8I9B

S-ECD (Omicron BA.2.75) in complex with PD of ACE2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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 structures of SARS-CoV-2 BA.2-derived subvariants spike in complex with ACE2 receptor.

Li, Y.Ren, C.Shen, Y.Zhang, Y.Chen, J.Zheng, J.Tian, R.Cao, L.Yan, R.

(2023) Cell Discov 9: 108-108


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,268Severe acute respiratory syndrome coronavirus 2Mutation(s): 44 
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Processed angiotensin-converting enzyme 2D [auth F],
E [auth D],
F [auth E]
624Homo sapiensMutation(s): 0 
Gene Names: ACE2UNQ868/PRO1885
EC: 3.4.17 (UniProt), 3.4.17.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens)
Explore Q9BYF1 
Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1
GTEx:  ENSG00000130234 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYF1
Glycosylation
Glycosylation Sites: 6Go to GlyGen: Q9BYF1-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D 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],
DA [auth d],
EA [auth e],
AA [auth a],
BA [auth b],
CA [auth c],
DA [auth d],
EA [auth e],
FA [auth f],
G,
GA [auth g],
H,
HA [auth h],
I,
IA [auth i],
J,
JA [auth j],
K,
KA [auth k],
L,
LA [auth l],
M,
MA [auth m],
N,
NA [auth n],
O,
OA [auth o],
P,
PA [auth p],
Q,
QA [auth q],
R,
S,
T,
U,
V,
W,
X,
Y,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
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 
AB [auth A]
BB [auth B]
CB [auth B]
DB [auth B]
EB [auth B]
AB [auth A],
BB [auth B],
CB [auth B],
DB [auth B],
EB [auth B],
FB [auth B],
GB [auth B],
HB [auth B],
IB [auth B],
JB [auth C],
KB [auth C],
LB [auth C],
MB [auth C],
NB [auth C],
OB [auth C],
PB [auth C],
QB [auth C],
RA [auth A],
RB [auth F],
SA [auth A],
SB [auth D],
TA [auth A],
TB [auth E],
UA [auth A],
VA [auth A],
WA [auth A],
XA [auth A],
YA [auth A],
ZA [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2020YFA0509301

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Data collection, Database references