8P5M | pdb_00008p5m

SARS-CoV-2 Spike RBD in complex with Mab-23 (Fab)

• PDB DOI: https://doi.org/10.2210/pdb8P5M/pdb
• EM Map EMD-17451: EMDB EMDataResource

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


• Deposited: 2023-05-24 Released: 2024-06-05 
• Deposition Author(s): Das, H., Hallberg, B.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Multi-compartmental diversification of neutralizing antibody lineages dissected in SARS-CoV-2 spike-immunized macaques.

Mandolesi, M., Das, H., de Vries, L., Yang, Y., Kim, C., Dhinakaran, M., Castro Dopico, X., Fischbach, J., Kim, S., Guryleva, M.V., Adori, M., Chernyshev, M., Stalmarck, A., Hanke, L., McInerney, G.M., Sheward, D.J., Corcoran, M., Hallberg, B.M., Murrell, B., Karlsson Hedestam, G.B.

(2024) Nat Commun 15: 6338-6338

• PubMed: 39068149 
• DOI: https://doi.org/10.1038/s41467-024-50286-0
• Primary Citation Related Structures: 
  8P5M, 8Q5Y


• PubMed Abstract: 
  

  The continued evolution of SARS-CoV-2 underscores the need to understand qualitative aspects of the humoral immune response elicited by spike immunization. Here, we combine monoclonal antibody (mAb) isolation with deep B cell receptor (BCR) repertoire sequencing of rhesus macaques immunized with prefusion-stabilized spike glycoprotein. Longitudinal tracing of spike-sorted B cell lineages in multiple immune compartments demonstrates increasing somatic hypermutation and broad dissemination of vaccine-elicited B cells in draining and non-draining lymphoid compartments, including the bone marrow, spleen and, most notably, periaortic lymph nodes. Phylogenetic analysis of spike-specific monoclonal antibody lineages identified through deep repertoire sequencing delineates extensive intra-clonal diversification that shaped neutralizing activity. Structural analysis of the spike in complex with a broadly neutralizing mAb provides a molecular basis for the observed differences in neutralization breadth between clonally related antibodies. Our findings highlight that immunization leads to extensive intra-clonal B cell evolution where members of the same lineage can both retain the original epitope specificity and evolve to recognize additional spike variants not previously encountered.

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Organizational Affiliation: 
• Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden. [e-mail].
Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 93.74 kDa 
• Atom Count: 3,258 
• Modeled Residue Count: 419 
• Deposited Residue Count: 852 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth I]	196	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mab-23 (Heavy chain variable domain)	B [auth G]	442	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mab-23 (Light chain variable domain)	C [auth L]	214	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19
RECONSTRUCTION	cryoSPARC	3.2.0
RECONSTRUCTION	cryoSPARC	4.1.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Das, H., Hallberg, B.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-05
  Type: Initial release
  
• Version 1.1: 2024-09-25
  Changes: Data collection, Source and taxonomy
• Version 1.2: 2024-10-23
  Changes: Data collection, Structure summary
• Version 1.3: 2024-12-18
  Changes: Data collection, Database references