8TC5

Cryo-EM Structure of Spike Glycoprotein from Civet Coronavirus SZ3 in Closed Conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.11 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 reveals variation in structural motifs within animal SARS-related coronavirus spike proteins

Bostina, M.Hills, F.R.Eruera, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,106Civet SARS CoV SZ3/2003Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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
D,
E,
F,
I [auth 5],
IA [auth f],
D,
E,
F,
I [auth 5],
IA [auth f],
L [auth I],
W [auth T]
2N-Glycosylation
Entity ID: 3
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-glucopyranose
BA [auth Y],
EA [auth b],
FA [auth c],
G [auth p],
H [auth 2],
BA [auth Y],
EA [auth b],
FA [auth c],
G [auth p],
H [auth 2],
LA [auth i],
NA [auth k],
P [auth M],
S [auth P],
T [auth Q],
Z [auth W]
3N-Glycosylation
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
DA [auth a],
GA [auth d],
J [auth G],
JA [auth g],
M [auth J],
DA [auth a],
GA [auth d],
J [auth G],
JA [auth g],
M [auth J],
PA [auth m],
R [auth O],
U [auth R],
X [auth U]
4N-Glycosylation
Entity ID: 5
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
AA [auth X],
HA [auth e],
K [auth H],
MA [auth j],
O [auth L],
AA [auth X],
HA [auth e],
K [auth H],
MA [auth j],
O [auth L],
V [auth S]
3N-Glycosylation
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
CA [auth Z],
KA [auth h],
N [auth K],
OA [auth l],
Q [auth N],
CA [auth Z],
KA [auth h],
N [auth K],
OA [auth l],
Q [auth N],
Y [auth V]
5N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EIC
Query on EIC

Download Ideal Coordinates CCD File 
RA [auth A],
VA [auth B],
YA [auth B]
LINOLEIC ACID
C18 H32 O2
OYHQOLUKZRVURQ-HZJYTTRNSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth C]
BB [auth C]
QA [auth A]
SA [auth A]
TA [auth A]
AB [auth C],
BB [auth C],
QA [auth A],
SA [auth A],
TA [auth A],
UA [auth B],
WA [auth B],
XA [auth B],
ZA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateNew Zealand--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Source and taxonomy