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 7EDF | pdb_00007edf

Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7), one RBD-up conformation 1


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 7EDF

This is version 1.3 of the entry. See complete history. 

Literature

Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function.

Yang, T.J., Yu, P.Y., Chang, Y.C., Liang, K.H., Tso, H.C., Ho, M.R., Chen, W.Y., Lin, H.T., Wu, H.C., Hsu, S.D.

(2021) Nat Struct Mol Biol 28: 731-739

  • DOI: https://doi.org/10.1038/s41594-021-00652-z
  • Primary Citation Related Structures: 
    7EDF, 7EDG, 7EDH, 7EDI, 7EDJ, 7EH5

  • PubMed Abstract: 

    The B.1.1.7 variant of SARS-CoV-2 first detected in the UK harbors amino-acid substitutions and deletions in the spike protein that potentially enhance host angiotensin conversion enzyme 2 (ACE2) receptor binding and viral immune evasion. Here we report cryo-EM structures of the spike protein of B.1.1.7 in the apo and ACE2-bound forms. The apo form showed one or two receptor-binding domains (RBDs) in the open conformation, without populating the fully closed state. All three RBDs were engaged in ACE2 binding. The B.1.1.7-specific A570D mutation introduces a molecular switch that could modulate the opening and closing of the RBD. The N501Y mutation introduces a π-π interaction that enhances RBD binding to ACE2 and abolishes binding of a potent neutralizing antibody (nAb). Cryo-EM also revealed how a cocktail of two nAbs simultaneously bind to all three RBDs, and demonstrated the potency of the nAb cocktail to neutralize different SARS-CoV-2 pseudovirus strains, including B.1.1.7.


  • Organizational Affiliation: 
    • Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 445.47 kDa 
  • Atom Count: 25,090 
  • Modeled Residue Count: 3,065 
  • Deposited Residue Count: 3,858 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,286Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 16Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
BA [auth b],
CA [auth c],
D,
DA [auth d],
AA [auth a],
BA [auth b],
CA [auth c],
D,
DA [auth d],
EA [auth e],
F,
FA [auth f],
G,
GA [auth g],
H,
HA [auth h],
I,
IA [auth i],
J,
JA [auth j],
K,
L,
M,
N,
O,
P,
Q,
R,
S,
T,
U,
V,
W,
X,
Y,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
KA [auth A]
LA [auth A]
MA [auth A]
NA [auth A]
OA [auth B]
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth B],
PA [auth B],
QA [auth B],
RA [auth B],
SA [auth B],
TA [auth B],
UA [auth C],
VA [auth C],
WA [auth C],
XA [auth C],
YA [auth C]
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 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan109-3114-Y-001-001
Academia Sinica (Taiwan)TaiwanAS-CDA-109-L08
Academia Sinica (Taiwan)TaiwanAS-CFII-108-110
Academia Sinica (Taiwan)TaiwanAS-CFII108-111

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2022-01-05
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-06-25
    Changes: Data collection