5F6I | pdb_00005f6i

Crystal Structure of Tier 2 Neutralizing Antibody DH428 from a Rhesus Macaque

• PDB DOI: https://doi.org/10.2210/pdb5F6I/pdb

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


• Deposited: 2015-12-06 Released: 2016-01-13 
• Deposition Author(s): Fera, D., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.265 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Structural Constraints of Vaccine-Induced Tier-2 Autologous HIV Neutralizing Antibodies Targeting the Receptor-Binding Site.

Bradley, T., Fera, D., Bhiman, J., Eslamizar, L., Lu, X., Anasti, K., Zhang, R., Sutherland, L.L., Scearce, R.M., Bowman, C.M., Stolarchuk, C., Lloyd, K.E., Parks, R., Eaton, A., Foulger, A., Nie, X., Karim, S.S., Barnett, S., Kelsoe, G., Kepler, T.B., Alam, S.M., Montefiori, D.C., Moody, M.A., Liao, H.X., Morris, L., Santra, S., Harrison, S.C., Haynes, B.F.

(2016) Cell Rep 14: 43-54

• PubMed: 26725118 
• DOI: https://doi.org/10.1016/j.celrep.2015.12.017
• Primary Citation Related Structures: 
  5F6H, 5F6I, 5F6J


• PubMed Abstract: 
  

  Antibodies that neutralize autologous transmitted/founder (TF) HIV occur in most HIV-infected individuals and can evolve to neutralization breadth. Autologous neutralizing antibodies (nAbs) against neutralization-resistant (Tier-2) viruses are rarely induced by vaccination. Whereas broadly neutralizing antibody (bnAb)-HIV-Envelope structures have been defined, the structures of autologous nAbs have not. Here, we show that immunization with TF mutant Envs gp140 oligomers induced high-titer, V5-dependent plasma neutralization for a Tier-2 autologous TF evolved mutant virus. Structural analysis of autologous nAb DH427 revealed binding to V5, demonstrating the source of narrow nAb specificity and explaining the failure to acquire breadth. Thus, oligomeric TF Envs can elicit autologous nAbs to Tier-2 HIVs, but induction of bnAbs will require targeting of precursors of B cell lineages that can mature to heterologous neutralization.

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Organizational Affiliation: 
• Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA. Electronic address: [e-mail].
Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
National Institute for Communicable Diseases, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2131, South Africa.
Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
Center for AIDS Program of Research in South Africa, University of KwaZulu-Natal, Durban 4013, South Africa; Columbia University, New York, NY 10032, USA.
Novartis Vaccines and Diagnostics, Inc., Cambridge, MA 02139, USA.
Boston University, Boston, MA 02118, USA.
National Institute for Communicable Diseases, Johannesburg 2131, South Africa; Center for AIDS Program of Research in South Africa, University of KwaZulu-Natal, Durban 4013, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2131, South Africa.
Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA.
Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.22 kDa 
• Atom Count: 3,225 
• Modeled Residue Count: 420 
• Deposited Residue Count: 443 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DH428 Antibody Heavy Chain	A [auth B]	227	Macaca mulatta	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DH428 Antibody Light Chain	B [auth C]	216	Macaca mulatta	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.265 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.106	α = 90
b = 74.628	β = 90
c = 102.62	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Fera, D., Harrison, S.C.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-01-20
  Changes: Database references
• Version 1.2: 2017-07-05
  Changes: Source and taxonomy
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary