5C7K

Crystal structure BG505 SOSIP gp140 HIV-1 Env trimer bound to broadly neutralizing antibodies PGT128 and 8ANC195


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.290 

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Literature

Complete epitopes for vaccine design derived from a crystal structure of the broadly neutralizing antibodies PGT128 and 8ANC195 in complex with an HIV-1 Env trimer.

Kong, L.Torrents de la Pena, A.Deller, M.C.Garces, F.Sliepen, K.Hua, Y.Stanfield, R.L.Sanders, R.W.Wilson, I.A.

(2015) Acta Crystallogr D Biol Crystallogr 71: 2099-2108

  • DOI: 10.1107/S1399004715013917
  • Primary Citation of Related Structures:  
    5C7K

  • PubMed Abstract: 
  • The HIV-1 envelope gp160 glycoprotein (Env) is a trimer of gp120 and gp41 heterodimers that mediates cell entry and is the primary target of the humoral immune response. Broadly neutralizing antibodies (bNAbs) to HIV-1 have revealed multiple epitopes or sites of vulnerability, but mapping of most of these sites is incomplete owing to a paucity of structural information on the full epitope in the context of the Env trimer ...

    The HIV-1 envelope gp160 glycoprotein (Env) is a trimer of gp120 and gp41 heterodimers that mediates cell entry and is the primary target of the humoral immune response. Broadly neutralizing antibodies (bNAbs) to HIV-1 have revealed multiple epitopes or sites of vulnerability, but mapping of most of these sites is incomplete owing to a paucity of structural information on the full epitope in the context of the Env trimer. Here, a crystal structure of the soluble BG505 SOSIP gp140 trimer at 4.6 Å resolution with the bNAbs 8ANC195 and PGT128 reveals additional interactions in comparison to previous antibody-gp120 structures. For 8ANC195, in addition to previously documented interactions with gp120, a substantial interface with gp41 is now elucidated that includes extensive interactions with the N637 glycan. Surprisingly, removal of the N637 glycan did not impact 8ANC195 affinity, suggesting that the antibody has evolved to accommodate this glycan without loss of binding energy. PGT128 indirectly affects the N262 glycan by a domino effect, in which PGT128 binds to the N301 glycan, which in turn interacts with and repositions the N262 glycan, thereby illustrating the important role of neighboring glycans on epitope conformation and stability. Comparisons with other Env trimer and gp120 structures support an induced conformation for glycan N262, suggesting that the glycan shield is allosterically modified upon PGT128 binding. These complete epitopes of two broadly neutralizing antibodies on the Env trimer can now be exploited for HIV-1 vaccine design.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody Fab PGT128 heavy chainA239Homo sapiensMutation(s): 0 
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Find proteins for S6B291 (Homo sapiens)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody Fab PGT128 light chainB211Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp120C487Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: env
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Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp41D153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody Fab 8ANC195 heavy chainE238Homo sapiensMutation(s): 0 
Gene Names: IGHG1
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Find proteins for P01857 (Homo sapiens)
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PHAROS:  P01857
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody Fab 8ANC195 light chainF215Homo sapiensMutation(s): 0 
Gene Names: IGKC
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens)
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PHAROS:  P01834
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  • Reference Sequence
Oligosaccharides

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Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG, H, I, J2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-glucopyranoseK, M9N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G68668TB
GlyCosmos:  G68668TB
GlyGen:  G68668TB
Entity ID: 9
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-glucopyranoseL10N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G40702WU
GlyCosmos:  G40702WU
GlyGen:  G40702WU
Entity ID: 10
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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-glucopyranoseN7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G46836GH
GlyCosmos:  G46836GH
GlyGen:  G46836GH
Entity ID: 11
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranoseO5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42227JK
GlyCosmos:  G42227JK
GlyGen:  G42227JK
Entity ID: 12
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseP, Q, R3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 13
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranoseS8N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G34499SX
GlyCosmos:  G34499SX
GlyGen:  G34499SX
Entity ID: 14
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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-glucopyranoseT11N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G60230HH
GlyCosmos:  G60230HH
GlyGen:  G60230HH
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.290 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 261.135α = 90
b = 261.135β = 90
c = 261.135γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-10-28
    Changes: Database references
  • Version 1.2: 2015-12-23
    Changes: Structure summary
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2017-11-01
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary