7Q0I

Crystal structure of the N-terminal domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-43


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.

Liu, C.Zhou, D.Nutalai, R.Duyvesteyn, H.M.E.Tuekprakhon, A.Ginn, H.M.Dejnirattisai, W.Supasa, P.Mentzer, A.J.Wang, B.Case, J.B.Zhao, Y.Skelly, D.T.Chen, R.E.Johnson, S.A.Ritter, T.G.Mason, C.Malik, T.Temperton, N.Paterson, N.G.Williams, M.A.Hall, D.R.Clare, D.K.Howe, A.Goulder, P.J.R.Fry, E.E.Diamond, M.S.Mongkolsapaya, J.Ren, J.Stuart, D.I.Screaton, G.R.

(2022) Cell Host Microbe 30: 53

  • DOI: https://doi.org/10.1016/j.chom.2021.11.013
  • Primary Citation of Related Structures:  
    7PRY, 7PRZ, 7PS0, 7PS1, 7PS2, 7PS3, 7PS4, 7PS5, 7PS6, 7PS7, 7Q0G, 7Q0H, 7Q0I, 7Q6E, 7Q9F, 7Q9G, 7Q9I, 7Q9J, 7Q9K, 7Q9M, 7Q9P

  • PubMed Abstract: 

    Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape from natural or vaccine-induced immunity. Beta is particularly difficult to neutralize using serum induced by early pandemic SARS-CoV-2 strains and is most antigenically separated from Delta. To understand this, we generated 674 mAbs from Beta-infected individuals and performed a detailed structure-function analysis of the 27 most potent mAbs: one binding the spike N-terminal domain (NTD), the rest the receptor-binding domain (RBD). Two of these RBD-binding mAbs recognize a neutralizing epitope conserved between SARS-CoV-1 and -2, while 18 target mutated residues in Beta: K417N, E484K, and N501Y. There is a major response to N501Y, including a public IgVH4-39 sequence, with E484K and K417N also targeted. Recognition of these key residues underscores why serum from Beta cases poorly neutralizes early pandemic and Delta viruses.


  • Organizational Affiliation

    Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-43 heavy chainA [auth H],
C [auth A]
231Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-43 Fab light chainB [auth L],
D [auth B]
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1E [auth D],
F [auth C]
311Severe acute respiratory syndrome coronavirus 2Mutation(s): 4 
Gene Names: S2
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: 7Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth E],
I [auth G]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth F]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth I]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(4-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth J]2N/AN-Glycosylation
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
DA [auth C]
W [auth D]
X [auth D]
BA [auth C],
CA [auth C],
DA [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4
Query on PG4

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AA [auth D]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

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O [auth L]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

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V [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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P [auth L],
R [auth A],
U [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth H]
M [auth H]
N [auth H]
Q [auth L]
S [auth A]
L [auth H],
M [auth H],
N [auth H],
Q [auth L],
S [auth A],
T [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.83α = 90
b = 66.964β = 92.544
c = 143.238γ = 90
Software Package:
Software NamePurpose
GDAdata collection
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CAMS Innovation Fund for Medical Sciences (CIFMS)United Kingdom2018-I2M-2-002
Medical Research Council (MRC, United Kingdom)United KingdomMR/N00065X/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2021-12-29
    Changes: Database references
  • Version 1.2: 2022-01-26
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description