7L09 | pdb_00007l09

Cryo-EM structure of SARS-CoV-2 2P S ectodomain bound domain-swapped antibody 2G12 from masked 3D refinement

• PDB DOI: https://doi.org/10.2210/pdb7L09/pdb
• EM Map EMD-23097: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-12-11 Released: 2020-12-30 
• Deposition Author(s): Manne, K., Henderson, R., 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: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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.

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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: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A3B2C2 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 481.36 kDa 
• Atom Count: 30,283 
• Modeled Residue Count: 3,776 
• Deposited Residue Count: 4,241 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,121	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 15		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2G12 heavy chain	D [auth H], G [auth M]	226	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
2G12 light chain	E [auth K], F [auth L]	213	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth D], K [auth G], L [auth I], M [auth J], N, O, P, Q, R, S	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth E]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth F]	8		N-Glycosylation
Glycosylation Resources
GlyTouCan: G14481TB GlyCosmos: G14481TB GlyGen: G14481TB

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	T	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G51945PF GlyCosmos: G51945PF GlyGen: G51945PF

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth C], RA [auth C], SA [auth C], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], Y [auth A], YA [auth C], Z [auth A], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK	D [auth H], G [auth M]	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-30 
Deposition Author(s): Manne, K., Henderson, R., 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: 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: 2024-11-13
  Changes: Data collection, Database references, Refinement description, Structure summary