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 3.1 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: 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: envpol
UniProt
Find proteins for Q0ED31 (Human immunodeficiency virus 1)
Explore Q0ED31 
Go to UniProtKB:  Q0ED31
Protein Feature View
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  • Reference Sequence
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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
Protein Feature View
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  • Reference Sequence
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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
Protein Feature View
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  • Reference Sequence
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, P5N-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-glucopyranoseO2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth G] , AB [auth D] , BB [auth D] , CA [auth A] , CB [auth D] , DA [auth A] , DB [auth D] , EA [auth A] , 
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 (Subject of Investigation/LOI)
Query on BGC

Download Ideal Coordinates CCD File 
BA [auth G] , CC [auth J] , LB [auth D] , MB [auth E] , QA [auth A] , RA [auth A] , SA [auth A] , TA [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

Download Ideal Coordinates CCD File 
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  



Entry History 

Deposition Data

  • Deposited Date: 2010-06-11 
  • Released Date: 2010-07-07 
  • Deposition Author(s): Zhou, T., Kwong, P.D.

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