7MDT | pdb_00007mdt

BG505 SOSIP.v5.2 in complex with the monoclonal antibody Rh4O9.8 (as Fab fragment)

• PDB DOI: https://doi.org/10.2210/pdb7MDT/pdb
• EM Map EMD-23779: EMDB EMDataResource

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


• Deposited: 2021-04-06 Released: 2022-01-26 
• Deposition Author(s): Antanasijevic, A., Ozorowski, G., Nogal, B., Ward, A.B.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

From structure to sequence: Antibody discovery using cryoEM.

Antanasijevic, A., Bowman, C.A., Kirchdoerfer, R.N., Cottrell, C.A., Ozorowski, G., Upadhyay, A.A., Cirelli, K.M., Carnathan, D.G., Enemuo, C.A., Sewall, L.M., Nogal, B., Zhao, F., Groschel, B., Schief, W.R., Sok, D., Silvestri, G., Crotty, S., Bosinger, S.E., Ward, A.B.

(2022) Sci Adv 8: eabk2039-eabk2039

• PubMed: 35044813 
• DOI: https://doi.org/10.1126/sciadv.abk2039
• Primary Citation Related Structures: 
  7MDT, 7MDU, 7MEP


• PubMed Abstract: 
  

  One of the rate-limiting steps in analyzing immune responses to vaccines or infections is the isolation and characterization of monoclonal antibodies. Here, we present a hybrid structural and bioinformatic approach to directly assign the heavy and light chains, identify complementarity-determining regions, and discover sequences from cryoEM density maps of serum-derived polyclonal antibodies bound to an antigen. When combined with next-generation sequencing of immune repertoires, we were able to specifically identify clonal family members, synthesize the monoclonal antibodies, and confirm that they interact with the antigen in a manner equivalent to the corresponding polyclonal antibodies. This structure-based approach for identification of monoclonal antibodies from polyclonal sera opens new avenues for analysis of immune responses and iterative vaccine design.

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Organizational Affiliation: 
• Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, WI 53706, USA.
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30329, USA.
Yerkes Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Yerkes Nonhuman Primate Genomics Core, Emory University, Atlanta, GA 30329, USA.
Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
International AIDS Vaccine Initiative-Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA.
The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A3B3C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A3B3C2 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 265.42 kDa 
• Atom Count: 15,956 
• Modeled Residue Count: 1,892 
• Deposited Residue Count: 2,225 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface protein gp120	A, E [auth C], F [auth E]	513	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6  Go to UniProtKB:  Q2N0S6
Glycosylation
Glycosylation Sites: 15

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein gp41	B, G [auth D], H [auth F]	153	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6  Go to UniProtKB:  Q2N0S6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Rh4O9.8 monoclonal antibody Light Chain	C [auth L]	110	Macaca mulatta	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Rh4O9.8 monoclonal antibody Heavy Chain	D [auth H]	117	Macaca mulatta	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], I [auth G], J [auth I], L [auth K], M, N, O, Q, R, S, T, U, W, X, Y, Z	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
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	K [auth J]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-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	AA [auth a], P, V	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AB [auth E], BB [auth E], CA [auth A], CB [auth E], DA [auth A], DB [auth E], EA [auth A], EB [auth E], FA [auth A], FB [auth E], GA [auth A], GB [auth E], HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth C], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], UA [auth C], VA [auth C], WA [auth C], XA [auth C], YA [auth E], ZA [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	RosettaEM

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-01-26 
Deposition Author(s): Antanasijevic, A., Ozorowski, G., Nogal, B., Ward, A.B.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1115782
Bill & Melinda Gates Foundation	United States	OPP1196345

Revision History  

• Version 1.0: 2022-01-26
  Type: Initial release
  
• Version 1.1: 2022-02-02
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary