8D0Y | pdb_00008d0y

Crystal Structure of HIV-1 BG505 SOSIPv8 Trimer in Complex with CD4bs targeting antibody 21N13 and interface targeting antibody 35O22 at 4.7 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.70 Å
  • R-Value Free: 
    0.298 (Depositor), 0.302 (DCC) 
  • R-Value Work: 
    0.268 (Depositor), 0.272 (DCC) 
  • R-Value Observed: 
    0.270 (Depositor) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Germline-targeting HIV vaccination induces neutralizing antibodies to the CD4 binding site.

Caniels, T.G.Medina-Ramirez, M.Zhang, S.Kratochvil, S.Xian, Y.Koo, J.H.Derking, R.Samsel, J.van Schooten, J.Pecetta, S.Lamperti, E.Yuan, M.Carrasco, M.R.Del Moral Sanchez, I.Allen, J.D.Bouhuijs, J.H.Yasmeen, A.Ketas, T.J.Snitselaar, J.L.Bijl, T.P.L.Martin, I.C.Torres, J.L.Cupo, A.Shirreff, L.Rogers, K.Mason, R.D.Roederer, M.Greene, K.M.Gao, H.Silva, C.M.Baken, I.J.L.Tian, M.Alt, F.W.Pulendran, B.Seaman, M.S.Crispin, M.van Gils, M.J.Montefiori, D.C.McDermott, A.B.Villinger, F.J.Koup, R.A.Moore, J.P.Klasse, P.J.Ozorowski, G.Batista, F.D.Wilson, I.A.Ward, A.B.Sanders, R.W.

(2024) Sci Immunol 9: eadk9550-eadk9550

  • DOI: https://doi.org/10.1126/sciimmunol.adk9550
  • Primary Citation of Related Structures:  
    8D01, 8D0Y, 8SW3, 8SW4

  • PubMed Abstract: 

    Eliciting potent and broadly neutralizing antibodies (bnAbs) is a major goal in HIV-1 vaccine development. Here, we describe how germline-targeting immunogen BG505 SOSIP germline trimer 1.1 (GT1.1), generated through structure-based design, engages a diverse range of VRC01-class bnAb precursors. A single immunization with GT1.1 expands CD4 binding site (CD4bs)-specific VRC01-class B cells in knock-in mice and drives VRC01-class maturation. In nonhuman primates (NHPs), GT1.1 primes CD4bs-specific neutralizing serum responses. Selected monoclonal antibodies (mAbs) isolated from GT1.1-immunized NHPs neutralize fully glycosylated BG505 virus. Two mAbs, 12C11 and 21N13, neutralize subsets of diverse heterologous neutralization-resistant viruses. High-resolution structures revealed that 21N13 targets the same conserved residues in the CD4bs as VRC01-class and CH235-class bnAbs despite its low sequence similarity (~40%), whereas mAb 12C11 binds predominantly through its heavy chain complementarity-determining region 3. These preclinical data underpin the ongoing evaluation of GT1.1 in a phase 1 clinical trial in healthy volunteers.


  • Organizational Affiliation
    • Amsterdam UMC, location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, Netherlands.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
35O22scFv Heavy Chain VariableA [auth D]128Macaca mulattaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
35O22scFv Light Chain VariableB [auth E]111Macaca mulattaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
21N13 Fab Heavy ChainC [auth H]225Macaca mulattaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
21N13 Fab Light ChainD [auth L]213Macaca mulattaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
BG505SOSIPv8 gp120E [auth G]455Human immunodeficiency virus 1Mutation(s): 0 
UniProt
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Go to UniProtKB:  Q2N0S6
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UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 13
Sequence Annotations
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
BG505SOSIPv8 gp41F [auth B]146Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
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Go to UniProtKB:  Q2N0S6
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UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D 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 A]7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G55220VL
GlyCosmos:  G55220VL
GlyGen:  G55220VL
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth C],
L [auth K]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranoseI [auth F]7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G23799GS
GlyCosmos:  G23799GS
GlyGen:  G23799GS
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-glucopyranoseJ [auth I]6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G34442SS
GlyCosmos:  G34442SS
GlyGen:  G34442SS
Entity ID: 11
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-glucopyranoseK [auth J],
M,
N,
O
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 12
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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
P
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.70 Å
  • R-Value Free:  0.298 (Depositor), 0.302 (DCC) 
  • R-Value Work:  0.268 (Depositor), 0.272 (DCC) 
  • R-Value Observed: 0.270 (Depositor) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 264.672α = 90
b = 264.672β = 90
c = 264.672γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
International AIDS Vaccine InitiativeUnited StatesINV-008352/OPP1153692
Consortia for HIV/AIDS Vaccine DevelopmentUnited StatesCHAVD 1UM1 AI144462
Other privateP01 AI110657

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection
  • Version 1.2: 2023-11-22
    Changes: Source and taxonomy
  • Version 1.3: 2024-05-15
    Changes: Database references, Structure summary
  • Version 1.4: 2024-11-20
    Changes: Structure summary
  • Version 1.5: 2026-01-14
    Changes: Database references, Structure summary