7SOB

SARS-CoV-2 S B.1.617.1 kappa variant + S309 + S2L20 Global Refinement


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants.

McCallum, M.Walls, A.C.Sprouse, K.R.Bowen, J.E.Rosen, L.E.Dang, H.V.De Marco, A.Franko, N.Tilles, S.W.Logue, J.Miranda, M.C.Ahlrichs, M.Carter, L.Snell, G.Pizzuto, M.S.Chu, H.Y.Van Voorhis, W.C.Corti, D.Veesler, D.

(2021) Science 374: 1621-1626

  • DOI: https://doi.org/10.1126/science.abl8506
  • Primary Citation of Related Structures:  
    7SO9, 7SOA, 7SOB, 7SOC, 7SOD, 7SOE, 7SOF

  • PubMed Abstract: 

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission leads to the emergence of variants, including the B.1.617.2 (Delta) variant of concern that is causing a new wave of infections and has become globally dominant. We show that these variants dampen the in vitro potency of vaccine-elicited serum neutralizing antibodies and provide a structural framework for describing their immune evasion. Mutations in the B.1.617.1 (Kappa) and Delta spike glycoproteins abrogate recognition by several monoclonal antibodies via alteration of key antigenic sites, including remodeling of the Delta amino-terminal domain. The angiotensin-converting enzyme 2 binding affinities of the Kappa and Delta receptor binding domains are comparable to the Wuhan-Hu-1 isolate, whereas B.1.617.2+ (Delta+) exhibits markedly reduced affinity.


  • Organizational Affiliation

    Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinA,
F [auth D],
K
1,277Severe acute respiratory syndrome coronavirus 2Mutation(s): 16 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
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UniProt GroupP0DTC2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
S2L20 Fab light chainB,
G [auth E],
L
107Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
S2L20 Fab heavy chainC,
H [auth F],
M
121Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
S309 Fab heavy chainD [auth G],
I [auth H],
N
128Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
S309 Fab light chainE [auth I],
J,
O
100Homo sapiensMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth K]
BA [auth A]
BB [auth K]
CA [auth A]
AA [auth A],
AB [auth K],
BA [auth A],
BB [auth K],
CA [auth A],
CB [auth K],
DA [auth A],
DB [auth K],
EA [auth A],
EB [auth K],
FA [auth A],
FB [auth K],
GA [auth D],
GB [auth K],
HA [auth D],
HB [auth K],
IA [auth D],
IB [auth K],
JA [auth D],
JB [auth K],
KA [auth D],
KB [auth K],
LA [auth D],
LB [auth K],
MA [auth D],
MB [auth K],
NA [auth D],
NB [auth K],
OA [auth D],
P [auth A],
PA [auth D],
Q [auth A],
QA [auth D],
R [auth A],
RA [auth D],
S [auth A],
SA [auth D],
T [auth A],
TA [auth D],
U [auth A],
UA [auth D],
V [auth A],
VA [auth D],
W [auth A],
WA [auth D],
X [auth A],
XA [auth K],
Y [auth A],
YA [auth K],
Z [auth A],
ZA [auth K]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • 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