7FD2

Cryo-EM structure of an alphavirus, Getah virus

  • Classification: VIRUS
  • Organism(s): Getah virus
  • Mutation(s): No 

  • Deposited: 2021-07-15 Released: 2022-08-10 
  • Deposition Author(s): Liu, Z., Liu, C., Wang, A.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 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

Structure of infective Getah virus at 2.8 angstrom resolution determined by cryo-electron microscopy.

Wang, A.Zhou, F.Liu, C.Gao, D.Qi, R.Yin, Y.Liu, S.Gao, Y.Fu, L.Xia, Y.Xu, Y.Wang, C.Liu, Z.

(2022) Cell Discov 8: 12-12

  • DOI: https://doi.org/10.1038/s41421-022-00374-6
  • Primary Citation of Related Structures:  
    7FD2

  • PubMed Abstract: 

    Getah virus (GETV), a member of the genus alphavirus, is a mosquito-borne pathogen that can cause pyrexia and reproductive losses in animals. Although antibodies to GETV have been found in over 10% of healthy people, there are no reports of clinical symptoms associated with GETV. The biological and pathological properties of GETV are largely unknown and antiviral or vaccine treatments against GETV are still unavailable due to a lack of knowledge of the structure of the GETV virion. Here, we present the structure of infective GETV at a resolution of 2.8 Å with the atomic models of the capsid protein and the envelope glycoproteins E1 and E2. We have identified numerous glycosylation and S-acylation sites in E1 and E2. The surface-exposed glycans indicate a possible impact on viral immune evasion and host cell invasion. The S-acylation sites might be involved in stabilizing the transmembrane assembly of E1 and E2. In addition, a cholesterol and a phospholipid molecule are observed in a transmembrane hydrophobic pocket, together with two more cholesterols surrounding the pocket. The cholesterol and phospholipid stabilize the hydrophobic pocket in the viral envelope membrane. The structural information will assist structure-based antiviral and vaccine screening, design, and optimization.


  • Organizational Affiliation

    Cryo-electron Microscopy Center, Southern University of Science and Technology, Shenzhen, Guangdong, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein 1A,
D [auth E],
G [auth I],
J [auth M]
438Getah virusMutation(s): 0 
EC: 3.4.21.90
UniProt
Find proteins for Q5Y388 (Getah virus)
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Go to UniProtKB:  Q5Y388
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5Y388
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein 2B,
E [auth F],
H [auth J],
K [auth N]
419Getah virusMutation(s): 0 
EC: 3.4.21.90
UniProt
Find proteins for Q5Y388 (Getah virus)
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Go to UniProtKB:  Q5Y388
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UniProt GroupQ5Y388
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
capsid proteinC,
F [auth G],
I [auth K],
L [auth O]
268Getah virusMutation(s): 0 
EC: 3.4.21.90
UniProt
Find proteins for Q5Y388 (Getah virus)
Explore Q5Y388 
Go to UniProtKB:  Q5Y388
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UniProt GroupQ5Y388
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-glucopyranoseM [auth D],
P,
S,
V
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseN [auth H],
Q,
T,
W
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
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-glucopyranoseO [auth L],
R,
U,
X
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCW (Subject of Investigation/LOI)
Query on PCW

Download Ideal Coordinates CCD File 
DB [auth M],
JA [auth E],
TA [auth I],
Z [auth A]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
CA [auth B]
DA [auth B]
EA [auth B]
GB [auth N]
HB [auth N]
CA [auth B],
DA [auth B],
EA [auth B],
GB [auth N],
HB [auth N],
IB [auth N],
MA [auth F],
NA [auth F],
OA [auth F],
UA [auth I],
XA [auth J],
YA [auth J]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
STE (Subject of Investigation/LOI)
Query on STE

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth J]
EB [auth M]
GA [auth B]
KA [auth E]
AA [auth A],
AB [auth J],
EB [auth M],
GA [auth B],
KA [auth E],
KB [auth N],
QA [auth F],
WA [auth J]
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
PLM (Subject of Investigation/LOI)
Query on PLM

Download Ideal Coordinates CCD File 
BA [auth A]
BB [auth J]
FA [auth B]
FB [auth M]
HA [auth B]
BA [auth A],
BB [auth J],
FA [auth B],
FB [auth M],
HA [auth B],
JB [auth N],
LA [auth E],
LB [auth N],
PA [auth F],
RA [auth F],
VA [auth I],
ZA [auth J]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
CB [auth M],
IA [auth E],
SA [auth I],
Y [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: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2
RECONSTRUCTIONRELION3.0.8

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81870246
National Natural Science Foundation of China (NSFC)China82070329

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release