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- PDB-7lih: CryoEM structure of Mayaro virus icosahedral subunit -

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Basic information

Entry
Database: PDB / ID: 7lih
TitleCryoEM structure of Mayaro virus icosahedral subunit
Components
  • Capsid proteinCapsid
  • E1 protein
  • E2 protein
KeywordsVIRAL PROTEIN / alphavirus / togavirus / enveloped virus / pathogen
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / membrane => GO:0016020 / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / membrane => GO:0016020 / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Togavirin / Togavirin / Structural polyprotein
Similarity search - Component
Biological speciesMayaro virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsChmielewski, D. / Kaelber, J.T. / Jin, J. / Weaver, S. / Auguste, A.J. / Chiu, W.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI120943 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P41GM103832 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K22AI125474 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI153433 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R24AI120942 United States
CitationJournal: To Be Published
Title: Near-atomic resolution Cryo-EM structure of Mayaro virus identifies key structural determinants of alphavirus particle formation
Authors: Chmielewski, D. / Kaelber, J.T. / Jin, J. / Weaver, S. / Auguste, A.J. / Chiu, W.
History
DepositionJan 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author
Item: _audit_author.name / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
F: Capsid protein
T: E1 protein
M: E2 protein
A: Capsid protein
H: E1 protein
D: E2 protein
B: Capsid protein
I: E1 protein
E: E2 protein
C: Capsid protein
J: E1 protein
G: E2 protein


Theoretical massNumber of molelcules
Total (without water)441,29412
Polymers441,29412
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area33680 Å2
ΔGint-186 kcal/mol
Surface area227750 Å2

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Components

#1: Protein
Capsid protein / Capsid


Mass: 17596.111 Da / Num. of mol.: 4 / Fragment: UNP residues 99-258 / Source method: isolated from a natural source / Source: (natural) Mayaro virus / References: UniProt: Q8QZ72
#2: Protein
E1 protein


Mass: 47182.426 Da / Num. of mol.: 4 / Fragment: UNP residues 807-1241 / Source method: isolated from a natural source / Source: (natural) Mayaro virus / References: UniProt: A0A0P0CE34
#3: Protein
E2 protein


Mass: 45544.910 Da / Num. of mol.: 4 / Fragment: UNP residues 331-740 / Source method: isolated from a natural source / Source: (natural) Mayaro virus / References: UniProt: A0A0P0BWJ4

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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

ComponentName: Mayaro virusMayaro virus disease / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mayaro virus
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Virus shellDiameter: 700 nm / Triangulation number (T number): 4
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 35 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1EMAN2particle selection
4jsprCTF correction
10jsprinitial Euler assignment
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 22314
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12219 / Symmetry type: POINT

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