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- EMDB-30278: Helical reconstruction of Dengue virus serotype 3 complexed with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-30278
TitleHelical reconstruction of Dengue virus serotype 3 complexed with Fab C10
Map datahelical reconstruction of DENV3 complexed with Fab C10
Sample
  • Complex: Helical reconstruction of Dengue virus serotype 3 complexed with Fab C10
    • Complex: C10 Fab
      • Protein or peptide: Heavy chain of Fab C10
      • Protein or peptide: light chain of Fab C10
    • Complex: Dengue virus serotype 3
      • Protein or peptide: envelope protein
Keywordsantibody / neutralization / VIRUS
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / viral RNA genome replication / serine-type endopeptidase activity / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / : / viral envelope / 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 non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / 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
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Dengue virus 3
Methodhelical reconstruction / cryo EM / Resolution: 10.4 Å
AuthorsMorrone S / Chew SV
Funding support Singapore, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-NRFI2016-01 Singapore
National Research Foundation (NRF, Singapore)NRF2016NRF-CRP001-063 Singapore
CitationJournal: Nat Commun / Year: 2020
Title: High flavivirus structural plasticity demonstrated by a non-spherical morphological variant.
Authors: Seamus R Morrone / Valerie S Y Chew / Xin-Ni Lim / Thiam-Seng Ng / Victor A Kostyuchenko / Shuijun Zhang / Melissa Wirawan / Pau-Ling Chew / Jaime Lee / Joanne L Tan / Jiaqi Wang / Ter Yong ...Authors: Seamus R Morrone / Valerie S Y Chew / Xin-Ni Lim / Thiam-Seng Ng / Victor A Kostyuchenko / Shuijun Zhang / Melissa Wirawan / Pau-Ling Chew / Jaime Lee / Joanne L Tan / Jiaqi Wang / Ter Yong Tan / Jian Shi / Gavin Screaton / Marc C Morais / Shee-Mei Lok /
Abstract: Previous flavivirus (dengue and Zika viruses) studies showed largely spherical particles either with smooth or bumpy surfaces. Here, we demonstrate flavivirus particles have high structural ...Previous flavivirus (dengue and Zika viruses) studies showed largely spherical particles either with smooth or bumpy surfaces. Here, we demonstrate flavivirus particles have high structural plasticity by the induction of a non-spherical morphology at elevated temperatures: the club-shaped particle (clubSP), which contains a cylindrical tail and a disc-like head. Complex formation of DENV and ZIKV with Fab C10 stabilize the viruses allowing cryoEM structural determination to ~10 Å resolution. The caterpillar-shaped (catSP) Fab C10:ZIKV complex shows Fabs locking the E protein raft structure containing three E dimers. However, compared to the original spherical structure, the rafts have rotated relative to each other. The helical tail structure of Fab C10:DENV3 clubSP showed although the Fab locked an E protein dimer, the dimers have shifted laterally. Morphological diversity, including clubSP and the previously identified bumpy and smooth-surfaced spherical particles, may help flavivirus survival and immune evasion.
History
DepositionMay 9, 2020-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7c2s
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7c2s
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30278.png

Downloads & links

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Map

FileDownload / File: emd_30278.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhelical reconstruction of DENV3 complexed with Fab C10
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.71 Å/pix.
x 256 pix.
= 437.76 Å		1.71 Å/pix.
x 256 pix.
= 437.76 Å		1.71 Å/pix.
x 256 pix.
= 437.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-2.4628282 - 5.963961
Average (Standard dev.)0.000000003710306 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 437.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.711.711.71
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z437.760437.760437.760
α/β/γ90.00090.00090.000
start NX/NY/NZ777686
NX/NY/NZ10710993
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.4635.9640.000

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Supplemental data

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Sample components

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Entire : Helical reconstruction of Dengue virus serotype 3 complexed with ...

EntireName: Helical reconstruction of Dengue virus serotype 3 complexed with Fab C10
Components
  • Complex: Helical reconstruction of Dengue virus serotype 3 complexed with Fab C10
    • Complex: C10 Fab
      • Protein or peptide: Heavy chain of Fab C10
      • Protein or peptide: light chain of Fab C10
    • Complex: Dengue virus serotype 3
      • Protein or peptide: envelope protein

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Supramolecule #1: Helical reconstruction of Dengue virus serotype 3 complexed with ...

SupramoleculeName: Helical reconstruction of Dengue virus serotype 3 complexed with Fab C10
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: C10 Fab

SupramoleculeName: C10 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Dengue virus serotype 3

SupramoleculeName: Dengue virus serotype 3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Dengue virus 3

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Macromolecule #1: envelope protein

MacromoleculeName: envelope protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Dengue virus 3
Molecular weightTheoretical: 43.322457 KDa
SequenceString: MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA ILPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLESIEGKV VQHENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST ...String:
MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA ILPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLESIEGKV VQHENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST VEAILPEYGT LGLECSPRTG LDFNEMILLT MKNKAWMVHR QWFFDLPLPW TSGATTETPT WNRKELLVTF KN AHAKKQE VVVLGSQEGA MHTALTGATE IQNSGGTSIF AGHLKCRLKM DKLELKGMSY AMCLNTFVLK KEVSETQHGT ILI KVEYKG EDAPCKIPFS TEDGQGKAHN GRLITANPVV TKKEEPVNIE AEPPFGESNI VIGIGDKALK INWYKKGS

UniProtKB: Genome polyprotein

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Macromolecule #2: Heavy chain of Fab C10

MacromoleculeName: Heavy chain of Fab C10 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.487058 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGAE VKKPGASVKV SCKASGYTFT SYAMHWVRQA PGQRLEWMGW INAGNGNTKY SQKFQDRVTI TRDTSASTAY MELSSLRSE DTAIYYCARD KVDDYGDYWF PTLWYFDYWG QGTLVTVS

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Macromolecule #3: light chain of Fab C10

MacromoleculeName: light chain of Fab C10 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.298362 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SALTQPASVS GSPGQSITIS CTGTSSDVGG FNYVSWFQQH PGKAPKLMLY DVTSRPSGVS SRFSGSKSGN TASLTISGLQ AEDEADYYC SSHTSRGTWV FGGGTKLTVL

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 18.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 18.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 102.3 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 10.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7051
Startup modelType of model: EMDB MAP
Final angle assignmentType: PROJECTION MATCHING

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