6XRJ | pdb_00006xrj

Crystal structure of the disulfide linked DH717.1 Fab dimer, derived from a macaque HIV-1 vaccine-induced Env glycan-reactive neutralizing antibody B cell lineage

• PDB DOI: https://doi.org/10.2210/pdb6XRJ/pdb

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


• Deposited: 2020-07-13 Released: 2020-12-30 
• Deposition Author(s): Manne, K., Nicely, N.I., Acharya, P.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.282 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.

Williams, W.B., Meyerhoff, R.R., Edwards, R.J., Li, H., Manne, K., Nicely, N.I., Henderson, R., Zhou, Y., Janowska, K., Mansouri, K., Gobeil, S., Evangelous, T., Hora, B., Berry, M., Abuahmad, A.Y., Sprenz, J., Deyton, M., Stalls, V., Kopp, M., Hsu, A.L., Borgnia, M.J., Stewart-Jones, G.B.E., Lee, M.S., Bronkema, N., Moody, M.A., Wiehe, K., Bradley, T., Alam, S.M., Parks, R.J., Foulger, A., Oguin, T., Sempowski, G.D., Bonsignori, M., LaBranche, C.C., Montefiori, D.C., Seaman, M., Santra, S., Perfect, J., Francica, J.R., Lynn, G.M., Aussedat, B., Walkowicz, W.E., Laga, R., Kelsoe, G., Saunders, K.O., Fera, D., Kwong, P.D., Seder, R.A., Bartesaghi, A., Shaw, G.M., Acharya, P., Haynes, B.F.

(2021) Cell 184: 2955

• PubMed: 34019795 
• DOI: https://doi.org/10.1016/j.cell.2021.04.042
• Primary Citation Related Structures: 
  6VTU, 6XRJ, 7L02, 7L06, 7L09, 7L6M, 7L6O, 7LU9, 7LUA


• PubMed Abstract: 
  

  Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (V _H ) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without V _H -swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgM ⁺ IgD ⁺ CD27 ⁺ , thus suggesting that they originated from a pool of antigen-experienced IgM ⁺ or marginal zone B cells.

---

Organizational Affiliation: 
• Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA. Electronic address: [e-mail].
Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA.
Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Duke Human Vaccine Institute, Durham, NC 27710, USA.
Department of Computer Science, Duke University, Durham, NC 27708, USA.
Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Department of Health and Human Services, Research Triangle Park, NC 27709, USA.
Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA.
Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA.
Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Pediatrics, Duke University, Durham, NC 27710, USA.
Department of Surgery, Duke University, Durham, NC 27710, USA.
Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA.
Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA.
Department of Medicine, Duke University, Durham, NC 27710, USA.
Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA; Avidea Technologies, Inc., Baltimore, MD, USA.
Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, Czech Republic.
Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA.
Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA.
Department of Computer Science, Duke University, Durham, NC 27708, USA; Department of Biochemistry, Duke University, Durham, NC 27705, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA.
Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA. Electronic address: [e-mail].
Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA; Department of Immunology, Duke University, 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)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 185.3 kDa 
• Atom Count: 12,965 
• Modeled Residue Count: 1,740 
• Deposited Residue Count: 1,748 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DH717.1 heavy chain Fab fragment	A, C, E, G [auth H]	226	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DH717.1 light chain Fab fragment	B, D, F, H [auth L]	211	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.282 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.587	α = 90
b = 201.587	β = 90
c = 154.327	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-30 
Deposition Author(s): Manne, K., Nicely, N.I., Acharya, P.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI145687

Revision History  

• Version 1.0: 2020-12-30
  Type: Initial release
  
• Version 1.1: 2021-06-02
  Changes: Database references
• Version 1.2: 2021-06-09
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary