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- EMDB-11371: Cryo-EM structure of mature Spondweni virus -

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Basic information

Entry
Database: EMDB / ID: EMD-11371
TitleCryo-EM structure of mature Spondweni virus
Map dataPost-processed RELION map
Sample
  • Virus: Spondweni virus
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Core protein / Genome polyprotein
Similarity search - Component
Biological speciesSpondweni virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsRenner M / Dejnirattisai W / Carrique L / Serna Martin I / Karia D / Ilca SL / Ho SF / Kotecha A / Keown JR / Mongkolsapaya J ...Renner M / Dejnirattisai W / Carrique L / Serna Martin I / Karia D / Ilca SL / Ho SF / Kotecha A / Keown JR / Mongkolsapaya J / Screaton GR / Grimes JM
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Wellcome Trust060208/Z/00/Z United Kingdom
Wellcome Trust093305/Z/10/Z United Kingdom
Wellcome Trust204703/Z/16/Z United Kingdom
Wellcome Trust200835/Z/16/Z United Kingdom
Wellcome Trust203141/Z/16/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Flavivirus maturation leads to the formation of an occupied lipid pocket in the surface glycoproteins.
Authors: Max Renner / Wanwisa Dejnirattisai / Loïc Carrique / Itziar Serna Martin / Dimple Karia / Serban L Ilca / Shu F Ho / Abhay Kotecha / Jeremy R Keown / Juthathip Mongkolsapaya / Gavin R ...Authors: Max Renner / Wanwisa Dejnirattisai / Loïc Carrique / Itziar Serna Martin / Dimple Karia / Serban L Ilca / Shu F Ho / Abhay Kotecha / Jeremy R Keown / Juthathip Mongkolsapaya / Gavin R Screaton / Jonathan M Grimes /
Abstract: Flaviviruses such as Dengue (DENV) or Zika virus (ZIKV) assemble into an immature form within the endoplasmatic reticulum (ER), and are then processed by furin protease in the trans-Golgi. To better ...Flaviviruses such as Dengue (DENV) or Zika virus (ZIKV) assemble into an immature form within the endoplasmatic reticulum (ER), and are then processed by furin protease in the trans-Golgi. To better grasp maturation, we carry out cryo-EM reconstructions of immature Spondweni virus (SPOV), a human flavivirus of the same serogroup as ZIKV. By employing asymmetric localised reconstruction we push the resolution to 3.8 Å, enabling us to refine an atomic model which includes the crucial furin protease recognition site and a conserved Histidine pH-sensor. For direct comparison, we also solve structures of the mature forms of SPONV and DENV to 2.6 Å and 3.1 Å, respectively. We identify an ordered lipid that is present in only the mature forms of ZIKV, SPOV, and DENV and can bind as a consequence of rearranging amphipathic stem-helices of E during maturation. We propose a structural role for the pocket and suggest it stabilizes mature E.
History
DepositionJul 10, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateAug 4, 2021-
Current statusAug 4, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zqv
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zqv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11371.png

Downloads & links

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Map

FileDownload / File: emd_11371.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed RELION map
Voxel sizeX=Y=Z: 0.845 Å
Density
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.011779605 - 0.035387862
Average (Standard dev.)0.0006446109 (±0.0024280874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions650650650
Spacing650650650
CellA=B=C: 549.25 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8450.8450.845
M x/y/z650650650
origin x/y/z0.0000.0000.000
length x/y/z549.250549.250549.250
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS650650650
D min/max/mean-0.0120.0350.001

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Supplemental data

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Mask #1

Fileemd_11371_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_11371_half_map_1.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_11371_half_map_2.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Spondweni virus

EntireName: Spondweni virus
Components
  • Virus: Spondweni virus
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine

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Supramolecule #1: Spondweni virus

SupramoleculeName: Spondweni virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Virus cultivated in C6/36 cells / NCBI-ID: 64318 / Sci species name: Spondweni virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Aedes circumluteolus (mosquito)

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Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Spondweni virus
Molecular weightTheoretical: 54.838207 KDa
SequenceString: IRCIGIGNRD FIEGMSGGTW VDIVLEHGGC VTVMSNNKPT LDFELVTTTA SNMAEVRSYC YEANISEMAS DSRCPTQGEA YLDKMADSQ FVCKRGYVDR GWGNGCGLFG KGSIVTCAKF TCVKKLTGKS IQPENLEYRV LVSVHASQHG GMINNDTNHQ H DKENRARI ...String:
IRCIGIGNRD FIEGMSGGTW VDIVLEHGGC VTVMSNNKPT LDFELVTTTA SNMAEVRSYC YEANISEMAS DSRCPTQGEA YLDKMADSQ FVCKRGYVDR GWGNGCGLFG KGSIVTCAKF TCVKKLTGKS IQPENLEYRV LVSVHASQHG GMINNDTNHQ H DKENRARI DITASAPRVE VELGSFGSIS MECEPRSGLN FGDLYYLTMN NKHWLVNRDW FHDLSLPWHT GATSNNHHWN NK EALVEFR EAHAKKQTAV VLGSQEGAVH AALAGALEAE SDGHKATIYS GHLKCRLKLD KLRLKGMSYA LCTGAFTFAR TPS ETIHGT ATVELQYAGE DGPCKVPIVI TSDTNSMAST GRLITANPVV TESGANSKMM VEIDPPFGDS YIIVGTGTTK ITHH WHRAG SSIGRAFEAT MRGAKRMAVL GDTAWDFGSV GGMFNSVGKF VHQVFGSAFK ALFGGMSWFT QLLIGFLLIW MGLNA RGGT VAMSFMGIGA MLIFLATSVS G

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Macromolecule #2: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Spondweni virus
Molecular weightTheoretical: 8.450787 KDa
SequenceString:
SITLPSHASQ KLETRSSTWL ESREYSKYLI KVENWILRNP GYALVAAVIG WTLGSSRSQK IIFVTLLMLV APAYS

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Macromolecule #4: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 4 / Number of copies: 3 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM / Phosphatidylethanolamine

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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

BufferpH: 7.4 / Details: PBS buffer
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV
DetailsUV inactivated

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 160341
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: EMDB MAP
EMDB ID:

7543

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 63222
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: CC
Output model

PDB-6zqv:
Cryo-EM structure of mature Spondweni virus

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