[English] 日本語
Yorodumi
- EMDB-27248: Sub-tomogram averaged map of full-length post-fusion CHIKV E1 gly... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27248
TitleSub-tomogram averaged map of full-length post-fusion CHIKV E1 glycoprotein trimer
Map dataSub-tomogram averaged map of membrane attached full-length post-fusion CHIKV E1 glycoprotein trimer
Sample
  • Complex: Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer from Chikungunya virus
    • Protein or peptide: Spike glycoprotein E1
  • Ligand: BROMIDE IONBromide
  • Ligand: HOLMIUM ATOM
  • Ligand: PHOSPHATE IONPhosphate
  • Ligand: water
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope ...togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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 speciesChikungunya virus strain S27-African prototype
Methodsubtomogram averaging / cryo EM / Resolution: 27.2 Å
AuthorsMangala Prasad V / Lee KK
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM099989 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
CitationJournal: Nat Commun / Year: 2022
Title: Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery.
Authors: Vidya Mangala Prasad / Jelle S Blijleven / Jolanda M Smit / Kelly K Lee /
Abstract: Chikungunya virus (CHIKV) is a human pathogen that delivers its genome to the host cell cytoplasm through endocytic low pH-activated membrane fusion mediated by class-II fusion proteins. Though ...Chikungunya virus (CHIKV) is a human pathogen that delivers its genome to the host cell cytoplasm through endocytic low pH-activated membrane fusion mediated by class-II fusion proteins. Though structures of prefusion, icosahedral CHIKV are available, structural characterization of virion interaction with membranes has been limited. Here, we have used cryo-electron tomography to visualize CHIKV's complete membrane fusion pathway, identifying key intermediary glycoprotein conformations coupled to membrane remodeling events. Using sub-tomogram averaging, we elucidate features of the low pH-exposed virion, nucleocapsid and full-length E1-glycoprotein's post-fusion structure. Contrary to class-I fusion systems, CHIKV achieves membrane apposition by protrusion of extended E1-glycoprotein homotrimers into the target membrane. The fusion process also features a large hemifusion diaphragm that transitions to a wide pore for intact nucleocapsid delivery. Our analyses provide comprehensive ultrastructural insights into the class-II virus fusion system function and direct mechanistic characterization of the fundamental process of protein-mediated membrane fusion.
History
DepositionJun 8, 2022-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateDec 21, 2022-
Current statusDec 21, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27248.png

Downloads & links

-
Map

FileDownload / File: emd_27248.map.gz / Format: CCP4 / Size: 251 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram averaged map of membrane attached full-length post-fusion CHIKV E1 glycoprotein trimer
Voxel sizeX=Y=Z: 6.612 Å
Density
Contour LevelBy AUTHOR: 1.55
Minimum - Maximum-5.7554083 - 9.380605
Average (Standard dev.)9.890514e-08 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-20-20-20
Dimensions404040
Spacing404040
CellA=B=C: 264.48 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Odd-half map

Fileemd_27248_half_map_1.map
AnnotationOdd-half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Even half map

Fileemd_27248_half_map_2.map
AnnotationEven half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer f...

EntireName: Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer from Chikungunya virus
Components
  • Complex: Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer from Chikungunya virus
    • Protein or peptide: Spike glycoprotein E1
  • Ligand: BROMIDE IONBromide
  • Ligand: HOLMIUM ATOM
  • Ligand: PHOSPHATE IONPhosphate
  • Ligand: water

-
Supramolecule #1: Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer f...

SupramoleculeName: Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer from Chikungunya virus
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Chikungunya virus strain S27-African prototype
Molecular weightTheoretical: 150 KDa

-
Macromolecule #1: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1
Details: The previously determined X-ray crystal structure PDB ID 1RER was rigidly docked into the sub-tomogram averaged map but no further refinement was performed
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain S27-African prototype
Molecular weightTheoretical: 42.690125 KDa
SequenceString: YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCRHDHA SAYKAHTASL KAKVRVMYGN VNQTVDVYVN GDHAVTIGGT Q FIFGPLSS ...String:
YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCRHDHA SAYKAHTASL KAKVRVMYGN VNQTVDVYVN GDHAVTIGGT Q FIFGPLSS AWTPFDNKIV VYKDEVFNQD FPPYGSGQPG RFGDIQSRTV ESNDLYANTA LKLARPSPGM VHVPYTQTPS GF KYWLKEK GTALNTKAPF GCQIKTNPVR AMNCAVGNIP VSMNLPDSAF TRIVEAPTII DLTCTVATCT HSSDFGGVLT LTY KTNKNG DCSVHSHSNV ATLQEATAKV KTAGKVTLHF STASASPSFV VSLCSARATC SASCEPPKDH IVPYA

-
Macromolecule #5: BROMIDE ION

MacromoleculeName: BROMIDE ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: BR
Molecular weightTheoretical: 79.904 Da
Chemical component information

ChemComp-BR:
BROMIDE ION / Bromide

-
Macromolecule #6: HOLMIUM ATOM

MacromoleculeName: HOLMIUM ATOM / type: ligand / ID: 6 / Number of copies: 4 / Formula: HO
Molecular weightTheoretical: 164.93 Da
Chemical component information

ChemComp-HO:
HOLMIUM ATOM

-
Macromolecule #7: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION / Phosphate

-
Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 139 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 5.1 / Details: Hepes Buffer Saline
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 7-8 seconds.
DetailsSub-volumes picked from liposome membrane surface

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 53000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 70.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 40 / Number images used: 591 / Reference model: crystal structure / Software - Name: PEET
Details: low pass filtered map of post-fusion E1--homotrimer crystal structure
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 27.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET / Number subtomograms used: 590
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

1rer

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8d87:
Fitted crystal structure of the homotrimer of fusion glycoprotein E1 from SFV into subtomogram averaged CHIKV E1 glycoprotein density

+
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