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 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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 ...

    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 LengthOrganismDetails
Antibody Fab PGT128 heavy chainA239Homo sapiensMutation(s): 0 
Find proteins for S6B291 (Homo sapiens)
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Go to UniProtKB:  S6B291
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp120C487Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
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Go to UniProtKB:  Q2N0S6
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp41D153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
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Go to UniProtKB:  Q2N0S6
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Antibody Fab 8ANC195 heavy chainE238Homo sapiensMutation(s): 0 
Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Explore P01857 
Go to UniProtKB:  P01857
NIH Common Fund Data Resources
PHAROS  P01857
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  • Reference Sequence

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Antibody Fab 8ANC195 light chainF215Homo sapiensMutation(s): 0 
Gene Names: IGKC
Find proteins for P01834 (Homo sapiens)
Explore P01834 
Go to UniProtKB:  P01834
NIH Common Fund Data Resources
PHAROS  P01834
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antibody Fab PGT128 light chainB211Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides
Entity ID: 7
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I, J
2 N-Glycosylation
Entity ID: 8
MoleculeChainsChain Length2D Diagram Glycosylation
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-glucopyranose
K, M
9 N-Glycosylation
Entity ID: 9
MoleculeChainsChain Length2D Diagram Glycosylation
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-glucopyranose
L
10 N-Glycosylation
Entity ID: 10
MoleculeChainsChain Length2D Diagram Glycosylation
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-glucopyranose
N
7 N-Glycosylation
Entity ID: 11
MoleculeChainsChain Length2D Diagram Glycosylation
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-glucopyranose
O
5 N-Glycosylation
Entity ID: 12
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
P, Q, R
3 N-Glycosylation
Entity ID: 13
MoleculeChainsChain Length2D Diagram Glycosylation
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-glucopyranose
S
8 N-Glycosylation
Entity ID: 14
MoleculeChainsChain Length2D Diagram Glycosylation
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-glucopyranose
T
11 N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
C, D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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 

  • 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