7L6M | pdb_00007l6m

Cryo-EM structure of DH898.1 Fab-dimer from local refinement of the Fab-dimer bound near the CD4 binding site of HIV-1 Env CH848 SOSIP trimer

• PDB DOI: https://doi.org/10.2210/pdb7L6M/pdb
• EM Map EMD-23145: EMDB EMDataResource

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


• Deposited: 2020-12-23 Released: 2021-02-10 
• Deposition Author(s): Manne, K., Edwards, R.J., Acharya, P.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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.

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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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 94.3 kDa 
• Atom Count: 6,638 
• Modeled Residue Count: 874 
• Deposited Residue Count: 874 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DH898.1 Fab light chain	A [auth g], D [auth j]	218	Macaca mulatta	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DH898.1 Fab heavy chain	B [auth h], C [auth i]	219	Macaca mulatta	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	ISOLDE

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Manne, K., Edwards, R.J., Acharya, P.

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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: 2021-02-10
  Type: Initial release
  
• Version 2.0: 2021-03-24
  Type: Coordinate replacement
  Reason: Sequence discrepancy
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2021-06-02
  Changes: Database references
• Version 2.2: 2021-06-09
  Changes: Database references
• Version 2.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary