7V7H

Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1), dimer of S trimer 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


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1), dimer of S trimer conformation 1

Yang, T.J.Yu, P.Y.Chang, Y.C.Hsu, S.T.D.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C, D, E
A, B, C, D, E, F
1,283Severe acute respiratory syndrome coronavirus 2Mutation(s): 12 
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 Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
AB [auth 0],
BA [auth b],
BB [auth 1],
CA [auth c],
AA [auth a],
AB [auth 0],
BA [auth b],
BB [auth 1],
CA [auth c],
CB [auth 2],
DA [auth d],
DB [auth 3],
EA [auth e],
EB [auth 4],
FA [auth f],
FB [auth 5],
G,
GA [auth g],
H,
HA [auth h],
HB [auth 7],
I,
IB [auth 8],
J,
JA [auth j],
JB [auth 9],
KA [auth k],
KB [auth AA],
L,
LA [auth l],
LB [auth BA],
M,
MA [auth m],
MB [auth CA],
N,
NA [auth n],
NB [auth DA],
O,
OA [auth o],
OB [auth EA],
P,
PA [auth p],
PB [auth FA],
Q,
QA [auth q],
QB [auth GA],
R,
RA [auth r],
RB [auth HA],
S,
SA [auth s],
T,
TA [auth t],
TB [auth JA],
U,
UB [auth KA],
V,
VA [auth v],
VB [auth LA],
WA [auth w],
WB [auth MA],
X,
XA [auth x],
XB [auth NA],
Y,
YA [auth y],
YB [auth OA],
Z,
ZA [auth z],
ZB [auth PA]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
GB [auth 6],
IA [auth i],
K,
SB [auth IA],
UA [auth u],
GB [auth 6],
IA [auth i],
K,
SB [auth IA],
UA [auth u],
W
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AC [auth A]
BC [auth A]
CC [auth A]
DC [auth A]
EC [auth B]
AC [auth A],
BC [auth A],
CC [auth A],
DC [auth A],
EC [auth B],
FC [auth B],
GC [auth B],
HC [auth B],
IC [auth C],
JC [auth C],
KC [auth C],
LC [auth C],
MC [auth D],
NC [auth D],
OC [auth D],
PC [auth D],
QC [auth E],
RC [auth E],
SC [auth E],
TC [auth E],
UC [auth F],
VC [auth F],
WC [auth F],
XC [auth F]
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
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: 2021-10-06
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary