9MID | pdb_00009mid

Crystal structure of the VRC01-class antibody 3G08, derived from GT1.1 vaccination, in complex with eOD-GT8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.247 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Precise targeting of HIV broadly neutralizing antibody precursors in humans.

Caniels, T.G.Prabhakaran, M.Ozorowski, G.MacPhee, K.J.Wu, W.van der Straten, K.Agrawal, S.Derking, R.Reiss, E.I.M.M.Millard, K.Turroja, M.Desrosiers, A.Bethony, J.Malkin, E.Liesdek, M.H.van der Veen, A.Klouwens, M.Snitselaar, J.L.Bouhuijs, J.H.Bronson, R.Jean-Baptiste, J.Gajjala, S.Rikhtegaran Tehrani, Z.Benner, A.Ramaswami, M.Duff, M.O.Liu, Y.W.Sato, A.H.Kim, J.Y.Baken, I.J.L.Mendes Silva, C.Bijl, T.P.L.van Rijswijk, J.Burger, J.A.Cupo, A.Yasmeen, A.Phulera, S.Lee, W.H.Randall Jr., K.N.Zhang, S.Corcoran, M.M.Regadas, I.Sullivan, A.C.Brown, D.M.Bohl, J.A.Greene, K.M.Gao, H.Yates, N.L.Sawant, S.Prins, J.M.Kootstra, N.A.Kaminsky, S.M.Barin, B.Rahaman, F.Meller, M.Philiponis, V.Laufer, D.S.Lombardo, A.Mwoga, L.Shotorbani, S.Holman, D.Koup, R.A.Klasse, P.J.Karlsson Hedestam, G.B.Tomaras, G.D.van Gils, M.J.Montefiori, D.C.McDermott, A.B.Hyrien, O.Moore, J.P.Wilson, I.A.Ward, A.B.Diemert, D.J.de Bree, G.J.Andrews, S.F.Caskey, M.Sanders, R.W.

(2025) Science 389: eadv5572-eadv5572

  • DOI: https://doi.org/10.1126/science.adv5572
  • Primary Citation of Related Structures:  
    9MI0, 9MIA, 9MIB, 9MIC, 9MID, 9MIF, 9MIH, 9MII, 9MJ3, 9MJ6, 9MJC, 9MJD, 9MJI, 9MK4

  • PubMed Abstract: 

    A protective HIV vaccine will need to induce broadly neutralizing antibodies (bnAbs) in humans, but priming rare bnAb precursor B cells has been challenging. In a double-blinded, placebo-controlled phase 1 human clinical trial, the recombinant, germline-targeting envelope glycoprotein (Env) trimer BG505 SOSIP.v4.1-GT1.1, adjuvanted with AS01 B , induced bnAb precursors of the VRC01-class at a high frequency in the majority of vaccine recipients. These bnAb precursors, that target the CD4 receptor binding site, had undergone somatic hypermutation characteristic of the VRC01-class. A subset of isolated VRC01-class monoclonal antibodies neutralized wild-type pseudoviruses and was structurally extremely similar to bnAb VRC01. These results further support germline-targeting approaches for human HIV vaccine design and demonstrate atomic-level manipulation of B cell responses with rational vaccine design.


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

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3G08 Fab Heavy ChainA [auth H]223Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
3G08 Fab Light ChainB [auth L]211Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
eOD-GT8 engineered mutant of gp120183Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.247 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.105α = 90
b = 44.474β = 119.89
c = 103.977γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
autoPROCdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States5P01AI110657

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Database references
  • Version 1.2: 2025-08-13
    Changes: Database references