8P5M

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

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

Das, H., Hallberg, B.M.

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: gel filtration

Macromolecule Content

• Total Structure Weight: 93.74 kDa 
• Atom Count: 3,258 
• Modelled 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