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- EMDB-9649: Cryo-EM structure of Immature Dengue virus serotype 3 in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-9649
TitleCryo-EM structure of Immature Dengue virus serotype 3 in complex with human antibody 1H10 Fab at pH 8.0.
Map dataCryo-EM density map of Immature Dengue virus serotype 3 in complex with human antibody 1H10 Fab at pH 8.0
Sample
  • Complex: Dengue virus 3 in complex with human antibody
    • Complex: Fab 1H10
      • Protein or peptide: Fab 1H10 heavy chain (V-region)
      • Protein or peptide: Fab 1H10 light chain (V-region)
    • Virus: Dengue virus 3
      • Protein or peptide: Envelope proteinViral envelope
    • Virus: Dengue virus 3
      • Protein or peptide: Premembrane protein
Keywordsimmature dengue virus / human antibody / 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 / viral capsid / : / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity ...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 / viral capsid / : / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / induction by virus of host autophagy / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / 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
Biological speciesHomo sapiens (human) / Dengue virus 3
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsWirawan M / Fibriansah G
Funding support Singapore, United States, 4 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-NRFI2016-01 Singapore
Ministry of Education (MoE, Singapore)MOE2012-T3-008 Singapore
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI057157 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K08 AI103038 United States
CitationJournal: Structure / Year: 2019
Title: Mechanism of Enhanced Immature Dengue Virus Attachment to Endosomal Membrane Induced by prM Antibody.
Authors: Melissa Wirawan / Guntur Fibriansah / Jan K Marzinek / Xin Xiang Lim / Thiam-Seng Ng / Adelene Y L Sim / Qian Zhang / Victor A Kostyuchenko / Jian Shi / Scott A Smith / Chandra S Verma / ...Authors: Melissa Wirawan / Guntur Fibriansah / Jan K Marzinek / Xin Xiang Lim / Thiam-Seng Ng / Adelene Y L Sim / Qian Zhang / Victor A Kostyuchenko / Jian Shi / Scott A Smith / Chandra S Verma / Ganesh Anand / James E Crowe / Peter J Bond / Shee-Mei Lok /
Abstract: Dengue virus (DENV) particles are released from cells in different maturation states. Fully immature DENV (immDENV) is generally non-infectious, but can become infectious when complexed with anti- ...Dengue virus (DENV) particles are released from cells in different maturation states. Fully immature DENV (immDENV) is generally non-infectious, but can become infectious when complexed with anti-precursor membrane (prM) protein antibodies. It is unknown how anti-prM antibody-coated particles can undergo membrane fusion since the prM caps the envelope (E) protein fusion loop. Here, we determined cryoelectron microscopy (cryo-EM) maps of the immDENV:anti-prM complex at different pH values, mimicking the extracellular (pH 8.0) or endosomal (pH 5.0) environments. At pH 5.0, there are two structural classes with fewer antibodies bound than at pH 8.0. These classes may represent different maturation states. Molecular simulations, together with the measured high-affinity pr:antibody interaction (versus the weak pr:E interaction) and also the low pH cryo-EM structures, suggest how antibody:pr complex can dislodge from the E protein at low pH. This exposes the E protein fusion loop enhancing virus interaction with endosomes.
History
DepositionSep 10, 2018-
Header (metadata) releaseDec 12, 2018-
Map releaseDec 12, 2018-
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: 2
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  • Surface view colored by radius
  • Surface level: 2
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  • Surface view with fitted model
  • Atomic models: PDB-6idi
  • Surface level: 2
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6idi
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9649.png

Downloads & links

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Map

FileDownload / File: emd_9649.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM density map of Immature Dengue virus serotype 3 in complex with human antibody 1H10 Fab at pH 8.0
Voxel sizeX=Y=Z: 1.7 Å
Density
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-7.6539693 - 10.648569
Average (Standard dev.)0.010382563 (±0.9794677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 870.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.71.71.7
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z870.400870.400870.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-7.65410.6490.010

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Supplemental data

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Sample components

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Entire : Dengue virus 3 in complex with human antibody

EntireName: Dengue virus 3 in complex with human antibody
Components
  • Complex: Dengue virus 3 in complex with human antibody
    • Complex: Fab 1H10
      • Protein or peptide: Fab 1H10 heavy chain (V-region)
      • Protein or peptide: Fab 1H10 light chain (V-region)
    • Virus: Dengue virus 3
      • Protein or peptide: Envelope proteinViral envelope
    • Virus: Dengue virus 3
      • Protein or peptide: Premembrane protein

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Supramolecule #1: Dengue virus 3 in complex with human antibody

SupramoleculeName: Dengue virus 3 in complex with human antibody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The virus was isolated from dengue patient. The immature dengue 3 virus was grown in Aedes Albopictus clone C6/36 cell. The anti-prM antibody 1H10 was generated from EBV-immortalized PBMC ...Details: The virus was isolated from dengue patient. The immature dengue 3 virus was grown in Aedes Albopictus clone C6/36 cell. The anti-prM antibody 1H10 was generated from EBV-immortalized PBMC that was obtained from dengue patient.

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Supramolecule #4: Fab 1H10

SupramoleculeName: Fab 1H10 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Dengue virus 3

SupramoleculeName: Dengue virus 3 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1 / NCBI-ID: 11069 / Sci species name: Dengue virus 3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Supramolecule #3: Dengue virus 3

SupramoleculeName: Dengue virus 3 / type: virus / ID: 3 / Parent: 1 / Macromolecule list: #2 / NCBI-ID: 11069 / Sci species name: Dengue virus 3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Envelope protein

MacromoleculeName: Envelope protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Dengue virus 3
Molecular weightTheoretical: 53.682484 KDa
Recombinant expressionOrganism: Aedes albopictus (Asian tiger mosquito)
SequenceString: MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA VLPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLEPIEGKV VQYENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST ...String:
MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA VLPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLEPIEGKV VQYENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST TEAILPEYGT LGLECSPRTG LDFNEMILLT MKNKAWMVHR QWFFDLPLPW ASGATTETPT WNRKELLVTF KN AHAKKQE VVVLGSQEGA MHTALTGATE IQNSGGTSIF AGHLKCRLKM DKLELKGMSY AMCTNTFVLK KEVSETQHGT ILI KVEYKG EDAPCKIPFS TEDGQGKAHN GRLITANPVV TKKEEPVNIE AEPPFGESNI VIGIGDNALK INWYKKGSSI GKMF EATAR GARRMAILGD TAWDFGSVGG VLNSLGKMVH QIFGSAYTAL FSGVSWVMKI GIGVLLTWIG LNSKNTSMSF SCIAI GIIT LYLGAVVQA

UniProtKB: Genome polyprotein

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Macromolecule #2: Premembrane protein

MacromoleculeName: Premembrane protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Dengue virus 3
Molecular weightTheoretical: 18.686615 KDa
Recombinant expressionOrganism: Aedes albopictus (Asian tiger mosquito)
SequenceString:
FHLTSRDGEP RMIVGKNERG KSLLFKTASG INMCTLIAMD LGEMCDDTVT YKCPHITEVE PEDIDCWCNL TSTWVTYGTC NQAGEHRRD KRSVALAPHV GMGLDTRTQT WMSAEGAWRQ VEKVETWALR HPGFTILALF LAHYIGTSLT QKVVIFILLM L VTPSMT

UniProtKB: Genome polyprotein

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Macromolecule #3: Fab 1H10 heavy chain (V-region)

MacromoleculeName: Fab 1H10 heavy chain (V-region) / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.319042 KDa
Recombinant expressionOrganism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
SequenceString:
QVQLVESGGG VVQPGRSLRL SCAASGFTFS NFAMHWVRQA PGKGLEWVSL ISYDGSNKYN ADSVRGRFSI SRDNSKNTLY LQMNSLRLE DTAVYYCVRV RQPWTQAWST NYFYYYGMDV WGQGTTVTVS SASTKGPS

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Macromolecule #4: Fab 1H10 light chain (V-region)

MacromoleculeName: Fab 1H10 light chain (V-region) / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.132362 KDa
Recombinant expressionOrganism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
SequenceString:
QSVLTQPPSA SGTPGQRVTI SCSGGSSNIG SSYVYWYKQV PGTAPKLLIY RNNERPSGVP DRFSGSKSGT SASLAISGLR SEDEADYYC AAWDDSLRGQ VFGGGTKLTV LGQPKAA

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 18.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 9193
Startup modelType of model: EMDB MAP
EMDB ID:

2141

Initial angle assignmentType: COMMON LINE / Software - Name: MPSA
Final angle assignmentType: COMMON LINE / Software - Name: MPSA
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: MPSA / Number images used: 2886
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4b03


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6idi:
Cryo-EM structure of Immature Dengue virus serotype 3 in complex with human antibody 1H10 Fab at pH 8.0.

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