8DAD | pdb_00008dad

SARS-CoV-2 receptor binding domain in complex with AZ090 Fab

• PDB DOI: https://doi.org/10.2210/pdb8DAD/pdb
• EM Map EMD-27270: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2022-06-13 Released: 2022-08-24 
• Deposition Author(s): Zong, S., Wang, Z., Gaebler, C., Nussenzweig, M.
• 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: 3.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

SARS-CoV-2 receptor binding domain in complex with AZ090 Fab

Zong, S.

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: 165.77 kDa 
• Atom Count: 3,255 
• Modeled Residue Count: 424 
• Deposited Residue Count: 1,486 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AZ090 Fab Heavy Chain	A [auth H]	123	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AZ090 Fab Light Chain	B [auth L]	107	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth B]	1,256	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 6  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

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth J], E [auth A]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Zong, S., Wang, Z., Gaebler, C., Nussenzweig, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	2U19AI111825

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2022-08-31
  Changes: Structure summary
• Version 1.2: 2024-10-30
  Changes: Data collection, Structure summary
• Version 1.3: 2025-05-14
  Changes: Data collection