[English] 日本語
Yorodumi
- EMDB-22961: Cryo-EM structure of the mature and infective Mayaro virus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22961
TitleCryo-EM structure of the mature and infective Mayaro virus
Map dataCryo-EM of the mature and infective Mayaro virus
Sample
  • Virus: Mayaro virus
Biological speciesMayaro virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsRibeiro Filho H / Coimbra LD / Cassago A / Rocha RFP / Padilha AC / Trivella DBB / Schatz M / Oliveira PSL / Portugal RV / Marques RE / van Heel M
Funding support Brazil, 3 items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2017/15340-2 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)440379/2016-4 Brazil
Sao Paulo Research Foundation (FAPESP)2018/03917-6 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 5, 2020-
Header (metadata) releaseApr 21, 2021-
Map releaseApr 21, 2021-
UpdateJun 9, 2021-
Current statusJun 9, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ko8
  • Surface level: 1.9
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ko8
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22961.png

Downloads & links

-
Map

FileDownload / File: emd_22961.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of the mature and infective Mayaro virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 800 pix.
= 885.92 Å		1.11 Å/pix.
x 800 pix.
= 885.92 Å		1.11 Å/pix.
x 800 pix.
= 885.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.9 / Movie #1: 1.9
Minimum - Maximum-7.5376306 - 9.131372
Average (Standard dev.)-3.04169e-05 (±0.55280685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 885.9199 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.10741.10741.1074
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z885.920885.920885.920
α/β/γ90.00090.00090.000
start NX/NY/NZ727265
NX/NY/NZ157157169
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS800800800
D min/max/mean-7.5389.131-0.000

-
Supplemental data

-
Sample components

-
Entire : Mayaro virus

EntireName: Mayaro virus
Components
  • Virus: Mayaro virus

-
Supramolecule #1: Mayaro virus

SupramoleculeName: Mayaro virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 59301 / Sci species name: Mayaro virus / Sci species strain: IQT4235 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Cs corrrector used to minimise the spherical aberration
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 9100 / Average exposure time: 4.26 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0 mm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 79000
CTF correctionSoftware - Name: IMAGIC (ver. 2019) / Software - details: Full data set CTF correction
Details: Per particle CTF correction based on IMAGIC movie spectra of all images simultaneously (Full data set CTF correction).
Startup modelType of model: OTHER / Details: Angular Reconstitution random startup
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 1/2 BIT CUT-OFF / Software - Name: IMAGIC (ver. 2019) / Software - details: with software extensions
Details: Random assignment of 3D membership to multiple 3D reconstructions during refinements, based on angular reconstitution.
Number images used: 40179
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC (ver. 2019)
Details: Angular reconstitution used originally in random startup mode, later in refinement mode using anchor sets
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC (ver. 2019)
Details: Angular reconstitution in refinement mode using anchor sets and local alignments
Final 3D classificationNumber classes: 30 / Avg.num./class: 1 / Software - Name: IMAGIC (ver. 2019)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more