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 7SO9

SARS-CoV-2 S B.1.617.2 delta variant + S2M11 + 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 1.4 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

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, F, K
1,275Severe acute respiratory syndrome coronavirus 2Mutation(s): 15 
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: 16Go to GlyGen: P0DTC2-1
Sequence AnnotationsExpand
  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
S2M11 Fab light chainB [auth D],
G,
L
104Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
S2M11 Fab heavy chainC [auth E],
H,
M
122Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
S2L20 Fab light chainD [auth B],
I,
N
107Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
S2L20 Fab heavy chainE [auth C],
J,
O
121Homo sapiensMutation(s): 0 
Entity Groups  
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
P, Q, R
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
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 A],
GB [auth K],
HA [auth F],
HB [auth K],
IA [auth F],
IB [auth K],
JA [auth F],
JB [auth K],
KA [auth F],
KB [auth K],
LA [auth F],
MA [auth F],
NA [auth F],
OA [auth F],
PA [auth F],
QA [auth F],
RA [auth F],
S [auth A],
SA [auth F],
T [auth A],
TA [auth F],
U [auth A],
UA [auth F],
V [auth A],
VA [auth F],
W [auth A],
WA [auth K],
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
  • Version 1.4: 2024-11-20
    Changes: Data collection, Structure summary