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- PDB-7ko8: Cryo-EM structure of the mature and infective Mayaro virus -

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Basic information

Entry
Database: PDB / ID: 7ko8
TitleCryo-EM structure of the mature and infective Mayaro virus
Components
  • Capsid protein
  • E1 glycoprotein
  • E2 glycoprotein
KeywordsVIRUS / alphavirus / mayaro virus / single particle cryo-EM / mature and infective viral particle
Biological speciesMayaro virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsRiberio-Filho, H.V. / Coimbra, L.D. / Cassago, A. / Rocha, R.P.F. / Padilha, A.C.M. / Schatz, M. / van Heel, M.G. / Portugal, R.V. / Trivella, D.B.B. / de Oliveira, P.S.L. / Marques, R.E.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2018/03917-6 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)440379/2016-4 Brazil
Sao Paulo Research Foundation (FAPESP)2018/00629 Brazil
Sao Paulo Research Foundation (FAPESP)2017/15340-2 Brazil
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM structure of the mature and infective Mayaro virus at 4.4 Å resolution reveals features of arthritogenic alphaviruses.
Authors: Helder V Ribeiro-Filho / Lais D Coimbra / Alexandre Cassago / Rebeca P F Rocha / João Victor da Silva Guerra / Rafael de Felicio / Carolina Moretto Carnieli / Luiza Leme / Antonio Cláudio ...Authors: Helder V Ribeiro-Filho / Lais D Coimbra / Alexandre Cassago / Rebeca P F Rocha / João Victor da Silva Guerra / Rafael de Felicio / Carolina Moretto Carnieli / Luiza Leme / Antonio Cláudio Padilha / Adriana F Paes Leme / Daniela B B Trivella / Rodrigo Villares Portugal / Paulo Sérgio Lopes-de-Oliveira / Rafael Elias Marques /
Abstract: Mayaro virus (MAYV) is an emerging arbovirus of the Americas that may cause a debilitating arthritogenic disease. The biology of MAYV is not fully understood and largely inferred from related ...Mayaro virus (MAYV) is an emerging arbovirus of the Americas that may cause a debilitating arthritogenic disease. The biology of MAYV is not fully understood and largely inferred from related arthritogenic alphaviruses. Here, we present the structure of MAYV at 4.4 Å resolution, obtained from a preparation of mature, infective virions. MAYV presents typical alphavirus features and organization. Interactions between viral proteins that lead to particle formation are described together with a hydrophobic pocket formed between E1 and E2 spike proteins and conformational epitopes specific of MAYV. We also describe MAYV glycosylation residues in E1 and E2 that may affect MXRA8 host receptor binding, and a molecular "handshake" between MAYV spikes formed by N262 glycosylation in adjacent E2 proteins. The structure of MAYV is suggestive of structural and functional complexity among alphaviruses, which may be targeted for specificity or antiviral activity.
History
DepositionNov 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.name ..._pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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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
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein
B: E1 glycoprotein
C: E2 glycoprotein
D: Capsid protein
E: E1 glycoprotein
F: E2 glycoprotein
G: Capsid protein
H: E1 glycoprotein
I: E2 glycoprotein
J: Capsid protein
L: E1 glycoprotein
M: E2 glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)499,36720
Polymers493,53912
Non-polymers5,8278
Water00
1
A: Capsid protein
B: E1 glycoprotein
C: E2 glycoprotein
D: Capsid protein
E: E1 glycoprotein
F: E2 glycoprotein
G: Capsid protein
H: E1 glycoprotein
I: E2 glycoprotein
J: Capsid protein
L: E1 glycoprotein
M: E2 glycoprotein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)29,962,0021200
Polymers29,612,363720
Non-polymers349,639480
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein
B: E1 glycoprotein
C: E2 glycoprotein
D: Capsid protein
E: E1 glycoprotein
F: E2 glycoprotein
G: Capsid protein
H: E1 glycoprotein
I: E2 glycoprotein
J: Capsid protein
L: E1 glycoprotein
M: E2 glycoprotein
hetero molecules
x 5


  • icosahedral pentamer
  • 2.5 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)2,496,834100
Polymers2,467,69760
Non-polymers29,13740
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: E1 glycoprotein
C: E2 glycoprotein
D: Capsid protein
E: E1 glycoprotein
F: E2 glycoprotein
G: Capsid protein
H: E1 glycoprotein
I: E2 glycoprotein
J: Capsid protein
L: E1 glycoprotein
M: E2 glycoprotein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 3 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)2,996,200120
Polymers2,961,23672
Non-polymers34,96448
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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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Protein , 3 types, 12 molecules ADGJBEHLCFIM

#1: Protein
Capsid protein


Mass: 29399.160 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mayaro virus / Strain: IQT4235
#2: Protein
E1 glycoprotein


Mass: 47339.621 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mayaro virus / Strain: IQT4235
#3: Protein
E2 glycoprotein


Mass: 46646.066 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mayaro virus / Strain: IQT4235

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Sugars , 3 types, 8 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Details

Has ligand of interestY
Has protein modificationY

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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 virus / Type: VIRUS / Details: Mayaro virus was purified from Vero CCL81 cells. / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Mayaro virus
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM softwareName: IMAGIC / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 1/2 BIT CUT-OFF / Num. of particles: 40179 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00631925
ELECTRON MICROSCOPYf_angle_d0.95743541
ELECTRON MICROSCOPYf_dihedral_angle_d20.06819050
ELECTRON MICROSCOPYf_chiral_restr0.0585048
ELECTRON MICROSCOPYf_plane_restr0.0075544

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