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- EMDB-8508: Cryo-EM Structure of Immature Zika Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-8508
TitleCryo-EM Structure of Immature Zika Virus
Map dataCryo-EM Reconstruction of Immature Zika Virus
Sample
  • Virus: Zika virus
    • Complex: Transmembrane domains
      • Protein or peptide: Protein E
      • Protein or peptide: M protein
    • Protein or peptide: E protein
    • Protein or peptide: pr domain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose
Keywordsimmature Zika virus / viral protein / VIRUS
Function / homology
Function and homology information


response to herbicide / photosystem II / flavivirin / photosynthetic electron transport in photosystem II / chlorophyll binding / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity ...response to herbicide / photosystem II / flavivirin / photosynthetic electron transport in photosystem II / chlorophyll binding / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis 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 / nucleoside-triphosphate phosphatase / channel activity / viral capsid / monoatomic ion transmembrane transport / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell surface / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / GTP binding / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Photosystem II protein D1 / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase ...Photosystem II protein D1 / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / 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, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein M / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus glycoprotein, immunoglobulin-like 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
Photosystem q(B) protein / Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
Methodsingle particle reconstruction / cryo EM / Resolution: 9.1 Å
AuthorsMangala Prasad V / Miller AS
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1 AI076331 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1 AI073755 United States
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: Structure of the immature Zika virus at 9 Å resolution.
Authors: Vidya Mangala Prasad / Andrew S Miller / Thomas Klose / Devika Sirohi / Geeta Buda / Wen Jiang / Richard J Kuhn / Michael G Rossmann /
Abstract: The current Zika virus (ZIKV) epidemic is characterized by severe pathogenicity in both children and adults. Sequence changes in ZIKV since its first isolation are apparent when pre-epidemic strains ...The current Zika virus (ZIKV) epidemic is characterized by severe pathogenicity in both children and adults. Sequence changes in ZIKV since its first isolation are apparent when pre-epidemic strains are compared with those causing the current epidemic. However, the residues that are responsible for ZIKV pathogenicity are largely unknown. Here we report the cryo-electron microscopy (cryo-EM) structure of the immature ZIKV at 9-Å resolution. The cryo-EM map was fitted with the crystal structures of the precursor membrane and envelope glycoproteins and was shown to be similar to the structures of other known immature flaviviruses. However, the immature ZIKV contains a partially ordered capsid protein shell that is less prominent in other immature flaviviruses. Furthermore, six amino acids near the interface between pr domains at the top of the spikes were found to be different between the pre-epidemic and epidemic ZIKV, possibly influencing the composition and structure of the resulting viruses.
History
DepositionDec 6, 2016-
Header (metadata) releaseDec 21, 2016-
Map releaseJan 11, 2017-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5u4w
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5u4w
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8508.png

Downloads & links

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Map

FileDownload / File: emd_8508.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM Reconstruction of Immature Zika Virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.6 Å/pix.
x 336 pix.
= 873.6 Å		2.6 Å/pix.
x 336 pix.
= 873.6 Å		2.6 Å/pix.
x 336 pix.
= 873.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum-32.937139999999999 - 22.248031999999998
Average (Standard dev.)0.055202045 (±1.5859408)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-168-168-168
Dimensions336336336
Spacing336336336
CellA=B=C: 873.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.62.62.6
M x/y/z336336336
origin x/y/z0.0000.0000.000
length x/y/z873.600873.600873.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-168-168-168
NC/NR/NS336336336
D min/max/mean-32.93722.2480.055

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Supplemental data

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Sample components

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Entire : Zika virus

EntireName: Zika virus
Components
  • Virus: Zika virus
    • Complex: Transmembrane domains
      • Protein or peptide: Protein E
      • Protein or peptide: M protein
    • Protein or peptide: E protein
    • Protein or peptide: pr domain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose

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Supramolecule #1: Zika virus

SupramoleculeName: Zika virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 64320 / Sci species name: Zika virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: prM-E glycoprotein / Diameter: 600.0 Å / T number (triangulation number): 1

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Supramolecule #2: Transmembrane domains

SupramoleculeName: Transmembrane domains / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Zika virus

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Macromolecule #1: E protein

MacromoleculeName: E protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Zika virus
Molecular weightTheoretical: 44.80141 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: GENLYFQGMR CIGMSNRDFV EGVSGGSWVD IVLEHGSCVT TMAKNKPTLD FELIKTEAKQ PATLRKYCIE AKLTNTTTES RCPTQGEPS LNEEQDKRFV CKHSMVDRGW GNGCGLFGKG GIVTCAMFRC KKNMEGKVVQ PENLEYTIVI TPHSGEEHAV G NDTGKHGK ...String:
GENLYFQGMR CIGMSNRDFV EGVSGGSWVD IVLEHGSCVT TMAKNKPTLD FELIKTEAKQ PATLRKYCIE AKLTNTTTES RCPTQGEPS LNEEQDKRFV CKHSMVDRGW GNGCGLFGKG GIVTCAMFRC KKNMEGKVVQ PENLEYTIVI TPHSGEEHAV G NDTGKHGK EIKITPQSSI TEAELTGYGT VTMECSPRTG LDFNEMVLLQ MENKAWLVHR QWFLDLPLPW LPGADTQGSN WI QKETLVT FKNPHAKKQD VVVLGSQEGA MHTALTGATE IQMSSGNLLF TGHLKCRLRM DKLQLKGMSY SMCTGKFKVV KEI AETQHG TIVIRVQYEG DGSPCKIPFE IMDLEKRHVL GRLITVNPIV TEKDSPVNIE AEPPFGDSYI IIGVEPGQLK LNWF KK

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Macromolecule #2: pr domain

MacromoleculeName: pr domain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Zika virus
Molecular weightTheoretical: 9.261531 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString:
FHLTTRNGEP HMIVSRQEKG KSLLFKTEDG VNMCTLMAMD LGELCEDTIT YKCPLLRQNE PEDIDCWCNS TSTWVTYGTC T

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Macromolecule #3: Protein E

MacromoleculeName: Protein E / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Zika virus
Molecular weightTheoretical: 6.892228 KDa
SequenceString:
GALNSLGKGI HQIFGAAFKS LFGGMSWFSQ ILIGTLLMWL GLNTKNGSIS LMCLALGGVL IFLSTA

UniProtKB: Genome polyprotein

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Macromolecule #4: M protein

MacromoleculeName: M protein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Zika virus
Molecular weightTheoretical: 5.984065 KDa
SequenceString:
REYTKHLIRV ENWIFRNPGF ALAAAAIAWL LGSSTSQKVI YLVMILLIAP AYS

UniProtKB: Genome polyprotein

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #6: beta-D-mannopyranose

MacromoleculeName: beta-D-mannopyranose / type: ligand / ID: 6 / Number of copies: 6 / Formula: BMA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BMA:
beta-D-mannopyranose

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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
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
20.0 mMC4H11NO3Tris
1.0 mMEDTA
GridModel: Ultrathin carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 3341 / Average exposure time: 7.6 sec. / Average electron dose: 4.7 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

Particle selectionNumber selected: 14351
Startup modelType of model: OTHER / Details: Random model generation
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 9315
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
Final angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
Final 3D classificationNumber classes: 50 / Avg.num./class: 200 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-5u4w:
Cryo-EM Structure of Immature Zika Virus

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