miniprotein M48U1E [auth K],
F [auth D],
G,
H [auth C]
28N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Llama single domain antibody, JM4I [auth H],
J [auth M],
K [auth L],
L [auth I]
129Lama glamaMutation(s): 0 
UniProt
Find proteins for A2KD57 (Lama glama)
Explore A2KD57 
Go to UniProtKB:  A2KD57
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2KD57
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
CA [auth F]
DA [auth F]
EA [auth F]
AA [auth F],
BA [auth F],
CA [auth F],
DA [auth F],
EA [auth F],
FA [auth A],
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
M [auth J],
MA [auth A],
N [auth J],
NA [auth A],
O [auth J],
P [auth J],
Q [auth J],
R [auth J],
RA [auth B],
S [auth J],
SA [auth B],
T [auth J],
TA [auth B],
U [auth J],
UA [auth B],
VA [auth B],
W [auth F],
WA [auth B],
X [auth F],
XA [auth B],
Y [auth F],
YA [auth B],
Z [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ACA
Query on ACA

Download Ideal Coordinates CCD File 
CB [auth B]6-AMINOHEXANOIC ACID
C6 H13 N O2
SLXKOJJOQWFEFD-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth B]
BB [auth B]
OA [auth A]
PA [auth A]
QA [auth A]
AB [auth B],
BB [auth B],
OA [auth A],
PA [auth A],
QA [auth A],
V [auth J],
ZA [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
U2X
Query on U2X
E [auth K],
F [auth D],
G,
H [auth C]
L-PEPTIDE LINKINGC16 H23 N O3TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.772α = 90
b = 86.221β = 102.88
c = 144.848γ = 90
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: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-08-21
    Changes: Structure summary
  • Version 1.2: 2013-09-04
    Changes: Database references
  • Version 1.3: 2014-04-09
    Changes: Source and taxonomy
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection