7LU9 | pdb_00007lu9

Cryo-EM structure of DH851.3 bound to HIV-1 CH505 Env

• PDB DOI: https://doi.org/10.2210/pdb7LU9/pdb
• EM Map EMD-23518: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Macaca mulatta, Human immunodeficiency virus 1
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-02-21 Released: 2021-03-24 
• 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: 5.60 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: Asymmetric - C1 
Global Stoichiometry: Hetero 18-mer - A6B6C3D3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 18-mer - A8B4C3D3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - C3D3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 500.61 kDa 
• Atom Count: 34,626 
• Modeled Residue Count: 4,383 
• Deposited Residue Count: 4,443 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DH851.3 light chain	A [auth k], H [auth j], L [auth r]	210	Macaca mulatta	Mutation(s): 0
UniProt
Find proteins for F7DKI0 (Macaca mulatta) Explore F7DKI0  Go to UniProtKB:  F7DKI0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DH851.3 heavy chain	B [auth l], G [auth i], K [auth q]	228	Macaca mulatta	Mutation(s): 0
UniProt
Find proteins for F6RL43 (Macaca mulatta) Explore F6RL43  Go to UniProtKB:  F6RL43

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DH851.3 heavy chain	C [auth m], F [auth h], J [auth p]	222	Macaca mulatta	Mutation(s): 0
UniProt
Find proteins for F6RL43 (Macaca mulatta) Explore F6RL43  Go to UniProtKB:  F6RL43

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DH851.3 light chain	D [auth n], E [auth g], I [auth o]	207	Macaca mulatta	Mutation(s): 0
UniProt
Find proteins for F7DKI0 (Macaca mulatta) Explore F7DKI0  Go to UniProtKB:  F7DKI0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	M [auth a], O [auth b], Q [auth c]	153	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6  Go to UniProtKB:  Q2N0S6
Glycosylation
Glycosylation Sites: 2

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	N [auth d], P [auth e], R [auth f]	461	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
UniProt
Find proteins for A0A0A7I3C6 (Human immunodeficiency virus type 1) Explore A0A0A7I3C6  Go to UniProtKB:  A0A0A7I3C6
Glycosylation
Glycosylation Sites: 6

Oligosaccharides

Help  

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth L], GA [auth O], KA [auth S], S [auth A], W [auth E], Z [auth H]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 8
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	AA [auth I], EA [auth M], HA [auth P], LA [auth T], T [auth B], X [auth F]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth J], IA [auth Q], U [auth C]	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G89445RP GlyCosmos: G89445RP GlyGen: G89445RP

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth K], JA [auth R], V [auth D]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G95663PY GlyCosmos: G95663PY GlyGen: G95663PY

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	FA [auth N], MA [auth U], Y [auth G]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	NA [auth a], OA [auth b], PA [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	A [auth k], H [auth j], L [auth r]	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.60 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: 2021-03-24 
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: 2021-03-24
  Type: Initial release
  
• Version 1.1: 2021-06-02
  Changes: Database references
• Version 1.2: 2021-06-09
  Changes: Database references
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Structure summary