8DPZ | pdb_00008dpz

Local refinement of SARS-CoV-2 vaccine induced antibody DH1338 bound to SARS-CoV-2 HexaPro RBD Spike ectodomain

• PDB DOI: https://doi.org/10.2210/pdb8DPZ/pdb
• EM Map EMD-27644: EMDB EMDataResource

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


• Deposited: 2022-07-18 Released: 2023-08-02 
• Deposition Author(s): Stalls, V., May, A.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: 3.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Local refinement of SARS-CoV-2 vaccine induced antibody Ab026500 bound to SARS-CoV-2 HexaPro RBD Spike ectodomain

Stalls, V., Acharya, P., May, A.J., Malewana, D.

To be published.

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: electron microscopy

Macromolecule Content 

• Total Structure Weight: 49.26 kDa 
• Atom Count: 3,326 
• Modeled Residue Count: 420 
• Deposited Residue Count: 440 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth B]	205	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: 1		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DH1338 Fab Heavy Chain	B [auth F]	128	Macaca mulatta	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DH1338 Fab Light Chain	C [auth G]	107	Macaca mulatta	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	D [auth A]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-02 
Deposition Author(s): Stalls, V., May, A.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	R01 AI165947

Revision History  

• Version 1.0: 2023-08-02
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Refinement description, Structure summary
• Version 1.2: 2025-05-21
  Changes: Data collection