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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Ligand Structure Quality Assessment 


This is version 3.2 of the entry. See complete history


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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160A [auth G],
D [auth A],
G [auth D],
J [auth I]
353Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: Envpol
UniProt
Find proteins for Q0ED31 (Human immunodeficiency virus 1)
Explore Q0ED31 
Go to UniProtKB:  Q0ED31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0ED31
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antigen binding fragment of heavy chain: Antibody VRC01B [auth H],
E [auth B],
H [auth E],
K [auth J]
224Homo sapiensMutation(s): 0 
Gene Names: Heavy chain
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antigen binding fragment of light chain: Antibody VRC01C [auth L],
F [auth C],
I [auth F],
L [auth K]
210Homo sapiensMutation(s): 0 
Gene Names: Light chain
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranose
M, N, P
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
O
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
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
BGC
Query on BGC

Download Ideal Coordinates CCD File 
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
TRS
Query on TRS

Download Ideal Coordinates CCD File 
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
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 


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
  • Version 3.2: 2023-09-06
    Changes: Data collection, Database references, Refinement description