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- PDB-7eak: Echovirus3 full particle in complex with 5G3 fab -

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Basic information

Entry
Database: PDB / ID: 7eak
TitleEchovirus3 full particle in complex with 5G3 fab
Components
  • (Capsid protein ...) x 4
  • heavy chain of 5G3 fab
  • light chain of 5G3 fab
KeywordsVIRUS / Echovirus3 / full particle / 5G3 fab
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MYRISTIC ACID / SPHINGOSINE / Genome polyprotein
Similarity search - Component
Biological speciesEchovirus E3
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsFeng, R.
CitationJournal: Cell Discov / Year: 2021
Title: Structural basis for neutralization of an anicteric hepatitis associated echovirus by a potent neutralizing antibody.
Authors: Rui Feng / Lei Wang / Dawei Shi / Binyang Zheng / Li Zhang / Hai Hou / Deju Xia / Lunbiao Cui / Xiangxi Wang / Sihong Xu / Kang Wang / Ling Zhu /
History
DepositionMar 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-31046
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  • Superimposition on EM map
  • EMDB-31046
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
F: heavy chain of 5G3 fab
L: light chain of 5G3 fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,3638
Polymers120,8356
Non-polymers5282
Water00
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
F: heavy chain of 5G3 fab
L: light chain of 5G3 fab
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,281,756480
Polymers7,250,084360
Non-polymers31,672120
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
F: heavy chain of 5G3 fab
L: light chain of 5G3 fab
hetero molecules
x 5


  • icosahedral pentamer
  • 607 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)606,81340
Polymers604,17430
Non-polymers2,63910
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
F: heavy chain of 5G3 fab
L: light chain of 5G3 fab
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 728 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)728,17648
Polymers725,00836
Non-polymers3,16712
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Capsid protein ... , 4 types, 4 molecules ABCD

#1: Protein Capsid protein VP1


Mass: 32801.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E3 / References: UniProt: A0A6M4MJE3
#2: Protein Capsid protein VP2


Mass: 29221.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E3 / References: UniProt: A0A6M4MJE3
#3: Protein Capsid protein VP3


Mass: 26281.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E3 / References: UniProt: A0A6M4MJE3
#4: Protein Capsid protein VP4


Mass: 7402.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E3 / References: UniProt: A0A6M4MJE3

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Antibody , 2 types, 2 molecules FL

#5: Antibody heavy chain of 5G3 fab


Mass: 12298.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#6: Antibody light chain of 5G3 fab


Mass: 12828.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 2 types, 2 molecules

#7: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#8: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Echovirus E3 in complex with 5G3 fabCOMPLEX#2-#3, #5-#60NATURAL
2Echovirus E3COMPLEX#2-#3, #5-#61NATURAL
35G3 fabCOMPLEX#5-#61NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Echovirus E347516
23Mus musculus (house mouse)10090
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70559 / Symmetry type: POINT

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