8CII

Delta-RBD complex with BA.2-07 fab, SARS1-34 fab and C1 nanobody

• PDB DOI: https://doi.org/10.2210/pdb8CII/pdb
• EM Map EMD-16676: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Homo sapiens, Lama glama
• Expression System: Homo sapiens, Cricetulus griseus, Escherichia coli
• Mutation(s): No 


• Deposited: 2023-02-09 Released: 2024-02-21 
• Deposition Author(s): Duyvesteyn, H.M.E., Ren, J., Stuart, D.I., Fry, E.E.
• Funding Organization(s): Wellcome Trust, Chinese Academy of Sciences, Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Potent cross-reactive mAbs from BA.4/5 breakthrough infection

Duyvesteyn, H.M.E., Screaton, G., Ren, J., Stuart, D.I., Fry, E.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 133.7 kDa 
• Atom Count: 9,024 
• Modelled Residue Count: 1,168 
• Deposited Residue Count: 1,219 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2'	A [auth E]	202	Homo sapiens	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
SARS1-34 fab Heavy Chain	B [auth H]	227	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS1-34 fab Light Chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
BA.2-07 fab Heavy Chain	D [auth A]	231	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
BA.2-07 fab Light Chain	E [auth B]	214	Homo sapiens	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
C1 nanobody	F [auth C]	131	Lama glama	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth D]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): Duyvesteyn, H.M.E., Ren, J., Stuart, D.I., Fry, E.E.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	203141/A/16/Z
Wellcome Trust	United Kingdom	101122/Z/13/Z
Chinese Academy of Sciences	China	2018-I2M-2-002
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N00065X/1

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Structure summary