7SOD

SARS-CoV-2 S NTD B.1.617.1 kappa variant S2L20 Local Refinement

• PDB DOI: https://doi.org/10.2210/pdb7SOD/pdb
• EM Map EMD-25267: 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: 2021-10-29 Released: 2021-11-17 
• Deposition Author(s): McCallum, M., Veesler, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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: 168.68 kDa 
• Atom Count: 3,830 
• Modelled Residue Count: 473 
• Deposited Residue Count: 1,505 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S2L20 Fab light chain	A [auth L]	107	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S2L20 Fab heavy chain	B [auth H]	121	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth A]	1,277	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 16  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

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 B]	2	N/A	N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-17 
Deposition Author(s): McCallum, M., Veesler, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2021-11-24
  Changes: Database references
• Version 1.2: 2021-12-01
  Changes: Database references
• Version 1.3: 2022-01-05
  Changes: Database references