9MJ6 | pdb_00009mj6

Crystal structure of the VRC01-class antibody 7A03 derived from GT1.1 vaccination

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-12-13 Released: 2025-05-28 
  • Deposition Author(s): Agrawal, S., Wilson, I.A.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 
    0.324 (Depositor), 0.320 (DCC) 
  • R-Value Work: 
    0.264 (Depositor), 0.264 (DCC) 
  • R-Value Observed: 
    0.267 (Depositor) 

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

Validation slider image for 9MJ6

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 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.

Macromolecule Content 

  • Total Structure Weight: 91.34 kDa 
  • Atom Count: 6,199 
  • Modeled Residue Count: 821 
  • Deposited Residue Count: 852 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
7A03 Fab heavy chainA [auth H],
C [auth E]
221Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
7A03 Fab light chainB [auth L],
D [auth F]
205Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free:  0.324 (Depositor), 0.320 (DCC) 
  • R-Value Work:  0.264 (Depositor), 0.264 (DCC) 
  • R-Value Observed: 0.267 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.483α = 90
b = 137.866β = 108.3
c = 62.983γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
autoPROCdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



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