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- EMDB-8734: Electron cryo-microscopy of "immature" Chikungunya VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-8734
TitleElectron cryo-microscopy of "immature" Chikungunya VLP
Map dataChikungunya virus strain Senegal 37997
Sample
  • Virus: Chikungunya virus strain Senegal 37997
    • Protein or peptide: E1 envelope glycoprotein
    • Protein or peptide: E3 envelope glycoprotein
    • Protein or peptide: capsid protein
    • Protein or peptide: E1 envelope glycoprotein
    • Protein or peptide: E2 envelope glycoprotein
KeywordsChikungunya / virus / immature / VIRUS LIKE PARTICLE
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 / virion attachment to host cell / host cell nucleus / 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 / virion attachment to host cell / host cell nucleus / 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 / Structural polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus strain Senegal 37997 / Chikungunya virus (strain 37997)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsRossmann MG / Yap ML / Sakurai A / Ishikawa M / Akahata W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095366 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Structural studies of Chikungunya virus maturation.
Authors: Moh Lan Yap / Thomas Klose / Akane Urakami / S Saif Hasan / Wataru Akahata / Michael G Rossmann /
Abstract: Cleavage of the alphavirus precursor glycoprotein p62 into the E2 and E3 glycoproteins before assembly with the nucleocapsid is the key to producing fusion-competent mature spikes on alphaviruses. ...Cleavage of the alphavirus precursor glycoprotein p62 into the E2 and E3 glycoproteins before assembly with the nucleocapsid is the key to producing fusion-competent mature spikes on alphaviruses. Here we present a cryo-EM, 6.8-Å resolution structure of an "immature" Chikungunya virus in which the cleavage site has been mutated to inhibit proteolysis. The spikes in the immature virus have a larger radius and are less compact than in the mature virus. Furthermore, domains B on the E2 glycoproteins have less freedom of movement in the immature virus, keeping the fusion loops protected under domain B. In addition, the nucleocapsid of the immature virus is more compact than in the mature virus, protecting a conserved ribosome-binding site in the capsid protein from exposure. These differences suggest that the posttranslational processing of the spikes and nucleocapsid is necessary to produce infectious virus.
History
DepositionMay 18, 2017-
Header (metadata) releaseAug 23, 2017-
Map releaseDec 6, 2017-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5vu2
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5vu2
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8734.png

Downloads & links

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Map

FileDownload / File: emd_8734.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChikungunya virus strain Senegal 37997
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 768 pix.
= 998.4 Å		1.3 Å/pix.
x 768 pix.
= 998.4 Å		1.3 Å/pix.
x 768 pix.
= 998.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-5.0 - 5.0
Average (Standard dev.)0.029038956 (±0.4375374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-384-384-384
Dimensions768768768
Spacing768768768
CellA=B=C: 998.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z768768768
origin x/y/z0.0000.0000.000
length x/y/z998.400998.400998.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-384-384-384
NC/NR/NS768768768
D min/max/mean-5.0005.0000.029

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Supplemental data

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Sample components

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Entire : Chikungunya virus strain Senegal 37997

EntireName: Chikungunya virus strain Senegal 37997
Components
  • Virus: Chikungunya virus strain Senegal 37997
    • Protein or peptide: E1 envelope glycoprotein
    • Protein or peptide: E3 envelope glycoprotein
    • Protein or peptide: capsid protein
    • Protein or peptide: E1 envelope glycoprotein
    • Protein or peptide: E2 envelope glycoprotein

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Supramolecule #1: Chikungunya virus strain Senegal 37997

SupramoleculeName: Chikungunya virus strain Senegal 37997 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 371095 / Sci species name: Chikungunya virus strain Senegal 37997 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: E1 envelope glycoprotein

MacromoleculeName: E1 envelope glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997
Molecular weightTheoretical: 95.538164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STKDNFNVYK ATRPYLAHCP DCGEGHSCHS PVALERIRNE ATDGTLKIQV SLQIGIKTDD SHDWTKLRYM DNHMPADAER AGLFVRTSA PCTITGTMGH FILARCPKGE TLTVGFTDSR KISHSCTHPF HHDPPVIGRE KFHSRPQHGK ELPCSTYVQS T AATTEEIE ...String:
STKDNFNVYK ATRPYLAHCP DCGEGHSCHS PVALERIRNE ATDGTLKIQV SLQIGIKTDD SHDWTKLRYM DNHMPADAER AGLFVRTSA PCTITGTMGH FILARCPKGE TLTVGFTDSR KISHSCTHPF HHDPPVIGRE KFHSRPQHGK ELPCSTYVQS T AATTEEIE VHMPPDTPDR TLMSQQSGNV KITVNGQTVR YKCNCGGSNE GLTTTDKVIN NCKVDQCHAA VTNHKKWQYN SP LVPRNAE LGDRKGKIHI PFPLANVTCR VPKARNPTVT YGKNQVIMLL YPDHPTLLSY RNMGEEPNYQ EEWVMHKKEV VLT VPTEGL EVTWGNNEPY KYWPQLSTNG TAHGHPHEII LYYYELYPTM TVVVVSVATF ILLSMVGMAA GMCMCARRRC ITPY ELTPG ATVPFLLSLI CCIRTAKAAT YQEAAIYLWN EQQPLFWLQA LIPLAALIVL CNCLRLLPCC CKTLAFLAVM SVGAH TVSA YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELLSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KNLPDY SCK VFTGVYPFMW GGAYCFCDAE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNITVTAYAN GDHAVTV KD AKFIVGPMSS AWTPFDNKIV VYKGDVYNMD YPPFGAGRPG QFGDIQSRTP ESKDVYANTQ LVLQRPAAGT VHVPYSQA P SGFKYWLKER GASLQHTAPF GCQIATNPVR AVNCAVGNMP ISIDIPEAAF TRVVDAPSLT DMSCEVPACT HSSDFGGVA IIKYAASKKG KCAVHSMTNA VTIREAEIEV EGNSQLQISF STALASAEFR VQVCSTQVHC AAECHP

UniProtKB: Structural polyprotein

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Macromolecule #2: E3 envelope glycoprotein

MacromoleculeName: E3 envelope glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997
Molecular weightTheoretical: 6.92699 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
PVMCLLANTT FPCSQPPCTP CCYEKEPEET LRMLEDNVMR PGYYQLLQAS LTCSPHRQRE

UniProtKB: Structural polyprotein

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Macromolecule #3: capsid protein

MacromoleculeName: capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus (strain 37997) / Strain: 37997
Molecular weightTheoretical: 16.229508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
CIFEVKHEGK VMGYACLVGD KVMKPAHVKG TIDNADLAKL AFKRSSKYDL ECAQIPVHMK SDASKFTHEK PEGYYNWHHG AVQYSGGRF TIPTGAGKPG DSGRPIFDNK GRVVAIVLGG ANEGARTALS VVTWNKDIVT KITPEGAEEW

UniProtKB: Structural polyprotein

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Macromolecule #4: E1 envelope glycoprotein

MacromoleculeName: E1 envelope glycoprotein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997
Molecular weightTheoretical: 4.810723 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
HTTLGVQDIS TTAMSWVQKI TGGVGLIVAV AALILIVVLC VSFSRH

UniProtKB: Structural polyprotein

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Macromolecule #5: E2 envelope glycoprotein

MacromoleculeName: E2 envelope glycoprotein / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997
Molecular weightTheoretical: 8.817458 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
STNGTAHGHP HEIILYYYEL YPTMTVVIVS VASFVLLSMV GTAVGMCVCA RRRCITPYEL TPGATVPFLL SLLCCVRTTK A

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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 72944
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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