3U4E

Crystal Structure of PG9 Fab in Complex with V1V2 Region from HIV-1 strain CAP45


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.

McLellan, J.S.Pancera, M.Carrico, C.Gorman, J.Julien, J.P.Khayat, R.Louder, R.Pejchal, R.Sastry, M.Dai, K.O'Dell, S.Patel, N.Shahzad-Ul-Hussan, S.Yang, Y.Zhang, B.Zhou, T.Zhu, J.Boyington, J.C.Chuang, G.Y.Diwanji, D.Georgiev, I.Do Kwon, Y.Lee, D.Louder, M.K.Moquin, S.Schmidt, S.D.Yang, Z.Y.Bonsignori, M.Crump, J.A.Kapiga, S.H.Sam, N.E.Haynes, B.F.Burton, D.R.Koff, W.C.Walker, L.M.Phogat, S.Wyatt, R.Orwenyo, J.Wang, L.X.Arthos, J.Bewley, C.A.Mascola, J.R.Nabel, G.J.Schief, W.R.Ward, A.B.Wilson, I.A.Kwong, P.D.

(2011) Nature 480: 336-343

  • DOI: 10.1038/nature10696
  • Primary Citation of Related Structures:  
    3TCL, 3U1S, 3U2S, 3U36, 3U46, 3U4B, 3U4E

  • PubMed Abstract: 
  • Variable regions 1 and 2 (V1/V2) of human immunodeficiency virus-1 (HIV-1) gp120 envelope glycoprotein are critical for viral evasion of antibody neutralization, and are themselves protected by extraordinary sequence diversity and N-linked glycosylation. Human antibodies such as PG9 nonetheless engage V1/V2 and neutralize 80% of HIV-1 isolates ...

    Variable regions 1 and 2 (V1/V2) of human immunodeficiency virus-1 (HIV-1) gp120 envelope glycoprotein are critical for viral evasion of antibody neutralization, and are themselves protected by extraordinary sequence diversity and N-linked glycosylation. Human antibodies such as PG9 nonetheless engage V1/V2 and neutralize 80% of HIV-1 isolates. Here we report the structure of V1/V2 in complex with PG9. V1/V2 forms a four-stranded β-sheet domain, in which sequence diversity and glycosylation are largely segregated to strand-connecting loops. PG9 recognition involves electrostatic, sequence-independent and glycan interactions: the latter account for over half the interactive surface but are of sufficiently weak affinity to avoid autoreactivity. The structures of V1/V2-directed antibodies CH04 and PGT145 indicate that they share a common mode of glycan penetration by extended anionic loops. In addition to structurally defining V1/V2, the results thus identify a paradigm of antibody recognition for highly glycosylated antigens, which-with PG9-involves a site of vulnerability comprising just two glycans and a strand.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
V1V2 region of HIV-1 on 1FD6 scaffoldA [auth G], B [auth J]124Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q1PHM9 (Human immunodeficiency virus 1)
Explore Q1PHM9 
Go to UniProtKB:  Q1PHM9
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PG9 Heavy ChainE [auth A], C [auth H]248Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PG9 Light ChainF [auth B], D [auth L]216Homo sapiensMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth C], I [auth E]7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G55220VL
GlyCosmos:  G55220VL
GlyGen:  G55220VL
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth D]6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G09724ZC
GlyCosmos:  G09724ZC
GlyGen:  G09724ZC
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth F]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranoseK [auth I]2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07696MJ
GlyCosmos:  G07696MJ
GlyGen:  G07696MJ
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
C [auth H], E [auth A]L-PEPTIDE LINKINGC5 H7 N O3GLN
TYS
Query on TYS
C [auth H], E [auth A]L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.026α = 90
b = 103.545β = 90
c = 186.373γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2011-12-21
    Changes: Database references
  • Version 2.0: 2019-12-25
    Changes: Advisory, Derived calculations, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary