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- EMDB-37421: CryoEM structure of non-structural protein 1 hexamer 1 from dengu... -

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Basic information

Entry
Database: EMDB / ID: EMD-37421
TitleCryoEM structure of non-structural protein 1 hexamer 1 from dengue virus type 4
Map data
Sample
  • Complex: dengue virus type 4 non-structural protein 1 hexamer
    • Protein or peptide: Genome polyprotein
  • Ligand: TRISTEAROYLGLYCEROL
Keywordsflavivirus / dimer / VIRAL PROTEIN
Function / homology
Function and homology information


flavivirin / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...flavivirin / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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
Biological speciesdengue virus type 4 / Dengue virus 4 Philippines/H241/1956
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsJiao HZ / Pan Q / Hu HL
Funding support1 items
OrganizationGrant numberCountry
Other governmentJCYJ20210324131802008
CitationJournal: Sci Adv / Year: 2024
Title: The step-by-step assembly mechanism of secreted flavivirus NS1 tetramer and hexamer captured at atomic resolution.
Authors: Qi Pan / Haizhan Jiao / Wanqin Zhang / Qiang Chen / Geshu Zhang / Jianhai Yu / Wei Zhao / Hongli Hu /
Abstract: Flaviviruses encode a conserved, membrane-associated nonstructural protein 1 (NS1) with replication and immune evasion functions. The current knowledge of secreted NS1 (sNS1) oligomers is based on ...Flaviviruses encode a conserved, membrane-associated nonstructural protein 1 (NS1) with replication and immune evasion functions. The current knowledge of secreted NS1 (sNS1) oligomers is based on several low-resolution structures, thus hindering the development of drugs and vaccines against flaviviruses. Here, we revealed that recombinant sNS1 from flaviviruses exists in a dynamic equilibrium of dimer-tetramer-hexamer states. Two DENV4 hexameric NS1 structures and several tetrameric NS1 structures from multiple flaviviruses were solved at atomic resolution by cryo-EM. The stacking of the tetrameric NS1 and hexameric NS1 is facilitated by the hydrophobic β-roll and connector domains. Additionally, a triacylglycerol molecule located within the central cavity may play a role in stabilizing the hexamer. Based on differentiated interactions between the dimeric NS1, two distinct hexamer models (head-to-head and side-to-side hexamer) and the step-by-step assembly mechanisms of NS1 dimer into hexamer were proposed. We believe that our study sheds light on the understanding of the NS1 oligomerization and contributes to NS1-based therapies.
History
DepositionSep 9, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37421.png

Downloads & links

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Map

FileDownload / File: emd_37421.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.6292472 - 6.0464187
Average (Standard dev.)0.0028046211 (±0.16975433)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 238.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_37421_additional_1.map
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Half map: #2

Fileemd_37421_half_map_1.map
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Histogram (log scale)

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Half map: #1

Fileemd_37421_half_map_2.map
Projections & Slices
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Sample components

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Entire : dengue virus type 4 non-structural protein 1 hexamer

EntireName: dengue virus type 4 non-structural protein 1 hexamer
Components
  • Complex: dengue virus type 4 non-structural protein 1 hexamer
    • Protein or peptide: Genome polyprotein
  • Ligand: TRISTEAROYLGLYCEROL

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Supramolecule #1: dengue virus type 4 non-structural protein 1 hexamer

SupramoleculeName: dengue virus type 4 non-structural protein 1 hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: dengue virus type 4

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Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Dengue virus 4 Philippines/H241/1956 / Strain: Philippines/H241/1956
Molecular weightTheoretical: 40.494758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DTGCAVSWSG KELKCGSGIF VIDNVHTWTE QYKFQPESPA RLASAILNAH EDGVCGIRST TRLENIMWKQ ITNELNYVLW EGGHDLTVV AGDVKGVLSK GKRALAPPVN DLKYSWKTWG KAKIFTPEAK NSTFLIDGPD TSECPNERRA WNFLEVEDYG F GMFTTNIW ...String:
DTGCAVSWSG KELKCGSGIF VIDNVHTWTE QYKFQPESPA RLASAILNAH EDGVCGIRST TRLENIMWKQ ITNELNYVLW EGGHDLTVV AGDVKGVLSK GKRALAPPVN DLKYSWKTWG KAKIFTPEAK NSTFLIDGPD TSECPNERRA WNFLEVEDYG F GMFTTNIW MKFREGSSEV CDHRLMSAAI KDQKAVHADM GYWIESSKNQ TWQIEKASLI EVKTCLWPKT HTLWSNGVLE SQ MLIPKAY AGPFSQHNYR QGYATQTVGP WHLGKLEIDF GECPGTTVTI QEDCDHRGPS LRTTTASGKL VTQWCCRSCT MPP LRFLGE DGCWYGMEIR PLSEKEENMV KSQVSAHHHH HH

UniProtKB: Genome polyprotein

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Macromolecule #2: TRISTEAROYLGLYCEROL

MacromoleculeName: TRISTEAROYLGLYCEROL / type: ligand / ID: 2 / Number of copies: 1 / Formula: TGL
Molecular weightTheoretical: 891.48 Da
Chemical component information

ChemComp-TGL:
TRISTEAROYLGLYCEROL

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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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101485
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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