3NGB

Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 gp120

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

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Literature

Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01.

Zhou, T., Georgiev, I., Wu, X., Yang, Z.Y., Dai, K., Finzi, A., Do Kwon, Y., Scheid, J.F., Shi, W., Xu, L., Yang, Y., Zhu, J., Nussenzweig, M.C., Sodroski, J., Shapiro, L., Nabel, G.J., Mascola, J.R., Kwong, P.D.

(2010) Science 329: 811-817

  • DOI: 10.1126/science.1192819
  • Primary Citation of Related Structures:  
    3NGB

  • PubMed Abstract: 

    • During HIV-1 infection, antibodies are generated against the region of the viral gp120 envelope glycoprotein that binds CD4, the primary receptor for HIV-1. Among these antibodies, VRC01 achieves broad neutralization of diverse viral strains. We determined the crystal structure of VRC01 in complex with a human immunodeficiency virus HIV-1 gp120 core ...

    During HIV-1 infection, antibodies are generated against the region of the viral gp120 envelope glycoprotein that binds CD4, the primary receptor for HIV-1. Among these antibodies, VRC01 achieves broad neutralization of diverse viral strains. We determined the crystal structure of VRC01 in complex with a human immunodeficiency virus HIV-1 gp120 core. VRC01 partially mimics CD4 interaction with gp120. A shift from the CD4-defined orientation, however, focuses VRC01 onto the vulnerable site of initial CD4 attachment, allowing it to overcome the glycan and conformational masking that diminishes the neutralization potency of most CD4-binding-site antibodies. To achieve this recognition, VRC01 contacts gp120 mainly through immunoglobulin V-gene regions substantially altered from their genomic precursors. Partial receptor mimicry and extensive affinity maturation thus facilitate neutralization of HIV-1 by natural human antibodies.

    Organizational Affiliation: 

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD 20892, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp160D [auth A],
G [auth D],
A [auth G],
J [auth I]		353Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env, pol
UniProt
Find proteins for Q0ED31 (Human immunodeficiency virus 1)
Explore Q0ED31 
Go to UniProtKB:  Q0ED31
Entity Groups  
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UniProt GroupQ0ED31
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Antigen binding fragment of heavy chain: Antibody VRC01E [auth B],
H [auth E],
B [auth H],
K [auth J]		224Homo sapiensMutation(s): 0 
Gene Names: Heavy chain
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Antigen binding fragment of light chain: Antibody VRC01F [auth C],
I [auth F],
L [auth K],
C [auth L]		210Homo sapiensMutation(s): 0 
Gene Names: Light chain
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Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM, N, P 5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseO 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
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AA [auth G],
AB [auth D],
BB [auth D],
CA [auth A],
CB [auth D],
AA [auth G],
AB [auth D],
BB [auth D],
CA [auth A],
CB [auth D],
DA [auth A],
DB [auth D],
EA [auth A],
EB [auth D],
FA [auth A],
FB [auth D],
GA [auth A],
GB [auth D],
HA [auth A],
HB [auth D],
IA [auth A],
IB [auth D],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
NB [auth I],
OB [auth I],
PB [auth I],
Q [auth G],
QB [auth I],
R [auth G],
RB [auth I],
S [auth G],
SB [auth I],
T [auth G],
TB [auth I],
U [auth G],
UB [auth I],
V [auth G],
VB [auth I],
W [auth G],
WB [auth I],
X [auth G],
XA [auth D],
XB [auth I],
Y [auth G],
YA [auth D],
Z [auth G],
ZA [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
BGC
Query on BGC
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BA [auth G],
CC [auth J],
LB [auth D],
MB [auth E],
QA [auth A],
BA [auth G],
CC [auth J],
LB [auth D],
MB [auth E],
QA [auth A],
RA [auth A],
SA [auth A],
TA [auth A],
UA [auth B],
VA [auth B],
WA [auth C],
YB [auth I],
ZB [auth I]
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N		 Ligand Interaction
TRS
Query on TRS
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AC [auth I],
BC [auth J],
DC [auth K],
JB [auth D],
KB [auth D],
AC [auth I],
BC [auth J],
DC [auth K],
JB [auth D],
KB [auth D],
OA [auth A],
PA [auth A]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.63α = 90
b = 98.275β = 99.68
c = 205.256γ = 90
Software Package:
Software NamePurpose
APSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 3.0: 2020-10-14
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 3.1: 2021-03-31
    Changes: Source and taxonomy