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- EMDB-21532: Native Mayaro virus cryo EM map, resolution 4.8 Angstroms -

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Basic information

Entry
Database: EMDB / ID: EMD-21532
TitleNative Mayaro virus cryo EM map, resolution 4.8 Angstroms
Map datamasked not sharpened
Sample
  • Complex: Native Mayaro Virus
    • Complex: Mayaro virus
      • Protein or peptide: Spike glycoprotein E1
      • Protein or peptide: Spike glycoprotein E2
Keywordsvirus
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 / 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 ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / 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 / structural molecule activity / virion membrane / proteolysis / RNA binding / membrane
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
Structural polyprotein
Similarity search - Component
Biological speciesMayaro virus / Mayaro virus (strain Brazil)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsMiller AS / Kuhn RJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Cell Host Microbe / Year: 2020
Title: Human mAbs Broadly Protect against Arthritogenic Alphaviruses by Recognizing Conserved Elements of the Mxra8 Receptor-Binding Site.
Authors: Laura A Powell / Andrew Miller / Julie M Fox / Nurgun Kose / Thomas Klose / Arthur S Kim / Robin Bombardi / Rashika N Tennekoon / A Dharshan de Silva / Robert H Carnahan / Michael S Diamond ...Authors: Laura A Powell / Andrew Miller / Julie M Fox / Nurgun Kose / Thomas Klose / Arthur S Kim / Robin Bombardi / Rashika N Tennekoon / A Dharshan de Silva / Robert H Carnahan / Michael S Diamond / Michael G Rossmann / Richard J Kuhn / James E Crowe /
Abstract: Mosquito inoculation of humans with arthritogenic alphaviruses results in a febrile syndrome characterized by debilitating musculoskeletal pain and arthritis. Despite an expanding global disease ...Mosquito inoculation of humans with arthritogenic alphaviruses results in a febrile syndrome characterized by debilitating musculoskeletal pain and arthritis. Despite an expanding global disease burden, no approved therapies or licensed vaccines exist. Here, we describe human monoclonal antibodies (mAbs) that bind to and neutralize multiple distantly related alphaviruses. These mAbs compete for an antigenic site and prevent attachment to the recently discovered Mxra8 alphavirus receptor. Three cryoelectron microscopy structures of Fab in complex with Ross River (RRV), Mayaro, or chikungunya viruses reveal a conserved footprint of the broadly neutralizing mAb RRV-12 in a region of the E2 glycoprotein B domain. This mAb neutralizes virus in vitro by preventing virus entry and spread and is protective in vivo in mouse models. Thus, the RRV-12 mAb and its defined epitope have potential as a therapeutic agent or target of vaccine design against multiple emerging arthritogenic alphavirus infections.
History
DepositionMar 8, 2020-
Header (metadata) releaseApr 8, 2020-
Map releaseOct 7, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 8.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6w2u
  • Surface level: 8.7
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6w2u
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21532.png

Downloads & links

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Map

FileDownload / File: emd_21532.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmasked not sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.62 Å/pix.
x 640 pix.
= 1036.8 Å		1.62 Å/pix.
x 640 pix.
= 1036.8 Å		1.62 Å/pix.
x 640 pix.
= 1036.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.699999999999999 / Movie #1: 8.7
Minimum - Maximum-16.887533000000001 - 22.502775
Average (Standard dev.)0.0731104 (±1.7308351)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-320-320-320
Dimensions640640640
Spacing640640640
CellA=B=C: 1036.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.621.621.62
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z1036.8001036.8001036.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ162182277
MAP C/R/S123
start NC/NR/NS-320-320-320
NC/NR/NS640640640
D min/max/mean-16.88822.5030.073

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Supplemental data

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Half map: half map not sharpened

Fileemd_21532_half_map_1.map
Annotationhalf map not sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map not sharpened

Fileemd_21532_half_map_2.map
Annotationhalf map not sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Native Mayaro Virus

EntireName: Native Mayaro Virus
Components
  • Complex: Native Mayaro Virus
    • Complex: Mayaro virus
      • Protein or peptide: Spike glycoprotein E1
      • Protein or peptide: Spike glycoprotein E2

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Supramolecule #1: Native Mayaro Virus

SupramoleculeName: Native Mayaro Virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Mayaro virus

SupramoleculeName: Mayaro virus / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Mayaro virus

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Macromolecule #1: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mayaro virus (strain Brazil) / Strain: Brazil
Molecular weightTheoretical: 41.612867 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: YEHTAIIPNQ VGFPYKAHVA REGYSPLTLQ MQVIETSLEP TLNLEYITCD YKTKVPSPYV KCCGTAECRT QDKPEYKCAV FTGVYPFMW GGAYCFCDSE NTQMSEAYVE RADVCKHDHA AAYRAHTASL RAKIKVTYGT VNQTVEAYVN GDHAVTIAGT K FIFGPVST ...String:
YEHTAIIPNQ VGFPYKAHVA REGYSPLTLQ MQVIETSLEP TLNLEYITCD YKTKVPSPYV KCCGTAECRT QDKPEYKCAV FTGVYPFMW GGAYCFCDSE NTQMSEAYVE RADVCKHDHA AAYRAHTASL RAKIKVTYGT VNQTVEAYVN GDHAVTIAGT K FIFGPVST PWTPFDTKIL VYKGELYNQD FPRYGAGQPG RFGDIQSRTL DSRDLYANTG LKLARPAAGN IHVPYTQTPS GF KTWQKDR DSPLNAKAPF GCIIQTNPVR AMNCAVGNIP VSMDIADSAF TRLTDAPVIS ELTCTVSTCT HSSDFGGIAV LSY KVEKSG RCDIHSHSNV AVLQEVSIET EGRSVIHFST ASASPSFVVS VCSSRATCTA KCEP

UniProtKB: Structural polyprotein

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Macromolecule #2: Spike glycoprotein E2

MacromoleculeName: Spike glycoprotein E2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mayaro virus (strain Brazil) / Strain: Brazil
Molecular weightTheoretical: 38.041957 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: STANHFNAYK LTRPYVAYCA DCGMGHSCHS PAMIENIQAD ATDGTLKIQF ASQIGLTKTD THDHTKIRYA EGHDIAEAAR STLKVHSSS ECTVTGTMGH FILAKCPPGE RISVSFVDSK NEHRTCRIAY HHEQRLIGRE RFTVRPHHGI ELPCTTYQLT T AETSEEID ...String:
STANHFNAYK LTRPYVAYCA DCGMGHSCHS PAMIENIQAD ATDGTLKIQF ASQIGLTKTD THDHTKIRYA EGHDIAEAAR STLKVHSSS ECTVTGTMGH FILAKCPPGE RISVSFVDSK NEHRTCRIAY HHEQRLIGRE RFTVRPHHGI ELPCTTYQLT T AETSEEID MHMPPDIPDR TILSQQSGNV KITVNGRTVR YSSSCGSQAV GTTTTDKTIN SCTVDKCQAY VTSHTKWQFN SP FVPRRMQ AERKGKVHIP FPLINTTCRV PLAPEALVRS GKREATLSLH PIHPTLLSYR TFGAERVFDE QWITAQTEVT IPV PVEGVE YQWGNHKPQR FVVA

UniProtKB: Structural polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
GridModel: C-flat / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 18000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 18410
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING / Software - Name: jspr

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6w2u:
Mayaro Virus glycoprotein E1 ectodomain and glycoportien E2 ectodomain asymmetric unit

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