7Y6T

Cryo-EM map of IPEC-J2 cell-derived PEDV PT52 S protein one D0-down and two D0-up


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

In situ structure and dynamics of an alphacoronavirus spike protein by cryo-ET and cryo-EM.

Huang, C.Y.Draczkowski, P.Wang, Y.S.Hsu, S.T.D.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinA,
C [auth B],
B [auth C]
1402Porcine epidemic diarrhea virusMutation(s): 2 
Gene Names: S
UniProt
Find proteins for A0A1Y0DD46 (Porcine epidemic diarrhea virus)
Explore A0A1Y0DD46 
Go to UniProtKB:  A0A1Y0DD46
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Y0DD46
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseBA [auth b],
D,
O
5N-Glycosylation Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
DA [auth d],
E,
F,
G,
GA [auth g],
DA [auth d],
E,
F,
G,
GA [auth g],
HA [auth h],
JA [auth j],
K,
Q,
T,
V,
X
3N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
EA [auth e],
H,
I,
IA [auth i],
J,
EA [auth e],
H,
I,
IA [auth i],
J,
L,
R,
U,
W,
Y
2N-Glycosylation Oligosaccharides Interaction
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseM, Z 3N-Glycosylation Oligosaccharides Interaction
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseAA [auth a],
KA [auth k],
N
4N-Glycosylation Oligosaccharides Interaction
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseCA [auth c],
FA [auth f],
P,
S
2N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth B],
BB [auth B],
CB [auth B],
LA [auth A],
MA [auth A],
AB [auth B],
BB [auth B],
CB [auth B],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth A],
PA [auth A],
QA [auth A],
RA [auth C],
SA [auth C],
TA [auth C],
UA [auth C],
VA [auth C],
WA [auth B],
XA [auth B],
YA [auth B],
ZA [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)TaiwanAS-CDA-109- L08
Academia Sinica (Taiwan)TaiwanAS-IDR- 110-08
Ministry of Science and Technology (MoST, Taiwan)TaiwanMOST 109-3114-Y-001-001
Ministry of Science and Technology (MoST, Taiwan)Taiwan110-2113-M-001- 050-MY3
Ministry of Science and Technology (MoST, Taiwan)Taiwan110-2311-B-001-013-MY3
Ministry of Science and Technology (MoST, Taiwan)TaiwanMOST 110-2811-B-001-560

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release